research paper topics in plant biotechnology

EDITORIAL article

Editorial: insights in plant biotechnology: 2021.

• 1 Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
• 2 Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, Quedlinburg, Germany
• 3 Crop Genetics and Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
• 4 CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China

Editorial on the Research Topic Insights in plant biotechnology: 2021

The Plant Biotechnology section at Frontiers in Plant Science mainly publishes applied studies examining how plants can be improved using modern genetic techniques ( Lloyd and Kossmann, 2021 ). This Research Topic was designed to allow editors from the section to highlight some of their own plant biotechnological work. There are many aspects of crops where this is needed - for example improving yields under changing climatic conditions will be crucial to help feed the growing world population - meaning that plant biotechnology is essential for food security. Plants are also good sources of pharmaceutically active compounds and can also be genetically manipulated to make them useful platforms for producing pharmaceutical proteins. Such plants where increased amounts of pharmaceuticals can be isolated, will help many medical treatments by reducing costs. Genetic manipulation of plants underlies much plant biotechnology and this can range from traditional plant breeding, through to transgenic and genome editing technologies. Understanding and improving the uses of these technologies will allow plant biotechnologists to improve plants in a more efficient manner. This Research Topic was designed to examine a wide range of different plant biotechnological issues, from understanding and overcoming abiotic stress tolerance, to manipulating specialized metabolism and the development of genome editing techniques.

One major aspect of plant biotechnology that will need much effort is to overcome different abiotic stresses as climate change is already affecting crop yields through increasing these types of stresses ( Ray et al., 2019 ) and will likely only be worsened by future climate change. Khan et al. examined this by testing how wheat can grow better under salt stress when exposed to an endophytic fungus. They showed that this interaction leads to alterations in primary and secondary metabolites through hormonal regulation that help overcome saline stress. The work highlights the potential of including plant-endophyte interactions when considering biotechnological means to improve plant stress tolerance. Iron deficiency or uptake efficiency can also be a considerable limit on plant growth and resilience. Liu et al. identified a tobacco mutant that grows better with little iron. They characterized it further phenotypically and employed transcriptome analyses showing differences in gene expression related to molecular and physiological changes. RT-qPCR-based gene expression studies heavily depend on the availability of appropriate reference genes. Li et al. identified a set of reference genes in ginger, suitable for studying abiotic stress responses and postharvest biology studies. Finally, El-Sappah et al. reviewed various aspects of heat stress that affect maize production and suggest crop management and molecular breeding approaches to mitigate the effects.

Crop losses due to biotic stresses can be devastating and two papers were published examining these. In one study Bettoni et al. use in vitro techniques and combined chemical and thermal treatments to eliminate multiple viruses from potato plants to allow the production of virus-free plants. This procedure can play an important role in production of virus-free potato plants for farmers and can significantly improve the production of good quality potatoes. He et al. utilized genomics approaches to help in speed breeding an already high-yielding rice variety to incorporate resistance to two different bacterial diseases. This variety will be important for farmers through producing higher yields with reduced need for application of antibacterial chemicals. Although microbial infections are important, many crop losses are caused by weeds ( Oerke, 2006 ) and Wong et al. provide a review on concepts how biotechnology (including gene drives) might serve weed management in the future.

Many compounds with pharmaceutical properties are found in plants. Further, understanding and manipulating specialized metabolism is a good way to identify and produce new drugs. A survey of orchid secondary metabolism was undertaken by Ghai et al. (2022) and utilized high throughput transcriptomics data to elucidate the role of potential candidates in secondary metabolite biosynthesis. Their findings may help in identifying interesting new compounds useful for drug development and the enzymes that synthesize them. Thorat et al. examined growth conditions that influenced accumulation of pharmaceutically important withanolides compounds in Withania somnifera . Using a transcriptomic approach they identified genes which are differentially expressed. Their findings could potentially be used to establish tools for rapid in vitro multiplication of Withania sp. and increase withanolides accumulation in this plant. In vitro cultivation and regeneration of plants is a key step for the biotechnological interventions in crops. Bull and Michelmore summarizes the current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis.

Plants can also be used to manufacture recombinant proteins (molecular farming), some of which can be used as pharmaceuticals or therapeutics. Such plant-based systems can have some advantages over production of the same proteins in microbes or mammalian cell cultures. One of these advantages is the easier production of heterologous glycoproteins. van der Kaaij et al. examined how this is advantageous to produce helminth glycoproteins with unusual glycan structures in plants, which can be used to treat autoimmune diseases. Two papers also reported on the production of active recombinant proteins in the forms of human transcriptional growth factor β1 ( Soni et al. ) or a bacterial laccase ( van Eerde et al. ). These proteins have pharmaceutical or biotechnological applications respectively and their production in plants should help reduce their cost.

Although modern biotechnological techniques, such as genome editing, offer novel and complementary options, traditional genetics are still crucial in improving crops. Coupled with genomic techniques this becomes increasingly important in identifying the genetic basis of traits and speed breeding these into elite varieties. Hu et al. describe the sequencing of three Chinese chestnut varieties and generation of a pangenome that will be incredibly useful for breeding efforts. Two other studies used genomic techniques: Wang et al. identify loci involved in wheat spike production through exome capture sequencing and RNAseq analysis. Similarly, Wen et al. performed a genome wide association study to improve biofortification by identifying genetic markers associated with lower phytate content in wheat grains. This will help increase availability of iron and zinc and improve the nutritional value of the grain. Finally, haplotype analysis of jujube chloroplasts was described, where they used information for 65 chloroplast genomes and will be useful for phylogenetic studies and breeding efforts in this plant ( Hu et al. ).

The importance of genome editing techniques in improving crop plants is broadly emphasized and a number of reviews on this subject were published. Dhugga highlighted that such techniques can speed up production of improved elite varieties with only 2-3 generations needed for variety development rather than the 5-6 that are currently required. Naik et al. examined potential interrelations between genome editing and nanotechnology for plant improvement, while Silva and Fontes examined how genome editing, especially using the CRISPR/Cas-system could help develop broad range viral resistance in plants. Despite the growing importance of genome editing for introducing mutations into plant genomes, post-transcriptional gene silencing can still play an important role in both gene function discovery and crop improvement. Imran et al. examined how nested secondary structure of miR159 influences silencing in Arabidopsis thaliana .

Perspective

This Research Topic scratches the surface of several aspects of plant biotechnology ranging from applied demonstrations of biotechnological solutions to problems, to descriptions of new technologies that will become increasingly important. Plant biotechnology is a broad topic which overlaps many different scientific fields. We hope that this contributes to helping the plant science community in understanding some aspects of applied plant science, how they are currently used and how they will be utilized in the future by plant biotechnologists.

Author contributions

JRL wrote the first draft of the manuscript and all authors contributed to, and approved the final version.

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Publisher’s note

All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.

Lloyd, J., Kossmann, J. (2021). Improving crops for a changing world. Front. Plant Sci. 12, 728328. doi: 10.3389/fpls.2021.728328

PubMed Abstract | CrossRef Full Text | Google Scholar

Oerke, E. C. (2006). Crop losses to pests. J. Agric. Sci. 144, 31–43. doi: 10.1017/S0021859605005708

CrossRef Full Text | Google Scholar

Ray, D. K., West, P. C., Clark, M., Gerber, J. S., Prishchepov, A. V., Chatterjee, S. (2019). Climate change has likely already affected global food production. PLos One 14, e0217148. doi: 10.1371/journal.pone.0217148

Keywords: abiotic and biotic stresses, plant biotechnology and breeding, pharmaceuticals, recombinant protein, genome edited crops

Citation: Lloyd JR, Wilhelm R, Sharma MK, Kossmann J and Zhang P (2023) Editorial: Insights in plant biotechnology: 2021. Front. Plant Sci. 14:1147930. doi: 10.3389/fpls.2023.1147930

Received: 19 January 2023; Accepted: 19 January 2023; Published: 30 January 2023.

Edited and Reviewed by:

Copyright © 2023 Lloyd, Wilhelm, Sharma, Kossmann and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) . The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: James R. Lloyd, [email protected]

Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.

• Open access
• Published: 15 July 2022

Bioinformatics approaches and applications in plant biotechnology

• Yung Cheng Tan 1 ,
• Asqwin Uthaya Kumar   ORCID: orcid.org/0000-0002-8785-6260 1 , 2 ,
• Ying Pei Wong 1 &
• Anna Pick Kiong Ling   ORCID: orcid.org/0000-0003-0930-0619 1  

Journal of Genetic Engineering and Biotechnology volume  20 , Article number:  106 ( 2022 ) Cite this article

12k Accesses

9 Citations

Metrics details

In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set.

Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the ‘omics’ approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed.

There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant’s genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.

Over the past decades, the term ‘bioinformatics’ has become a buzzword in all areas of research in biological science. With the continuous development and advancement in molecular biology, the explosive growth of biological information required a more organized, computerized system to collect, store, manage, and analyse the vast amount of biological data generated in the experiments from all fields [ 1 ]. Bioinformatics, as a new emerging interdisciplinary field for the past few decades, has many tools and techniques that are essential for efficient sorting and organizing of biological data into databases [ 1 , 2 ]. Bioinformatics can be referred as a computer-based scientific field which applies mathematics, biology, and computer science to form into a single discipline for the analyses and interpretation of genomics and proteomics data [ 2 , 3 ]. In short, the main components of bioinformatics are (a) the collection and analysis of database and (b) the development of software tools and algorithm as a tool for interpretation of biological data [ 2 ]. Bioinformatics played a crucial role in many areas of biology as its applications provide various types of data, including nucleotide and amino acid sequences, protein domains and structure as well as expression patterns from various organisms [ 3 ]. Similarly, the field of plant biotechnology has also taken advantages of bioinformatics, which provides full genomic information of various plant species to allow for efficient exploration into plants as biological resource to humans [ 1 , 3 , 4 ]. The intention of this article is to describe some of the key concepts, tools, and its applications in bioinformatics that are relevant to plant biotechnologies. The current challenges and limitations for improvement and continuous development of bioinformatics in plant science are also described.

Applications of bioinformatics in plant biotechnology

The introduction of bioinformatics and computational biology into the area of plant biology is drastically accelerating scientific invention in life science. With the aid of sequencing technology, scientists in plant biology have revealed the genetic architecture of various plant and microorganism species, such as proteome, transcriptome, metabolome, and even their metabolic pathway [ 1 ]. Sequence analysis is the most fundamental approach to obtain the whole genome sequence such as DNA, RNA, and protein sequence from an organism’s genome in modern science. The sequencing of whole genome permits the determination of organization of different species and provides a starting point to understand their functionality. A complete sequence data consists of coding and non-coding regions, which can act as a necessary precursor for any functional gene that determines the unique traits possessed by organisms. The resulting sequence includes all regions such as exons, introns, regulator, and promoter, which often leads to a vastly large amount of genome information [ 5 ]. With the emergence of next-generation sequencing (NGS) and some other omics technologies used to examine plants genomics, more and more sequenced plants genome will be revealed [ 1 , 6 , 7 , 8 ]. To deal with these vast amounts of data, the development and implementation of bioinformatics allow scientists to capture, store, and organize them in a systematic database [ 1 , 5 ].

Bioinformatics databases and tools for plant biotechnology

In the field of bioinformatics, there are a variety of options of databases and tools that are available to perform analysis related to plant biotechnology. Next-generation sequencing (NGS) and bioinformatics analysis on the plant genomes over the years have generated a large amount of data. All these data are submitted to various and multiple databases that are publicly available online. Each database is unique and has its focus. For instance, CottonGen, database is solely dedicated to obtaining genomics and breeding information of any cotton species of interest [ 9 ]. The establishment of such database eases the researchers who are working on cotton genomic studies by focussing on using just one database instead of searching through other available databases. However, some databases are established and designed to cater not only to one specific species or genus, but focus on all the plant species, such as the National Center for Biotechnology Information (NCBI) ( https://www.ncbi.nlm.nih.gov/ ) database, which as of 2021 possesses almost 21,000 plant genomes that are available for access [ 10 ]. Such a database is useful for studies that do not focus on one specific genus or species. This eases the researchers in accessing to all kinds of genomic data in one database. This section will briefly discuss some of the available plant genome databases, which are publicly accessible and not designated for one genus or species alone.

First would be the globally known and recognized database by all the researchers and biologists, which is the NCBI database. NCBI has been dedicated for gathering and analysing information about molecular biology, biochemistry, and genetics. In the NCBI database, one can download the genome information of the plant species of interest from either gene expression omnibus (GEO) ( https://www.ncbi.nlm.nih.gov/geo/ ) or sequence read archive (SRA) ( https://www.ncbi.nlm.nih.gov/sra ) by simply stating the scientific name of the plant in the search bar and the entire genomic information of the plant can then be obtained. The GEO and SRA comprise processed or raw gene expression data or RNA sequencing of plants that are reposited in the repository. For instance, to obtain the genomics of Rosa chinensis (Rose plant), by inputting the name in the search bar, it will direct to the search result page where the researcher can select the most recent or suitable datasets with specific accession number. Depending on the profiling platform used in each dataset, researchers could retrieve either gene symbols, Ensemble ID, open reading frame, chromosomal location, regulatory elements, etc. The information allows researcher to further analyse the subject of study using bioinformatics tools such as gene ontology ( http://geneontology.org/ ), Database for Annotation, Visualization and integration Discovery (DAVID) ( https://david.ncifcrf.gov/ ), Basic Local Alignment Search Tool (BLAST) ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ), and others that is relevant for the study.

Another database that is available for accessing plant genome database is EnsemblPlants ( https://plants.ensembl.org/index.html ). Unlike the NCBI database, which is not only dedicated to plant genomes, EnsemblPlants is specifically dedicated to accessing plant genomes. EnsemblPlant is part of the Ensembl project that started in 1999, where the project aimed to automatically annotate the genome and integrate the outcome of the annotation with other publicly available biological data and establish an open access archive or database online for the use of the research community [ 11 ]. Ensembl project later launched the taxonomic specific websites designated for each taxon under their project that also includes the plants. The database is a user-friendly integrative platform, where it is continuously updated with the new addition of plant species every time a plant genome is completely sequenced. Compared to the NCBI database mentioned earlier, EnsemblPlant not only provides genome sequence, gene models, and functional annotation of the plant species of interest, but also includes the polymorphic loci, population structure, genotype, linkage, and phenotype information [ 11 , 12 ]. Unlike, NCBI, EnsemblPlant does also provide comparative genomics data of the plant species of interest. This indicates that the platform does not only offer genome sequence data but provide additional analytical data about the plant species of interest and help the researchers who are working on plant bioinformatics to save a lot of time by reducing the tedious work in running the analysis. Yet, the researchers could re-assess the data if necessary, depending on the stringency of their work.

Aside from the abovementioned databases that are widely used for retrieving plant genome sequence, there are still other plant databases such as PlantGDB, MaizeDIG, and Phytozome that can also be considered. Table 1 lists the available database and tools that are widely applied in plant biotechnology.

Biotechnology and bioinformatics for plant breeding

Plant breeding can be defined as the changing or improvement of desired traits in plants to produce improved new crop cultivars for the benefits of humankind [ 8 ]. Jhansi and Usha [ 13 ] mentioned a few benefits brought by genetically engineered plants such as improved quality, enhanced nutritional value, and maximized yield. The revolution of life science in molecular biology and genomics has enabled the leaps forward in plant breeding by applying the knowledge and biological data obtained in genomics research on crops [ 6 , 8 , 13 ]. In modern agriculture, transgenic technology on plants refers to genetic modification, which is done on plants or crops by altering or introducing foreign genes into the plant, to make them useful and productive and enhance their characteristic [ 13 , 14 ]. As mentioned above, the evolution of next-generation sequencing (NGS) and other sequencing technologies produces a large size of biological data which require databases to store the information. The accessibility of whole genome sequences in databases allows free association across genomes with respect to gene sequence, putative function, or genetic map position. With the aid of software, it is possible to formulate predictive hypothesis and incorporate the desired phenotypes from a complex combination into plants by looking at those genetic markers which score well and gives a higher reliability in breeding [ 2 , 15 ]. Other than genome sequence information, databases which store the information of metabolites also play a crucial role in the study of interaction with proteomics and genomics to reflect the changes in phenotype and specific function of an organism [ 1 ]. Some of the most widely used metabolomics databases for plants and crops such as Metlin ( http://metlin.scripps.edu ), provides multiple metabolite searching and about 240,000 metabolites, nearly 72,000 high-resolution MS/MS spectra, and PlantCyc ( https://plantcyc.org/ ), a database which stores information about biochemical pathway and their catalytic enzyme and genes from plants [ 1 , 16 ]. Moreover, single-nucleotide polymorphism markers also benefit from the revolution of NGS and other sequencing technologies. By using NGS, RNA sequencing (RNA-seq) allows direct measure of mRNA profile in order to identify known single-nucleotide polymorphism (SNP) [ 1 ]. SNP is the unique allelic variation within a genome of same species, which can be used as biological markers to locate the genes associated with desired traits in plants [ 17 , 18 ]. Besides, transcriptome resequencing using NGS allows rapid and inexpensive SNP discovery within a large, complex gene with highly repetitive regions of a genome such as wheat, maize, sugarcane, avocado, and black currant [ 17 ]. Figure 1 illustrates briefly the process involved in plant breeding using NGS and bioinformatics.

Brief process of plant breeding involving NGS and bioinformatics

Ever since the first transgenic rice production in 2000, there has been a significant revolution in crop genome sequencing projects, along with the advancement in technologies, rapidly increasing the pace in genetically modified organism (GMO) [ 2 , 13 , 19 ]. Among all the products in rice biotechnology, one of the most widely known GM rice is golden rice. Golden rice is a variety of rice engineered by introducing the biosynthetic pathway to produce β-carotene (pro-vitamin A) into staple food in order to resolve vitamin A deficiency. The World Health Organization has classified vitamin A deficiency as public health problem as it causes half a million of children to childhood blindness [ 13 ]. Vitamin A is an essential nutrient to humans as it helps with development of vision, growth, cellular differentiation, and proliferation of immune system; insufficient intake of vitamin A may lead to childhood blindness, anaemia, and reduced immune responsiveness against infection [ 20 ]. Being the first crop genome to be sequenced, rice has become the most suitable model to initiate the development and improvement of other species in genomic aspect [ 21 , 22 , 23 , 24 ]. The particular reason is due to its small genome size and diploidy, which enables rice to be an excellent model for other cereal crops with larger genomes, such as maize and wheat [ 21 , 23 ]. Song et al. [ 22 ] reported the complete genome sequence of two rice subspecies, japonica and indica , in 2005 that laid a strong foundation for molecular studies and plant breeding research [ 22 , 24 ]. With recent advancement in bioinformatics, it is now possible to run the sequence alignment between large and complex genome from other crop species with genomic data available from rice, by using different software or tools, in order to find out the shared conserved sequence through comparative genomics [ 2 , 7 ]. Vassilev et al. stated some of the most commonly used programmes such as BLAST and FASTA format allowed rapid sequence searching in databases and give the best possible alignment to each sequence [ 25 ]. The programming algorithm calculates the alignment score to measure the proportion of homology matching residue between sequence from related species [ 2 ].

Wheat, as the most widely grown consumed crops, together with rice and maize contributes more than 60% of the calories and protein for our daily life [ 26 , 27 ]. To meet the demands of human population growth, it is necessary to achieve more understanding in wheat research and breeding in order to accelerate the production of wheat yield by 2050 [ 26 , 27 , 28 ]. Despite its importance, the improvement of wheat has been challenging as the researchers have to overcome the complexity of the wheat genome such as highly repetitive and large polyploid in order to get a fully sequenced reference genome [ 26 , 29 ]. Advances in next-generation sequencing (NGS) platforms and other bioinformatics tools have revealed the extensive structural rearrangements and complex gene content in wheat, which revolutionized wheat genomics with the improvement of wheat yield and its adaptation to diversed environments [ 26 , 29 ]. The NGS platforms allow the swift detection of DNA markers from the huge genome data in a short period of time. These NGS-based approaches have undoubtedly revolutionized the allele discovery and genotype-by-sequencing (GBS). By providing a high-quality reference genome of wheat in databases, it allows more sequence comparison between wheat and other species to find out more homologous gene. Moreover, the development of sequencing technologies in both high-throughput genotyping and read length, combining with biological databases, allow the rapid development of novel algorithm to complex wheat genome [ 29 , 30 ]. For instance, genome-wide association studies (GWAS) are an approach used in genome research which allows rapid screening of raw data to select specific regions with agronomic traits [ 29 , 31 ]. It allows multiple genetic variants across genome to be tested to study the genotype-phenotype association; thus, this method can be used to facilitate improvement in crop breeding via genomic selection and genetic modification [ 16 , 29 ].

Maize, a globally important crop, not only has a wide variety of uses in terms of economic impact, but can also serve as genetic model species in genotype to phenotype relationship in plant genomic studies [ 32 , 33 ]. Besides, due to its extremely high level of gene diversity, maize has high potential in the improvement of yield to meet the demands of population growth [ 33 ]. Despite the combination of economic and genomic impact, the progress in generating a whole genome sequence in maize has been a computational challenge due to the presence of tremendous structural variation (SV) in its genome [ 34 ]. The introduction of NGS techniques in several crops including maize allowed the rapid de novo genome sequencing and production of huge amount genomics and phenomics information [ 1 , 35 ]. A better integration of data within multiple genome assemblies is much needed to study the connection between phenotype and genotype in order to achieve yield and quality improvement of maize [ 35 ]. Nowadays, some user-friendly online databases such as qTeller, MaizeDIG, and MaizeMine are designed to ease the comparison and visualization of relationships between genotypes and phenotypes [ 36 ]. MaizeGDB, a model organism database for maize, provides the access of data on genes, alleles, molecular markers, metabolic pathway information, phenotypic images with description, and more which are useful for maize research [ 35 , 36 ]. MaizeMine is a data mining resource under MaizeGDB, which was designed to accelerate the genomics analysis by allowing the researchers to better script their own research data in downstream analysis [ 36 ] whereas MaizeDIG is a genotype-phenotype database which allows the users to link the association of genotype with phenotype expressed by image [ 35 , 36 ]. Cho et al. [ 35 ] reported that with the accessibility via image search tool, the relationship between a gene and its phenotype features can be visualized within image. The integration and visualization of high-quality data with these tools enables quick prioritizing phenotype of interest in crops, which play a crucial role in the improvement of plant breeding.

Bioinformatics for studying stress resistance in plants

The understanding of the stress response on plants is vital for the improvement of breeding efforts in agriculture, and to predict the fate of natural plants under abiotic change especially in the current era of continuous climate change [ 37 ]. Stress response in plants can be divided into biotic and abiotic. Biotic stress mainly refers to negative influence caused by living organism such as virus, fungi, bacteria, insects, nematodes, and weeds [ 38 ] while abiotic stress refers to factors such as extreme temperature, drought, flood, salinity, and radiation which dramatically affect the crop yield [ 37 ]. NGS technologies and other potent computational tools, which allowed sequencing of whole genome and transcriptome, have led to the extensive studies of plants towards stress response on a molecular basis [ 1 , 2 , 37 ]. The tremendous amount of plant genome data obtained from genome sequencing allows the investigation of correlations between the molecular backbone of living organism and their adaptations towards the environment [ 16 ].

Biotic and abiotic stress management

How the plants and crops respond towards stress environment is the key to ensure their growth and development, and to avoid the great crop yield penalty caused by harsh condition [ 35 , 39 ]. Therefore, the utilization of bioinformatic tools is important to study and analyse the plant transcriptome in response to biotic and abiotic stress. Besides, the application of bioinformatics tools on plants and crops genome can benefit the agricultural community by searching the desired gene among genome from different species and elucidate their function on the crops [ 35 ]. The genome databases play a crucial role in storing and mining large and complex genome sequence from the plants. Besides data storage, some genome databases are also able to perform gene expression profiling to predict the pattern of gene expressed at the level of transcript in cell or tissues. By using in silico genomic technologies, the disease resistance gene-enzyme with their respective transcription factor, which plays a role in defence mechanism against stress, are able to be identified [ 40 , 41 ]. For instance, a large-scale transcriptome sequencing of chrysanthemum plants was carried out by Xu et al. [ 40 ] to study the dehydration stress in chrysanthemum plants. An online database called Chrysanthemum Transcriptome Database ( http://www.icugi.org/chrysanthemum ) was developed to allow the storage and distribution of transcriptome sequence and its analysis result among research community [ 40 ]. With the aid of different protein databases, the biochemical pathway and kinase activity of chrysanthemum in response to dehydration stress are able to be predicted [ 40 ]. Xu et al. [ 40 ] also reported a total of 306 transcription factor and 228 protein kinase that are important upstream regulator in plants when encountered with various biotic and abiotic stresses.

Bioinformatics approaches to study resistance to plant pathogen

One of the challenges in modern agriculture to supply the nutrition’s demand along with the world population growth is the crop loss due to disease. The study of plant pathogen plays an essential role in the study of plant diseases, including pathogen identification, disease aetiology, disease resistance, and economic impact, among others [ 41 ]. Plants protect themselves through a complex defence system against variety of pathogen, including insects, bacteria, fungi, and viruses. Plant-pathogen interaction is a multicomponent system mediated by the detection of pathogen-derived molecules in the form of protein, sugar, and polysaccharide, by pattern recognition receptor (PRRs) within the plants [ 42 , 43 , 44 , 45 ]. After the recognition of enemy molecules, signal transduction is carried out accordingly and plant immune systems will respond defensively through different pathways involving different genes [ 42 ]. According to Schneider et al. [ 46 ], the development of molecular plant pathology can be broadly divided into three eras, begins with the disease physiology starting from early 1900s until 1980s [ 46 ]. In the second era of molecular plant genetic studies, one or a few genes of bacterial pathogens were focused whereas the third era of plant genomic studies began in 2000 with the sequencing of genome, and the first complete genome of bacterial pathogen, Xylella fastidiosa , was obtained [ 46 ]. The recent advance in DNA sequence technologies allow researchers to study the immune system of plants on genomic and transcriptomics level [ 1 , 41 , 42 ]. Genomics has revealed the mystery and complexity and consequently the various information about phytopathogen. A clearer picture of plant-pathogen interactions in the context of transcriptomic and proteomics can be visualized through the application of different bioinformatics tools, which in turn made feasible the engineering resistance to microbial pathogen in plant [ 43 ].

PRGdb: bioinformatics web for plant pathogen resistance gene analysis

Plants have developed a wide range of defence mechanism against different pathogen and ultimately inhibit growth and spread of pathogen [ 47 , 48 ]. Plant defence system is mediated by resistance (R) gene [ 47 ]. R gene plays an important role in defence mechanism. They encode for protein that recognizes specific avirulent (Avr) pathogen proteins and initiated the defence mechanism through one or more signal transduction pathway in a hypersensitive response (HR) [ 41 , 47 , 48 ]. However, the essential components needed for protein to exert their resistance are still unidentified [ 48 ]. With the intention to study and identify more novel R gene, high-throughput genomic experiments and plant genomic sequence are essential to explore their function and new R gene discovery [ 47 ]. In 2009, Plant Disease Resistance Gene database (PRGdb), a comprehensive bioinformatics resource across hundreds of plant species, was launched in order to facilitate the plant genome research on discovery and predict plant disease resistance gene [ 47 , 48 ]. To date, PRGdb 3.0 has been released with 153 reference resistance genes and 177,072 annotated candidate pathogen receptor genes (PRGs) [ 49 ]. This database act as an important reference site and repository to all the research studies on exploration and use of plant resistance genes [ 48 , 49 ].

Apart from resistance gene storage, this easily accessible platform also allows different tools that are essential for exploration and discovery of novel R gene. For instance, the DRAGO 2.0 tool, which was built to explore known and novel disease resistance gene, can be launched on any transcriptome or proteome to annotate and predict PRG from DNA or amino acid with high accuracy [ 49 ]. Besides, BLAST search tools available in PRGdb provide comparison of different sequences which allowed the determination of gene homology and expression analysis. Apart from the database, plant pathology field also benefited from whole genome sequence technologies. The new DNA sequencing technologies such as NGS and Sanger sequencing allowed the study of genomics, proteomics, metabolomics, and transcriptomics on both the host plant and the pathogen [ 1 ]. The phytopathogen genomes which have been sequenced are expected to provide valuable information on the molecular basis for infection of plant host and explore the potential novel virulence factors [ 1 ]. Figure 2 illustrates a brief process involved in producing stress-resistant plant using bioinformatics approach.

Brief process involved in producing stress-resistant plant using bioinformatics approach

Metagenomics in plant biotechnology and Cas9 modification

The effects of environment microorganisms’ community, especially soil microorganism on plants, may contribute to plant’s growth and pathogenesis. Through metagenomics approaches, the soil microorganism community that contributed to plant growth may provide a great genomic insight into physiology and pathology [ 50 , 51 , 52 , 53 ]. In metagenomics approaches, the overall genetic materials obtained from soil are sequenced and advancing to microbial community analysis via data analytics [ 53 , 54 , 55 ]. The extracted genetic materials from the soil were subjected to high-throughput metagenomics analysis via various NGS approaches such as 16S rRNA sequencing, shotgun metagenomic sequencing, MiSeq sequencing [ 54 , 55 , 56 ] for microbial species identification, functional genomics study, and structural metagenomic analysis. A NGS produces huge genomics data for each study; thus, application of bioinformatics tools would add value in the metagenomics analysis as the target genes identified could advance into elucidation of plant growth, plant disease, soil contamination, and microbial taxonomy [ 52 ]. For example, the use of UNITE ( https://unite.ut.ee/ ) for fungi identification [ 57 ], SILVA ( https://www.arb-silva.de/ ) for 16S rRNA [ 58 ], and MGnify ( https://www.ebi.ac.uk/metagenomics/ ) possesses metagenomics data of microbiome [ 59 ]. These databases allow the researchers to retrieve and analyse the relevant metagenomic sequenced data for a specific study.

Since metagenomics analysis provides the greater output on plant-microbe interaction, the genes that are responsible for plant immunity may play a crucial role in protecting against disease-causing microorganism [ 60 , 61 ]. With the emergence of Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) gene editing technique, Cas9 modification could produce a better plant trait and disease-resistant plant [ 62 , 63 ]. The CRISPR/Cas9 system is employed in studying the functional genomics in plants in relation to plant-microbe interaction. CRISPR/Cas9 system facilitated the gene editing by creating a mutant through double-stranded break forming a targeted gene mutation and followed by genome repair [ 63 , 64 , 65 ]. The CRISPR/Cas9 modification on OsSWEET14 genes protects the Super Basmati Rice from bacterial blight causes by Xanthomonas oryzae pv. oryzae [ 66 ]. Gene editing to knockout OsMPK5 and OsERF922 genes in rice protects against Magnaporthe grisea and Magnaporthe oryzae , respectively [ 67 , 68 , 69 ]. Besides that, Cas9 modification on Cs WRKY22 and TcNPR3 increased host defence immunity through regulating salicylic acid in Citrus sinensis and Theobroma cacao , respectively [ 70 , 71 ]. Thus, CRISPR/Cas9 modification could be one of important science advancements to validate the metagenomics analysis on plant-microbe interaction.

Current challenges of bioinformatics applications in plant biotechnology

Despite the beneficial prospect of the bioinformatics applied in plant biotechnology, there are many challenges and limitations must be addressed in order to fully utilize their potentials [ 1 ]. Along with the rapid growth in plant genome data mining and database development, there are a few challenges faced by bioinformaticians and scientists which can be divided into number of areas as mentioned in the subsections below.

Bioinformatic data management and organization and synchronize update resources

Since the introduction of the next-generation sequencing (NGS), which is commercially available in 2004, enormous amount of data has been generated in plant genome research. Thousands of Gb of plants sequences are deposited in various public databases monthly [ 1 , 72 , 73 ]. Moreover, the constantly sequenced and re-sequenced of the plant genome has developed a vast amount of new genome sequence in all public databases. The increase in sequenced plant genome driven by technological improvement has led to a problem that arises along with the storage and update of a large amount of data [ 72 , 74 ]. The update process should occur in all the comparative databases, not just solely individual genome database [ 72 ]. With this, the synchronized update of genome data resources among different plant genomic platform is able to provide a strong, updated, reliable database community that all the plant researchers can rely on [ 72 ].

Complexity of plant genetic content

Other than the tremendous amount of genome sequence generated, the complexity of the plant genetic content is also a challenging issue faced by plant research community. Even though the arrival of next-generation sequencing technologies has allowed the rapid DNA sequencing for non-model or orphan plant species, the sequencing pace for plants is far from that of animal and microorganism [ 74 ]. The main factor which contributes to this situation is because sometimes the plant genome can be nearly hundred times larger than the currently sequenced animal and microorganism genome [ 73 ]. Needless to say, some of the plant genome even can have polyploidy, a duplication of an entire genome, which is estimated to occur in 80% of the plant species [ 73 , 75 ]. According to Schatz et al., the genome assembly in the case of large size plant genome with abundance of repetitive sequence can be metaphorically described as build-up of a large puzzle consisting of blue sky separated by nearly indistinguishable white clouds of small gene [ 73 ]. The particular reason for this is mainly because the sequence length in NGS is relatively shorter than in Sanger sequencing and required dedicated assembly algorithm [ 74 ]. Therefore, most plant genomes sequenced by NGS can only be used for establishing gene catalogues, interpreting the repeat content, glimpsing evolutionary mechanism, and performing on comparative genomics in early study [ 74 ].

Advance in sequencing technologies

There are two basic approaches to genome assembly, i.e. comparative genome assembly and de novo genome assembly [ 75 ]. It is important to distinguish between these two different approaches. Comparative is a reference-guided method which use a genome or transcriptome, or both, for guidance, whereas de novo assembly refers to reconstruction of a genome from organisms that have not been sequenced before [ 74 , 75 ]. Table 2 compares some of the available assembly and NGS technology available for genome sequencing. However, these two approaches are not completely exclusive due to a lack of bioinformatic tools designed to cope with the unique and challenging features of plant genomes [ 74 , 75 ]. One of the biggest challenges in the development of bioinformatic software is the algorithm development [ 76 ]. As is known, all the programmes or software in bioinformatic are very computationally intensive. As most of the assemblies available now solely rely on single assembly, a development in better algorithm in terms of resource requirement is essential for combining different assemblers by using a different underlying algorithm in order to give a more credible final assembly [ 74 , 76 ].

Database accessibility

To date, there are about 374,000 known plant species in the world [ 77 ]. The first full plant genome sequencing was completed on A rabidopsis thaliana through Sanger sequencing methods in 2000 [ 78 ]. Although introduction of molecular biology decades ago may have facilitated the species identification, obtaining the full plant genomic data remains challenging due to the genome complexity. The development of NGS platform may foster the plant genome sequencing, yet there are limited sequenced datasets reposited to the database. To date, there are only 29 plant genome databases accessible in PlantGDB genome browser allowing researchers to retrieve the information about gene structure, matched GSS contigs, similar protein, spliced alignments EST, etc. Besides, the PlaD database ( http://systbio.cau.edu.cn/plad/index.php ) that focuses on the microarray data of the plants developed by China Agricultural University comprises transcriptomic database for plant defence against pathogen. However, it is limited to Arabidopsis , rice, maize, and wheat [ 79 ]. The Plant Omics Data Center ( http://plantomics.mind.meiji.ac.jp/podc/ ) is another publicly available web-based plant database featuring omics data for co-expressed profile, regulatory network, and plant ontology information [ 80 ]. Although curated omics datasets could be retrieved from PODC, information are restricted for certain plants and crops such as Arabidopsis , tobacco, earthmoss, barrelclover, soybean, potato, rice, tomato, grape, maize, and sorghum. Furthermore, all these publicly available databases require constant updating with new released data or resequencing data so that the researcher could obtain the most updated version of genome datasets for their research.

The application of bioinformatics in plant biotechnology represents a fundamental shift in the way scientists study living organisms. Bioinformatics play a significant role in the development of agriculture sector as it helps to study the stress resistance and plant pathogen, which are critical in advancing crop breeding [ 75 ]. NGS and other sequencing technologies will make more plant genome data accessible in all public databases and enable the identification of genomic variants and prediction of protein structure and function [ 75 , 76 ]. Moreover, GWAS, which allows the identification of loci and allelic variation related to valuable traits, eased the crop modification and improvement [ 74 ]. In brief, the advance in bioinformatics application in plant biotechnology enables researchers to achieve fundamental and systematic understanding of economically important plant. However, despite all these exciting achievement by the application of bioinformatic on plant biotechnology, it is still a long way from automated full genome sequencing and assembly at a low cost [ 76 ]. There is a critical need for effective bioinformatic tools which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant’s genome. To achieve this, an enhanced algorithm development is essential to enable data mining and analysis, comparison, and so on. Therefore, bioinformaticians and experts with mathematical and programming skills will play an important role in bringing fresh approaches and knowledge into bioinformatics, not only for the advancement in plant biotechnology and agriculture sector, but the future of humanity as well.

Availability of data and materials

Not applicable.

Abbreviations

Genome-wide association studies

Next-generation sequencing

Plant Disease Resistance Gene database

RNA sequencing

Single-nucleotide polymorphism

Gomez-Casati DF, Busi MV, Barchiesi J, Peralta DA, Hedin N, Bhadauria V (2018) Applications of bioinformatics to plant biotechnology. Curr Issues Mol Biol 27:89–104. https://doi.org/10.21775/cimb.027.089

Article   Google Scholar  

Zhang SY, Liu SL (2013) Bioinformatics. In: Maloy S, Hughes K (eds) Brenner’s Encyclopedia of Genetics, 2nd edn. Academic Press, London. https://doi.org/10.1016/B978-0-12-374984-0.00155-8

Chapter   Google Scholar  

Tiwari A, Singh P, Kumawat S (2020) Applications of bioinformatics in plant breeding system. Int J Curr Microbial App Sci. 11:2825–2831

Google Scholar  

Rhee SY, Dickerson J, Xu D (2006) Bioinformatics and its applications in plant biology. Annu Rev Plant Biol 57:335–360. https://doi.org/10.1146/annurev.arplant.56.032604.144103

Normand EA, Van den Veyyer IB (2019) Next-generation sequencing for gene panels and clinical exomes. In: Leung PCK, Qiao J (eds) Human Reproductive and Prenatal Genetics, 1st edn. Academic Press, London. https://doi.org/10.1016/B978-0-12-813570-9.00025-5

Blätke MA, Szymanski JJ, Gladilin E, Scholz U, Beier S (2021) Editorial: advances in applied bioinformatics in crops. Front Plant Sci 12:640394. https://doi.org/10.3389/fpls.2021.640394

Kushwaha UKS, Deo I, Jaiswal JP, Prasad B (2017) Role of bioinformatics in crop improvement. Glob J Sci Front Res D Agric Vet 17(1):13–23

Caligari PDS, Brown J (2017) Plant Breeding, Practice. In: Thomas B, Murray BG, Murphy DJ (eds) Encyclopedia of Applied Plant Sciences, 2nd edn. Academic Press, London. https://doi.org/10.1016/B978-0-12-394807-6.00195-7

Yu J, Jung S, Cheng CH, Lee T, Zheng P, Buble K et al (2021) CottonGen: the community database for cotton genomics, genetics, and breeding research. Plants. 10(12):2805. https://doi.org/10.3390/plants10122805

Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC et al (2022) Database resources of the national center for biotechnology information. Nucleic Acids Res 50(D1):D20–D26. https://doi.org/10.1093/nar/gkab1112

Howe KL, Contreras-Moreira B, De Silva N, Maslen G, Akanni W, Allen J et al (2019) Ensembl Genomes 2020 – enabling non-vertebrate genomic research. Nucleic Acids Res 48(D1):D689–D695. https://doi.org/10.1093/nar/gkz890

Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomics data. In: Edwards D (ed) Plant Bioinformatics. Methods in Molecular Biology, vol 1374. Humana Press. https://doi.org/10.1007/978-1-4939-3167-5_6

Jhansi Rani S, Usha R (2013) Transgenic plants: Types, benefits, public concerns and future. J Pharm Res 6(8):879–883. https://doi.org/10.1016/j.jopr.2013.08.008

Barragán-Ocaña A, Reyes-Ruiz G, Olmos-Peña S, Gómez-Viquez H (2019) Transgenic crops: trends and dynamics in the world and in Latin America. Transgenic Res 28(3-4):391–399. https://doi.org/10.1007/s11248-019-00123-8

Platten JD, Cobb JN, Zantua RE (2019) Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection. PLoS One 14(1):e0210529. https://doi.org/10.1371/journal.pone.0210529

Filho HA, Machicao J, Bruno OM (2018) A hierarchical model of metabolic machinery based on the kcore decomposition of plant metabolic networks. PLoS One 13(5):e0195843. https://doi.org/10.1371/journal.pone.0195843

Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 728398:1–11. https://doi.org/10.1155/2012/728398

Hoskins RA, Phan AC, Naeemuddin M, Mapa FA, Ruddy DA, Ryan JJ et al (2001) Single nucleotide polymorphism markers for genetics mapping in Drosophila melanogaster . Genome Res 11(6):1100–1113. https://doi.org/10.1101/gr.gr-1780r

Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 8(1):2–9. https://doi.org/10.1111/j.1467-7652.2009.00459.x

Tang G, Qin J, Dolnikowski GG, Russell RM, Grusak MA (2009) Golden Rice is an effective source of vitamin A. Am J Clin Nutr 89(6):1776–1783. https://doi.org/10.3945/ajcn.2008.27119

Yu J, Hu S, Wang J, Wong GKS, Li S, Liu B et al (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. Indica ). Science. 296(5565):79–92. https://doi.org/10.1126/science.1068037

Song S, Tian D, Zhang Z, Hu S, Yu J (2018) Rice genomics: over the past two decades and into the future. Genomics Proteomics Bioinformatics 16(6):397–404. https://doi.org/10.1016/j.gpb.2019.01.001

Jackson SA (2016) Rice: The First Crop Genome. Rice. 9(14). https://doi.org/10.1186/s12284-016-0087-4

Jain R, Jenkins J, Shu S, Chern M, Martin JA, Copetti D et al (2019) Genome sequence of the model rice variety KitaakeX. BMC Genomics 20(905). https://doi.org/10.1186/s12864-019-6262-4

Vassilev D, Leunissen J, Atanassov A, Nenov A, Dimov G (2005) Application of bioinformatics in plant breeding. Biotechnol Biotechnol Equip 19(sup3):139–152. https://doi.org/10.1080/13102818.2005.10817293

Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J et al (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature. 588(7837):277–283. https://doi.org/10.1038/s41586-020-2961-x

Appels R, Eversole K, Stein N, Feuillet C, Keller B, Rogers J et al (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science. 361(6403). https://doi.org/10.1126/science.aar7191

Gill BS, Appels R, Borta-Oberholster AM, Buell CR, Bennetzen JL, Chalhoub B et al (2004) A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium. Genetics. 168(2):1087–1096. https://doi.org/10.1534/genetics.104.034769

Babu P, Baranwal DK, Harikrishna PD, Bharti H, Joshi P et al (2020) Application of genomics tools in wheat breeding to attain durable rust resistance. Front Plant Sci 11:567147. https://doi.org/10.3389/fpls.2020.567147

Guan J, Garcia DF, Zhou Y, Appels R, Li A, Mao L (2020) The battle to sequence the bread wheat genome: a tale of the three kingdoms. Genomics Proteomics Bioinformatics 18(3):221–229. https://doi.org/10.1016/j.gpb.2019.09.005

Bolser D, Staines DM, Pritchard E, Kersey P (2016) Ensembl plants: integrating tools for visualizing, mining and analyzing plant genomics data. Methods Mol Biol 1374:115–140. https://doi.org/10.1007/978-1-4939-3167-5_6

Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G et al (2005) Structure and architecture of the maize genome. Plant Physiol 139(4):1612–1624. https://doi.org/10.1104/pp.105.068718

Li C, Song W, Luo Y, Gao S, Zhang R, Shi Z et al (2019) The HuangZaoSi maize genome provides insights into genomic variation and improvement history of maize. Mol Plant 12(3):402–409. https://doi.org/10.1016/j.molp.2019.02.009

Lu F, Romay MC, Glaubitz JC, Bradbury PJ, Elshire RJ, Wang T et al (2015) High-resolution genetic mapping of maize pan-genome sequence anchors. Nat Commun 6:6914. https://doi.org/10.1038/ncomms7914

Cho KT, Portwood JL, Gardiner JM, Harper LC, Lawrence-Dill CJ, Friedberg I et al (2019) MaizeDIG: maize database of images and genomes. Front Plant Sci 10:1050. https://doi.org/10.3389/fpls.2019.01050

Portwood JL, Woodhouse MR, Cannon EK, Gardiner JM, Harper LC, Schaeffer ML et al (2018) MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Res 47(D1):D1146–D1154. https://doi.org/10.1093/nar/gky1046

Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML (2020) Bioinformatics resources for plant abiotic stress responses: state of the art and opportunities in the fast evolving -omics era. Plants. 9(5):591. https://doi.org/10.3390/plants9050591

Singla J, Krattinger SG (2016) Biotic stress resistance genes in wheat. Reference Module in Food Science. https://doi.org/10.1016/B978-0-08-100596-5.00229-8

Costa MCD, Farrant JM (2019) Plant resistance to abiotic stresses. Plants (Basel) 8(12):553. https://doi.org/10.3390/plants8120553

Xu Y, Gao S, Yang Y, Huang M, Cheng L, Wei Q et al (2013) Transcriptome sequencing and whole genome expression profiling of chrysanthemum under dehydration stress. BMC Genomics 14:662. https://doi.org/10.1186/1471-2164-14-662

Nishad R, Ahmed T, Rahman VJ, Kareem A (2020) Modulation of plant defense system in response to microbial interactions. Front Microbiol 11:1298. https://doi.org/10.3389/fmicb.2020.01298

Andersen EJ, Ali S, Byamukama E, Yen Y, Nepal MP (2018) Disease resistance mechanisms in plants. Genes (Basel) 9(7):339. https://doi.org/10.3390/genes9070339

Dong OX, Ronald PC (2019) Genetic engineering for disease resistance in plants: recent progress and future perspectives. Plant Physiol 180(1):26–38. https://doi.org/10.1104/pp.18.01224

Abdulkhair WM, Alghuthaymi MA (2016) Plant pathogens. In: Rigobelo EC (ed) Plant Growth, 1st edn. InTechOpen. https://doi.org/10.5772/65325 Available from: https://www.intechopen.com/chapters/52387

Gupta R, Lee SE, Agrawal GK, Rakwal R, Sangryeol P, Wang Y et al (2015) Understanding the plant-pathogen interactions in the context of proteomics-generated apoplastic proteins inventory. Front Plant Sci 6:352. https://doi.org/10.3389/fpls.2015.00352

Schneider DJ, Collmer A (2010) Studying plant-pathogen interactions in the genomics era: beyond Molecular Koch’s postulates to systems biology. Annu Rev Phytopathol 48:457–479. https://doi.org/10.1146/annurev-phyto-073009-114411

Sanseverino W, Hermoso A, D’Alessandro R, Vlasova A, Andolfo G, Frusciante L et al (2013) PRGdb 2.0: towards a community-based database model for the analysis of R-genes in plants. Nucleic Acids Res 41(Database Issue):D1167–D1171. https://doi.org/10.1093/nar/gks1183

Sanseverino W, Roma G, Simone MD, Faino L, Melito S, Stupka E et al (2010) PRGdb: a bioinformatics platform for plant resistance gene analysis. Nucleic Acids Res 38(Database Issue):D814–D821. https://doi.org/10.1093/nar/gkp978

Osuna-Cruz CM, Paytuvi-Gallart A, Donato AD, Sundesha V, Andolfo G, Cigliano RA et al (2018) PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. Nucleic Acids Res 46(D1):D1197–D1201. https://doi.org/10.1093/nar/gkx1119

Hily JM, Demanèche S, Poulicard N, Tannières M, Djennane S, Beuve M et al (2018) Metagenomic-based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome. Plant Biotechnol J 16(1):208–220. https://doi.org/10.1111/pbi.12761

Fadiji AE, Babalola OO (2020) Metagenomics methods for the study of plant-associated microbial communities: a review. J Microbiol Methods 70:105860. https://doi.org/10.1016/j.mimet.2020.105860

Piombo E, Abdelfattah A, Droby S, Wisniewski M, Spadaro D, Schena L (2021) Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms. 9(1):188. https://doi.org/10.3390/microorganisms9010188

Chaudhary P, Khati P, Chaudhary A, Maithani D, Kumar G, Sharma A (2021) Cultivable and metagenomic approach to study the combined impact of nanogypsum and Pseudomonas taiwanensis on maize plant health and its rhizospheric microbiome. PLoS One 16(4):e0250574. https://doi.org/10.1371/journal.pone.0250574

Chukwuneme CF, Ayangbenro AS, Babalola OO (2021) Metagenomic analyses of plant growth-promoting and carbon-cycling genes in maize rhizosphere soils with distinct land-use and management histories. Genes (Basel) 12(9):1431. https://doi.org/10.3390/genes12091431

Zhao J, Ma J, Yang Y, Yu H, Zhang S, Chen F (2021) Response of soil microbial community to vegetation reconstruction modes in mining areas of the Loess Plateau, China. Front Microbiol 12:714967. https://doi.org/10.3389/fmicb.2021.714967

Babalola OO, Fadiji AE, Ayangbenro AS (2020) Shotgun metagenomic data of root endophytic microbiome of maize ( Zea mays L.). Data Brief 31(105893). https://doi.org/10.1016/j.dib.2020.105893

Nilsson RH, Larsson KH, Taylor AFS, Bengtsson-Palme J, Jeppesen TS, Schigel D et al (2019) The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Res 47(D1):D259–D264. https://doi.org/10.1093/nar/gky1022

Quast C, Pruesse E, Yilmaz P et al (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41(Database issue):D590–D596. https://doi.org/10.1093/nar/gks1219

Mitchell AL, Almeida A, Beracochea M, Boland M, Burgin J, Cochrane G et al (2020) MGnify: the microbiome analysis resource in 2020. Nucleic Acids Res 48(D1):D570–D578. https://doi.org/10.1093/nar/gkz1035

Musidlak O, Buchwald W, Nawrot R (2014) Plant defense responses against viral and bacterial pathogen infections. Focus on RNA-binding proteins (RBPs). Herba Polonica 60:60–73. https://doi.org/10.1515/hepo-2015-0005

Silva MS, Arraes FBM, Campos MDA, Grossi-de-Sa M, Fernandez D, Cândido EDS et al (2018) Review: potential biotechnological assets related to plant immunity modulation applicable in engineering disease-resistant crops. Plant Sci 270:72–84. https://doi.org/10.1016/j.plantsci.2018.02.013

Feng Z, Zhang B, Ding W, Liu X, Yang DL, Wei P et al (2013) Efficient genome editing in plants using a CRISPR/Cas system. Cell Res 23(10):1229–1232. https://doi.org/10.1038/cr.2013.114

Wada N, Ueta R, Osakabe Y, Osakabe K (2020) Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering. BMC Plant Biol 20:234. https://doi.org/10.1186/s12870-020-02385-5

Nekrasov V, Staskawicz B, Weigel D, Jones JD, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31(8):691–693. https://doi.org/10.1038/nbt.2655

Langner T, Kamoun S, Belhaj K (2018) CRISPR crops: plant genome editing toward disease resistance. Annu Rev Phytopathol 56:479–512. https://doi.org/10.1146/annurev-phyto-080417-050158

Zafar K, Khan MZ, Amin I, Mukhtar Z, Yasmin S, Arif M et al (2020) Precise CRISPR-Cas9 mediated genome editing in super basmati rice for resistance against bacterial blight by targeting the major susceptibility gene. Front Plant Sci 11:575. https://doi.org/10.3389/fpls.2020.00575

Xie K, Yang Y (2013) RNA-guided genome editing in plants using a CRISPR-Cas system. Mol Plant 6(6):1975–1983. https://doi.org/10.1093/mp/sst119

Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y et al (2016) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11(4):e0154027. https://doi.org/10.1371/journal.pone.0154027

Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T et al (2019) Broad-spectrum resistance to bacterial blight in rice using genome editing. Nat Biotechnol 37(11):1344–1350. https://doi.org/10.1038/s41587-019-0267-z

Wang L, Chen S, Peng A, Xie Z, He Y, Zou X (2019) CRISPR/CAS9 -mediated editing of CsWRKY22 reduces susceptibility to Xanthomonas citri subsp. citri in Wanjincheng orange ( Citrus sinensis (L.) Osbeck). Plant Biotechnol Rep 13(5):501–510. https://doi.org/10.1007/s11816-019-00556-x

Fister AS, Landherr L, Maximova SN, Guiltinan MJ (2018) Transient expression of CRISPR/Cas9 machinery targeting TcNPR3 Enhances defense response in theobroma cacao. Front Plant Sci 9:268. https://doi.org/10.3389/fpls.2018.00268

Ong Q, Nguyen P, Thao NP, Le L (2016) Bioinformatics approach in plant genomic research. Curr Genomics 17(4):368–378. https://doi.org/10.2174/1389202917666160331202956

Schatz MC, Witkowski J, McCombie WR (2012) Current challenges in de novo plant genome sequencing and assembly. Genome Biol 13(4):243. https://doi.org/10.1186/gb-2012-13-4-243

Claros MG, Bautista R, Guerrero-Fernández D, Benzerki H, Seoane P, Fernández-Pozo N (2012) Why assembling plant genome sequences is so challenging. Biology (Basel) 1(2):439–459. https://doi.org/10.3390/biology1020439

Kyriakidou M, Tai HH, Anglin NL, Ellis D, Strömvik MV (2018) Current strategies of polyploid plant genome sequence assembly. Front Plant Sci 9:1660. https://doi.org/10.3389/fpls.2018.01660

Mathur M (2018) Bioinformatics challenges: a review. Int J Adv Sci Res 3(6):29–33

Fazan L, Song YG, Kozlowski G (2020) The woody planet: from past triumph to manmade decline. Plants (Basel) 9(11):1593. https://doi.org/10.3390/plants9111593

Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408(6814):796–815. https://doi.org/10.1038/35048692

Qi H, Jiang Z, Zhang K, Yang S, He F, Zhang Z (2018) PlaD: a transcriptomics database for plant defense responses to pathogens, providing new insights into plant immune system. Genomics Proteomics Bioinformatics 16(4):283–293. https://doi.org/10.1016/j.gpb.2018.08.002

Ohyanagi H, Takano T, Terashima S, Kobayashi M, Kanno M, Morimoto K et al (2015) Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. Plant Cell Physiol 56(1):e9. https://doi.org/10.1093/pcp/pcu188

Download references

Acknowledgements

The authors wish to thank Prof. Hoe I. Ling of Columbia University (New York, USA) for his editorial input and proofread the manuscript.

Author information

Authors and affiliations.

Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia

Yung Cheng Tan, Asqwin Uthaya Kumar, Ying Pei Wong & Anna Pick Kiong Ling

School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Malaysia

Asqwin Uthaya Kumar

You can also search for this author in PubMed   Google Scholar

Contributions

YCT designed the content and was a major contributor in writing the manuscript. AUK and YPW edited the manuscript. APKL designed and edited the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Anna Pick Kiong Ling .

Ethics declarations

Ethics approval and consent to participate, consent for publication, competing interests.

The authors declare that they have no competing interests.

Additional information

Publisher’s note.

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ .

Reprints and permissions

About this article

Cite this article.

Tan, Y.C., Kumar, A.U., Wong, Y.P. et al. Bioinformatics approaches and applications in plant biotechnology. J Genet Eng Biotechnol 20 , 106 (2022). https://doi.org/10.1186/s43141-022-00394-5

Download citation

Received : 30 November 2021

Accepted : 05 July 2022

Published : 15 July 2022

DOI : https://doi.org/10.1186/s43141-022-00394-5

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

• Bioinformatics
• Biotic and abiotic
• Plant breeding
• Plant sequencing
• Plant pathogen
• PRGdb sequence analysis

Information

• Author Services

Initiatives

You are accessing a machine-readable page. In order to be human-readable, please install an RSS reader.

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess .

Feature papers represent the most advanced research with significant potential for high impact in the field. A Feature Paper should be a substantial original Article that involves several techniques or approaches, provides an outlook for future research directions and describes possible research applications.

Feature papers are submitted upon individual invitation or recommendation by the scientific editors and must receive positive feedback from the reviewers.

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

Original Submission Date Received: .

• Active Journals
• Find a Journal
• Proceedings Series
• For Authors
• For Reviewers
• For Editors
• For Librarians
• For Publishers
• For Societies
• For Conference Organizers
• Open Access Policy
• Institutional Open Access Program
• Special Issues Guidelines
• Editorial Process
• Research and Publication Ethics
• Article Processing Charges
• Testimonials
• Preprints.org
• SciProfiles
• Encyclopedia

Article Menu

• Subscribe SciFeed
• PubMed/Medline
• Google Scholar
• on Google Scholar
• Table of Contents

Find support for a specific problem in the support section of our website.

Please let us know what you think of our products and services.

Visit our dedicated information section to learn more about MDPI.

JSmol Viewer

Plant biotechnology—an indispensable tool for crop improvement.

1. Introduction

2. cereal crops, 3. pulse crops, 4. root and tuber crops, 5. industrial crops, 6. new crops for arid regions, 7. ornamental crops, 8. development of new methodologies in plant biotechnology, author contributions, conflicts of interest, abbreviations.

List of Contributions

• Nowicka, B. Modifications of Phytohormone Metabolism Aimed at Stimulation of Plant Growth, Improving Their Productivity and Tolerance to Abiotic and Biotic Stress Factors. Plants 2022 , 11 , 3430.
• Hamdan, M.F.; Karlson, C.K.S.; Teoh, E.Y.; Lau, S.-E.; Tan, B.C. Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses. Plants 2022 , 11 , 2625.
• Buzdin, A.V.; Patrushev, M.V.; Sverdlov, E.D. Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population? Plants 2021 , 10 , 1667.
• Zhao, Y.; Feng, M.; Paudel, D.; Islam, T.; Momotaz, A.; Luo, Z.; Zhao, Z.; Wei, N.; Li, S.; Xia, Q.; et al. Advances in Genomics Approaches Shed Light on Crop Domestication. Plants 2021 , 10 , 1571.
• Prieto, P.; Palomino, C.; Cifuentes, Z.; Cabrera, A. Analysis of chromosome associations during early meiosis in wheat lines carrying chromosome introgressions from Agropyron cristatum . Plants 2021 , 10 , 2292, https://doi.org/10.3390/plants10112292 .
• Dreiseitl, A.; Nesvadba, Z. Powdery mildew resistance genes in single-plant progenies derived from accessions of a winter barley core collection. Plants 2021 , 10 , 1988, https://doi.org/10.3390/plants10101988 .
• Numan, M.; Khan, A.L.; Asaf, S.; Salehin, M.; Beyene, G.; Tadele, Z.; Ligaba-Osena, A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [Eragrostis tef (Zucc.) Trotter]. Plants 2021 , 10 , 628.
• Tigist, S.G.; Sibiya, J.; Amelework, A.; Keneni, G. Agromorphological and physiological performance of Ethiopian common bean ( Phaseolus vulgaris L.) Genotypes Under Different Agroecological Conditions. Plants 2023 , 12 , 2342, https://doi.org/10.3390/plants12122342 .
• Purdy, S.J.; Fuentes, D.; Ramamoorthy, P.; Nunn, C.; Kaiser, B.N.; Merchant, A. The metabolic profile of young, watered chickpea plants can be used as a biomarker to predict seed number under terminal drought. Plants 2023 , 12 , 2172.
• Adly, W.M.R.M.; Niedbała, G.; EL-Denary, M.E.; Mohamed, M.A.; Piekutowska, M.; Wojciechowski, T.; Abd El-Salam, E.-S.T.; Fouad, A.S. Somaclonal variation for genetic improvement of starch accumulation in potato ( Solanum tuberosum ) tubers. Plants 2023 , 12 , 232.
• Amelework, A.B.; Bairu, M.W.; Marx, R.; Laing, M.; Venter, S.L. Genotype x Environment Interaction and stability analysis of selected cassava cultivars in South Africa. Plants 2023 , 12 , 2490.
• Nokihara, K.; Okada, Y.; Ohata, S.; Monden, Y. Transcriptome analysis reveals key genes involved in weevil resistance in the hexaploid sweetpotato. Plants 2021 , 10 , 1535.
• Roy, C.B.; Goonetilleke, S.N.; Joseph, L.; Krishnan, A.; Saha, T.; Kilian, A.; Mather, D.E. Analysis of genetic diversity and resistance to foliar pathogens based on genotyping-by-sequencing of a para rubber diversity panel and progeny of an interspecific cross. Plants 2022 , 11 , 3418.
• Carra, A.; Catalano, C.; Pathirana, R.; Sajeva, M.; Inglese, P.; Motisi, A.; Carimi, F. Increased Zygote-Derived Plantlet Formation through In Vitro Rescue of Immature Embryos of Highly Apomictic Opuntia ficus-indica (Cactaceae). Plants 2023 , 12 , 2758.
• Vilcherrez-Atoche, J.A.; Silva, J.C.; Clarindo, W.R.; Mondin, M.; Cardoso, J.C. In Vitro Polyploidization of Brassolaeliocattleya Hybrid Orchid. Plants 2023 , 12 , 281.
• Sherpa, R.; Devadas, R.; Bolbhat, S.N.; Nikam, T.D.; Penna, S. Gamma Radiation Induced In-Vitro Mutagenesis and Isolation of Mutants for Early Flowering and Phytomorphological Variations in Dendrobium ‘Emma White’. Plants 2022 , 11 , 3168.
• Lim, S.-H.; Kim, D.-H.; Cho, M.-C.; Lee, J.-Y. Chili pepper AN2 ( CaAN2 ): A visible selection marker for nondestructive monitoring of transgenic plants. Plants 2022 , 11 , 820.
• FAO; IFAD; UNICEF; WFP; WHO. The State of Food Security and Nutrition in the World 2023 ; FAO: Rome, Italy, 2023. [ Google Scholar ]
• Pathirana, R.; Carimi, F. Management and utilization of plant genetic resources for a sustainable agriculture. Plants 2022 , 11 , 2038. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Pingali, P.L. Green Revolution: Impacts, limits, and the path ahead. Proc. Natl. Acad. Sci. USA 2012 , 109 , 12302–12308. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• UNDESA. UN/DESA Policy Brief #102: Population, Food Security, Nutrition and Sustainable Development. Available online: https://www.un.org/development/desa/dpad/publication/un-desa-policy-brief-102-population-food-security-nutrition-and-sustainable-development/ (accessed on 19 March 2024).
• Hemathilake, D.M.K.S.; Gunathilake, D.M.C.C. Chapter 31—Agricultural productivity and food supply to meet increased demands. In Future Foods ; Bhat, R., Ed.; Academic Press: Cambridge, MA, USA, 2022; pp. 539–553. [ Google Scholar ]
• Wijerathna-Yapa, A.; Pathirana, R. Sustainable agro-food systems for addressing climate change and food security. Agriculture 2022 , 12 , 1554. [ Google Scholar ] [ CrossRef ]
• Gill, G.P.; Harvey, C.F.; Gardner, R.C.; Fraser, L.G. Development of sex-linked PCR markers for gender identification in Actinidia . Theor. Appl. Genet. 1998 , 97 , 439–445. [ Google Scholar ] [ CrossRef ]
• Guo, D.; Wang, R.; Fang, J.; Zhong, Y.; Qi, X. Development of sex-linked markers for gender identification of Actinidia arguta. Sci. Rep. 2023 , 13 , 12780. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Bharadwaj, C.; Jorben, J.; Rao, A.; Roorkiwal, M.; Patil, B.S.; Jayalakshmi; Ahammed, S.K.; Saxena, D.R.; Yasin, M.; Jahagirdar, J.E.; et al. Development of high yielding fusarium wilt resistant cultivar by pyramiding of “genes” through marker-assisted backcrossing in chickpea ( Cicer arietinum L.). Front. Genet. 2022 , 13 , 924287. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Mei, J.; Shao, C.; Yang, R.; Feng, Y.; Gao, Y.; Ding, Y.; Li, J.; Qian, W. Introgression and pyramiding of genetic loci from wild Brassica oleracea into B. napus for improving Sclerotinia resistance of rapeseed. Theor. Appl. Genet. 2020 , 133 , 1313–1319. [ Google Scholar ] [ CrossRef ]
• Benitez-Alfonso, Y.; Soanes, B.K.; Zimba, S.; Sinanaj, B.; German, L.; Sharma, V.; Bohra, A.; Kolesnikova, A.; Dunn, J.A.; Martin, A.C.; et al. Enhancing climate change resilience in agricultural crops. Curr. Biol. 2023 , 33 , R1246–R1261. [ Google Scholar ] [ CrossRef ]
• Crews, T.E.; Carton, W.; Olsson, L. Is the future of agriculture perennial? Imperatives and opportunities to reinvent agriculture by shifting from annual monocultures to perennial polycultures. Glob. Sustain. 2018 , 1 , e11. [ Google Scholar ] [ CrossRef ]
• Soto-Gómez, D.; Pérez-Rodríguez, P. Sustainable agriculture through perennial grains: Wheat, rice, maize, and other species. A review. Agric. Ecosyst. Environ. 2022 , 325 , 107747. [ Google Scholar ] [ CrossRef ]
• Baik, B.-K.; Hoagland, L.A.; Jones, S.S.; Murphy, K.M.; Reeves, P.G. Nutritional and quality characteristics expressed in 31 perennial wheat breeding lines. Renew. Agric. Food Syst. 2009 , 24 , 285–292. [ Google Scholar ] [ CrossRef ]
• Zhang, X.; Sallam, A.; Gao, L.; Kantarski, T.; Poland, J.; DeHaan, L.R.; Wyse, D.L.; Anderson, J.A. Establishment and optimization of genomic selection to accelerate the domestication and improvement of intermediate wheatgrass. Plant Genome 2016 , 9 , 1–18. [ Google Scholar ] [ CrossRef ]
• Dorn, K.M.; Poland, J. Thinopyrum intermedium v2.1. Available online: https://phytozome-next.jgi.doe.gov/info/Tintermedium_v2_1 (accessed on 23 January 2024).
• Zhang, S.; Huang, G.; Zhang, Y.; Lv, X.; Wan, K.; Liang, J.; Feng, Y.; Dao, J.; Wu, S.; Zhang, L.; et al. Sustained productivity and agronomic potential of perennial rice. Nat. Sustain. 2023 , 6 , 28–38. [ Google Scholar ] [ CrossRef ]
• Yan, X.; Cheng, M.; Li, Y.; Wu, Z.; Li, Y.; Li, X.; He, R.; Yang, C.; Zhao, Y.; Li, H.; et al. Tripsazea, a Novel Trihybrid of Zea mays, Tripsacum dactyloides, and Zeaperennis. G3 Genes|Genomes|Genet. 2020 , 10 , 839–848. [ Google Scholar ] [ CrossRef ]
• Kruglova, N.N.; Zinatullina, A.E. In Vitro Culture of Autonomous Embryos as a Model System for the Study of Plant Stress Tolerance to Abiotic Factors (on the Example of Cereals). Biol. Bull. Rev. 2022 , 12 , 201–211. [ Google Scholar ] [ CrossRef ]
• Pathirana, R.; Wijithawarna, W.A.; Jagoda, K.; Ranawaka, A.L. Selection of rice for iron toxicity tolerance through irradiated caryopsis culture. Plant Cell Tissue Organ Cult. 2002 , 70 , 83–90. [ Google Scholar ]
• Abate, E.; Hussien, S.; Laing, M.; Mengistu, F. Aluminium toxicity tolerance in cereals: Mechanisms, genetic control and breeding methods. Afr. J. Agric. Res. 2013 , 8 , 711–722. [ Google Scholar ] [ CrossRef ]
• Krishania, S. Abiotic Stress Tolerance in Eleusine coracana (L.) Gaertn by Manipulation of Tissue Culture Media ; IIS University: Jaipur, India, 2010. [ Google Scholar ]
• Pathirana, R. Mutations in plant evolution, crop domestication and breeding. Trop. Agric. Res. Ext. 2021 , 24 , 124–157. [ Google Scholar ] [ CrossRef ]
• Acevedo-Garcia, J.; Spencer, D.; Thieron, H.; Reinstädler, A.; Hammond-Kosack, K.; Phillips, A.L.; Panstruga, R. mlo -based powdery mildew resistance in hexaploid bread wheat generated by a non-transgenic TILLING approach. Plant Biotechnol. J. 2017 , 15 , 367–378. [ Google Scholar ] [ CrossRef ]
• Bigini, V.; Camerlengo, F.; Botticella, E.; Sestili, F.; Savatin, D.V. Biotechnological Resources to Increase Disease-Resistance by Improving Plant Immunity: A Sustainable Approach to Save Cereal Crop Production. Plants 2021 , 10 , 1146. [ Google Scholar ] [ CrossRef ]
• Ceoloni, C.; Kuzmanovic, L.; Forte, P.; Virili, M.E.; Bitti, A. Wheat-perennial Triticeae introgressions: Major achievements and prospects. In Alien Introgression in Wheat: Cytogenetics, Molecular Biology, and Genomics ; Molnár-Láng, M., Ceoloni, C., Doležel, J., Eds.; Springer International Publishing: Cham, Switzerland, 2015; pp. 273–313. [ Google Scholar ]
• FAO. International Year of Pulses 2016. Available online: https://www.fao.org/pulses-2016/en/ (accessed on 22 November 2023).
• FAO. World Pulse Day/10 February. Available online: https://www.fao.org/world-pulses-day/en/ (accessed on 22 November 2023).
• FAO. FAOSTAT ; Food and Agriculture Organisation of the United Nations: Rome, Italy, 2020. [ Google Scholar ]
• Bernard, R.L. Two genes affecting stem termination in soybeans. Crop Sci. 1972 , 12 , 235–239. [ Google Scholar ] [ CrossRef ]
• Krylova, E.A.; Khlestkina, E.K.; Burlyaeva, M.O.; Vishnyakova, M.A. Determinate growth habit of grain legumes: Role in domestication and selection, genetic control. EcoGen 2020 , 18 , 43–58. [ Google Scholar ] [ CrossRef ]
• Sharma, K.K.; Dumbala, S.R.; Bhatnagar-Mathur, P. Biotech Approaches for Crop Improvement in the Semi-arid Tropics. In Plant Biotechnology: Experience and Future Prospects ; Ricroch, A., Chopra, S., Fleischer, S.J., Eds.; Springer International Publishing: Cham, Switzerland, 2014; pp. 193–207. [ Google Scholar ]
• Raman, R.B.; Sinhamahapatra, S.P. A dwarf determinate plant type for achieving higher and stable yield in blackgram ( Vigna mungo L. Hepper). Bioscan 2014 , 9 , 497–500. [ Google Scholar ]
• Duc, G.; Agrama, H.; Bao, S.; Berger, J.; Bourion, V.; De Ron, A.M.; Gowda, C.L.L.; Mikic, A.; Millot, D.; Singh, K.B.; et al. Breeding annual grain legumes for sustainable agriculture: New methods to approach complex traits and target new cultivar ideotypes. Crit. Rev. Plant Sci. 2015 , 34 , 381–411. [ Google Scholar ] [ CrossRef ]
• IAEA. International Atomic Energy Agency, Mutant Database. Available online: https://nucleus.iaea.org/sites/mvd/SitePages/Home.aspx (accessed on 20 January 2024).
• Bohra, A.; Singh, N.P. Whole genome sequences in pulse crops: A global community resource to expedite translational genomics and knowledge-based crop improvement. Biotechnol. Lett. 2015 , 37 , 1529–1539. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Jacob, C.; Carrasco, B.; Schwember, A.R. Advances in breeding and biotechnology of legume crops. Plant Cell Tiss Organ Cult 2016 , 127 , 561–584. [ Google Scholar ] [ CrossRef ]
• Jegadeesan, S.; Raizada, A.; Dhanasekar, P.; Suprasanna, P. Draft genome sequence of the pulse crop blackgram [ Vigna mungo (L.) Hepper] reveals potential R-genes. Sci. Rep. 2021 , 11 , 11247. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Varshney, R.K.; Pandey, M.K.; Bohra, A.; Singh, V.K.; Thudi, M.; Saxena, R.K. Toward the sequence-based breeding in legumes in the post-genome sequencing era. Theor. Appl. Genet. 2019 , 132 , 797–816. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Kumar, A.; Bohra, A.; Mir, R.R.; Sharma, R.; Tiwari, A.; Khan, M.A.; Varshney, R.K. Next generation breeding in pulses: Present status and future directions. Crop Breed. Appl. Biotechnol. 2021 , 21 , 1–22. [ Google Scholar ] [ CrossRef ]
• Asati, R.; Tripathi, M.K.; Tiwari, S.; Yadav, R.K.; Tripathi, N. Molecular breeding and drought tolerance in chickpea. Life 2022 , 12 , 1846. [ Google Scholar ] [ CrossRef ]
• Diaz, L.M.; Ricaurte, J.; Tovar, E.; Cajiao, C.; Teran, H.; Grajales, M.; Polania, J.; Rao, I.; Beebe, S.; Raatz, B. QTL analyses for tolerance to abiotic stresses in a common bean ( Phaseolus vulgaris L.) population. PLoS ONE 2018 , 13 , e0202342. [ Google Scholar ] [ CrossRef ]
• Sultana, R.; Choudhary, A.K.; Pal, A.K.; Saxena, K.B.; Prasad, B.D.; Singh, R. Abiotic stresses in major pulses: Current status and strategies. In Approaches to Plant Stress and their Management ; Gaur, R.K., Sharma, P., Eds.; Springer: New Delhi, India, 2014; pp. 173–190. [ Google Scholar ]
• Koundinya, A.V.V.; Das, A.; Hegde, V. Mutation breeding in tropical root and ruber crops. In Mutation Breeding for Sustainable Food Production and Climate Resilience ; Penna, S., Jain, S.M., Eds.; Springer Nature: Singapore, 2023; pp. 779–809. [ Google Scholar ]
• Bradshaw, J.E. A Brief History of the Impact of Potato Genetics on the Breeding of Tetraploid Potato Cultivars for Tuber Propagation. Potato Res. 2022 , 65 , 461–501. [ Google Scholar ] [ CrossRef ]
• Yan, M.; Nie, H.; Wang, Y.; Wang, X.; Jarret, R.; Zhao, J.; Wang, H.; Yang, J. Exploring and exploiting genetics and genomics for sweetpotato improvement: Status and perspectives. Plant Commun. 2022 , 3 , 100332. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• FAO. What is Hidden Hunger. In Proceedings of the Second International Confefrence on Nutrition, Rome, Italy, 19–21 November 2014; Available online: https://www.fao.org/about/meetings/icn2/news-archive/news-detail/en/c/265240 (accessed on 22 January 2024).
• Howeler, R.; Lutaladio, N.; Thomas, G. Save and Grow: Cassava. A Guide to Sustainable Production Intensification ; FAO: Rome, Italy, 2013. [ Google Scholar ]
• Chavez, A.L.; Bedoya, J.; Sánchez, T.; Iglesias, C.; Ceballos, H.; Roca, W. Iron, carotene, and ascorbic acid in cassava roots and leaves. Food Nutr. Bull. 2000 , 21 , 410–413. [ Google Scholar ]
• Narayanan, N.; Beyene, G.; Chauhan, R.D.; Gaitán-Solís, E.; Gehan, J.; Butts, P.; Siritunga, D.; Okwuonu, I.; Woll, A.; Jiménez-Aguilar, D.M.; et al. Biofortification of field-grown cassava by engineering expression of an iron transporter and ferritin. Nat. Biotechnol. 2019 , 37 , 144–151. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Landi, M.; Shah, T.; Falquet, L.; Niazi, A.; Stavolone, L.; Bongcam-Rudloff, E.; Gisel, A. Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 ( Manihot esculenta ). Sci. Data 2023 , 10 , 887. [ Google Scholar ] [ CrossRef ]
• Patil, B.L.; Fauquet, C.M. Cassava mosaic geminiviruses: Actual knowledge and perspectives. Mol. Plant Pathol. 2009 , 10 , 685–701. [ Google Scholar ] [ CrossRef ]
• Beyene, G.; Chauhan, R.D.; Ilyas, M.; Wagaba, H.; Fauquet, C.M.; Miano, D.; Alicai, T.; Taylor, N.J. A virus-derived stacked RNAi construct confers robust resistance to cassava brown streak disease. Front. Plant Sci. 2017 , 7 , 240414. [ Google Scholar ]
• Mmbando, G.S. The legal aspect of the current use of genetically modified organisms in Kenya, Tanzania, and Uganda. GM Crops Food 2023 , 14 , 1–12. [ Google Scholar ] [ CrossRef ]
• ACB. Push Back against Risky and Unsafe RNAi GM Cassava Cultivation in Kenya. Available online: https://acbio.org.za/gm-biosafety/push-back-against-risky-unsafe-rnai-gm-cassava-cultivation-kenya/ (accessed on 14 February 2024).
• Kimno, L.C.; Kinyua, M.G.; Bimpong, I.K.; Were, J.O. Field screening of elite cassava ( Manihot esculenta ) mutant lines for their response to mosaic and brown streak viruses. J. Exp. Agric. Int. 2023 , 45 , 205–215. [ Google Scholar ] [ CrossRef ]
• Sapakhova, Z.; Raissova, N.; Daurov, D.; Zhapar, K.; Daurova, A.; Zhigailov, A.; Zhambakin, K.; Shamekova, M. Sweet potato as a key crop for food security under the conditions of global climate change: A Review. Plants 2023 , 12 , 2516. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Anil, S.R.; Sheela, M.N.; Visalakshi Chandra, C.; Krishna Radhika, N.; Asha, K.I. Status of biofortification in tropical root and tuber crops. Curr. Sci. 2023 , 120 , 169–175. [ Google Scholar ]
• Yang, J.; Bi, H.P.; Fan, W.J.; Zhang, M.; Wang, H.X.; Zhang, P. Efficient embryogenic suspension culturing and rapid transformation of a range of elite genotypes of sweet potato ( Ipomoea batatas [L.] Lam.). Plant Sci. 2011 , 181 , 701–711. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Lou, H.R.; Maria, M.S.; Benavides, J.; Zhang, D.P.; Zhang, Y.Z.; Ghislain, M. Rapid genetic transformation of sweetpotato ( Ipomoea batatas (L.) Lam) via organogenesis. Afr. J. Biotechnol. 2006 , 5 , 1851–1857. [ Google Scholar ]
• Choi, H.J.; Chandrasekhar, T.; Lee, H.-Y.; Kim, K.-M. Production of herbicide-resistant transgenic sweet potato plants through Agrobacterium tumefaciens method. Plant Cell Tissue Organ Cult. 2007 , 91 , 235–242. [ Google Scholar ] [ CrossRef ]
• Yang, K.Y.; Yi, G.B.; Kim, Y.M.; Choi, G.; Shin, B.C.; Shin, Y.M.; Kim, K.M. Production of transgenic sweet potato (Ipomoea batatas (L.) Lam.) lines via microprojectile bombardment. Korean J. Breed. 2005 , 37 , 236–240. [ Google Scholar ]
• Okada, Y.; Saito, A.; Nishiguchi, M.; Kimura, T.; Mori, M.; Hanada, K.; Sakai, J.; Miyazaki, C.; Matsuda, Y.; Murata, T. Virus resistance in transgenic sweetpotato [ Ipomoea batatas L. (Lam)] expressing the coat protein gene of sweet potato feathery mottle virus. Theor. Appl. Genet. 2001 , 103 , 743–751. [ Google Scholar ] [ CrossRef ]
• Leclerc, Y.; Donnelly, D.J.; Coleman, W.K.; King, R.R. Microtuber dormancy in three potato cultivars. Am. Potato J. 1995 , 72 , 215–223. [ Google Scholar ]
• Suttle, J.C. Involvement of ethylene in potato microtuber dormancy. Plant Physiol. 1998 , 118 , 843–848. [ Google Scholar ]
• Pathirana, R.; Harris, J.C.; McKenzie, M.J. A comparison of microtubers and field-grown tubers of potato ( Solanum tuberosum L.) for hexoses, sucrose and their ratios following postharvest cold storage. Postharvest Biol. Technol. 2008 , 49 , 180–184. [ Google Scholar ] [ CrossRef ]
• Zhang, Z.; Mao, B.; Li, H.; Zhou, W.; Takeuchi, Y.; Yoneyama, K. Effect of salinity on physiological characteristics, yield and quality of microtubers in vitro in potato. Acta Physiol. Plant. 2005 , 27 , 481–489. [ Google Scholar ]
• Wang, X.; Gu, X.; Xu, Z.; Yin, Z.; Yang, X.; Lin, R.; Zhou, Q.; Huang, H.; Huang, T. Current achievements and future challenges of genotype-dependent somatic embryogenesis techniques in Hevea brasiliensis . Forests 2023 , 14 , 1891. [ Google Scholar ] [ CrossRef ]
• Rahman, A.Y.A.; Usharraj, A.O.; Misra, B.B.; Thottathil, G.P.; Jayasekaran, K.; Feng, Y.; Hou, S.; Ong, S.Y.; Ng, F.L.; Lee, L.S.; et al. Draft genome sequence of the rubber tree Hevea brasiliensis . BMC Genom. 2013 , 14 , 75. [ Google Scholar ] [ CrossRef ]
• Lau, N.-S.; Makita, Y.; Kawashima, M.; Taylor, T.D.; Kondo, S.; Othman, A.S.; Shu-Chien, A.C.; Matsui, M. The rubber tree genome shows expansion of gene family associated with rubber biosynthesis. Sci. Rep. 2016 , 6 , 28594. [ Google Scholar ] [ CrossRef ]
• Tang, C.; Yang, M.; Fang, Y.; Luo, Y.; Gao, S.; Xiao, X.; An, Z.; Zhou, B.; Zhang, B.; Tan, X.; et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat. Plants 2016 , 2 , 16073. [ Google Scholar ] [ CrossRef ]
• Pootakham, W.; Sonthirod, C.; Naktang, C.; Ruang-Areerate, P.; Yoocha, T.; Sangsrakru, D.; Theerawattanasuk, K.; Rattanawong, R.; Lekawipat, N.; Tangphatsornruang, S. De novo hybrid assembly of the rubber tree genome reveals evidence of paleotetraploidy in Hevea species. Sci. Rep. 2017 , 7 , 41457. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Chao, J.; Wu, S.; Shi, M.; Xu, X.; Gao, Q.; Du, H.; Gao, B.; Guo, D.; Yang, S.; Zhang, S.; et al. Genomic insight into domestication of rubber tree. Nat. Commun. 2023 , 14 , 4651. [ Google Scholar ] [ CrossRef ] [ PubMed ]
• Priyadarshan, P.M. Molecular markers to devise predictive models for juvenile selection in Hevea rubber. Plant Breed. 2022 , 141 , 159–183. [ Google Scholar ] [ CrossRef ]
• Hajek, O.L.; Knapp, A.K. Shifting seasonal patterns of water availability: Ecosys-tem responses to an unanticipated dimension of climate change. New Phytol. 2022 , 233 , 119–125. [ Google Scholar ] [ CrossRef ]
• FAO. Food and Agriculture Organization, Water. Available online: https://www.fao.org/water/en/ (accessed on 20 January 2024).
• WEF. The World Economic Forum’s Global Risks Report 2021. The Global Risks Report 2021 , 16th ed. 2021. ISBN: 978-2-940631-24-7. Available online: http://www3.weforum.org/docs/WEF_The_Global_Risks_Report_2021.pdf (accessed on 22 November 2023).
• Mishra, B.K.; Kumar, P.; Saraswat, C.; Chakraborty, S.; Gautam, A. Water security in a changing environment: Concept, challenges and solutions. Water 2021 , 13 , 490. [ Google Scholar ] [ CrossRef ]
• Shedbalkar, U.U.; Adki, V.S.; Jadhav, J.P.; Bapat, V.A. Opuntia and other cacti: Applications and biotechnological insights. Trop. Plant Biol. 2010 , 3 , 136–150. [ Google Scholar ]
• Gabellini, S.; Scaramuzzi, S. Evolving consumption trends, marketing strategies, and governance settings in ornamental horticulture: A grey literature review. Horticulturae 2022 , 8 , 234. [ Google Scholar ] [ CrossRef ]
• Francini, A.; Romano, D.; Toscano, S.; Ferrante, A. The contribution of ornamental plants to urban ecosystem services. Earth 2022 , 3 , 1258–1274. [ Google Scholar ] [ CrossRef ]
• Rihn, A.L.; Knuth, M.J.; Behe, B.K.; Hall, C.R. Benefit information’s impact on ornamental plant value. Horticulturae 2023 , 9 , 740. [ Google Scholar ] [ CrossRef ]
• Cardoso, J.C.; Martinelli, A.P.; Teixeira da Silva, J.A. A novel approach for the selection of Cattleya hybrids for precocious and season-independent flowering. Euphytica 2016 , 210 , 143–150. [ Google Scholar ] [ CrossRef ]

Click here to enlarge figure

Share and Cite

Pathirana, R.; Carimi, F. Plant Biotechnology—An Indispensable Tool for Crop Improvement. Plants 2024 , 13 , 1133. https://doi.org/10.3390/plants13081133

Pathirana R, Carimi F. Plant Biotechnology—An Indispensable Tool for Crop Improvement. Plants . 2024; 13(8):1133. https://doi.org/10.3390/plants13081133

Pathirana, Ranjith, and Francesco Carimi. 2024. "Plant Biotechnology—An Indispensable Tool for Crop Improvement" Plants 13, no. 8: 1133. https://doi.org/10.3390/plants13081133

Article Metrics

Article access statistics, further information, mdpi initiatives, follow mdpi.

Subscribe to receive issue release notifications and newsletters from MDPI journals

Recent Advances in Plant Biotechnology

• © 2009
• Ara Kirakosyan 0 ,
• Peter B. Kaufman 1

University of Michigan, Ann Arbor, U.S.A.

You can also search for this author in PubMed   Google Scholar

• Presents a full overview of plant biotechnology from the history to applications
• Approach includes associated risks and the effects of plant biotechnology on global warming, alternative energy initiatives, food production, and medicine
• Includes supplementary material: sn.pub/extras

33k Accesses

81 Citations

4 Altmetric

This is a preview of subscription content, log in via an institution to check access.

Access this book

Subscribe and save.

• Get 10 units per month
• Download Article/Chapter or eBook
• 1 Unit = 1 Article or 1 Chapter
• Cancel anytime
• Available as EPUB and PDF
• Read on any device
• Instant download
• Own it forever
• Compact, lightweight edition
• Dispatched in 3 to 5 business days
• Free shipping worldwide - see info
• Durable hardcover edition

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

About this book

Similar content being viewed by others.

Creating Products and Services in Plant Biotechnology

Plant tissue culture and biotechnology: perspectives in the history and prospects of the International Association of Plant Biotechnology (IAPB)

The Evolution of Agriculture and Tools for Plant Innovation

• agriculture
• alternative energy
• bioremediation
• biotechnology
• genetically modified plants
• herbal medicine
• herbal products
• plant biotechnology
• transgenic plants

Table of contents (16 chapters)

Front matter, plant biotechnology from inception to the present, overview of plant biotechnology from its early roots to the present.

• Ara Kirakosyan, Peter B. Kaufman, Leland J. Cseke

The Use of Plant Cell Biotechnology for the Production of Phytochemicals

• Ara Kirakosyan, Leland J. Cseke, Peter B. Kaufman

Molecular Farming of Antibodies in Plants

• Rainer Fischer, Stefan Schillberg, Richard M. Twyman

Use of Cyanobacterial Proteins to Engineer New Crops

• Matias D. Zurbriggen, Néstor Carrillo, Mohammad-Reza Hajirezaei

Molecular Biology of Secondary Metabolism: Case Study for Glycyrrhiza Plants

• Hiroaki Hayashi

Applications of Plant Biotechnology in Agriculture and Industry

New developments in agricultural and industrial plant biotechnology, phytoremediation: the wave of the future.

• Jerry S. Succuro, Steven S. McDonald, Casey R. Lu

Biotechnology of the Rhizosphere

• Beatriz Ramos Solano, Jorge Barriuso Maicas, Javier Gutierrez Mañero

Plants as Sources of Energy

• Leland J. Cseke, Gopi K. Podila, Ara Kirakosyan, Peter B. Kaufman

Use of Plant Secondary Metabolites in Medicine and Nutrition

Interactions of bioactive plant metabolites: synergism, antagonism, and additivity.

• John Boik, Ara Kirakosyan, Peter B. Kaufman, E. Mitchell Seymour, Kevin Spelman

The Use of Selected Medicinal Herbs for Chemoprevention and Treatment of Cancer, Parkinson’s Disease, Heart Disease, and Depression

• Maureen McKenzie, Carl Li, Peter B. Kaufman, E. Mitchell Seymour, Ara Kirakosyan

Regulating Phytonutrient Levels in Plants – Toward Modification of Plant Metabolism for Human Health

Risks and benefits associated with plant biotechnology, risks and benefits associated with genetically modified (gm) plants.

• Peter B. Kaufman, Soo Chul Chang, Ara Kirakosyan

Risks Involved in the Use of Herbal Products

• Peter B. Kaufman, Maureen McKenzie, Ara Kirakosyan

Risks Associated with Overcollection of Medicinal Plants in Natural Habitats

• Maureen McKenzie, Ara Kirakosyan, Peter B. Kaufman

Authors and Affiliations

Ara Kirakosyan, Peter B. Kaufman

About the authors

Bibliographic information.

Book Title : Recent Advances in Plant Biotechnology

Authors : Ara Kirakosyan, Peter B. Kaufman

DOI : https://doi.org/10.1007/978-1-4419-0194-1

Publisher : Springer New York, NY

eBook Packages : Biomedical and Life Sciences , Biomedical and Life Sciences (R0)

Copyright Information : The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2009

Hardcover ISBN : 978-1-4419-0193-4 Published: 30 July 2009

Softcover ISBN : 978-1-4899-7916-2 Published: 23 August 2016

eBook ISBN : 978-1-4419-0194-1 Published: 15 August 2009

Edition Number : 1

Number of Pages : XIV, 405

Topics : Plant Genetics and Genomics , Plant Sciences

• Publish with us

Policies and ethics

• Find a journal
• Track your research

An official website of the United States government

The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

• Publications
• Account settings

Preview improvements coming to the PMC website in October 2024. Learn More or Try it out now .

• Advanced Search
• Journal List
• Plants (Basel)
• PMC11054891

Plant Biotechnology—An Indispensable Tool for Crop Improvement

Ranjith pathirana.

1 School of Agriculture, Food and Wine, Waite Campus, University of Adelaide, Urrbra, SA 5064, Australia

Francesco Carimi

2 Istituto di Bioscienze e BioRisorse (IBBR), Consiglio Nazionale delle Ricerche, Via Ugo la Malfa, 153, 90146 Palermo, Italy; [email protected]

1. Introduction

Traditional plant breeding has helped to increase food production dramatically over the past five decades, and many countries have managed to produce enough food for the growing population, particularly in the developing world. Sustaining these gains in crop productivity and adapting to climate change are becoming urgent concerns in modern times. In fact, yield increases in our major cereals have slowed down in the past 20 years. Global hunger is still above pre-pandemic levels, with around 690–783 million people faced with hunger in 2022, and meeting Sustainable Development Goal 2 of ending hunger by 2030 has become a daunting task [ 1 ]. Although increased yields through the Green Revolution helped to cultivate an additional 18–27 million hectares, this increased food production was accompanied by environmental degradation and micronutrient deficiencies across populations [ 2 , 3 ]. Developing crop cultivars that meet the present-day requirements of agriculture and horticulture is challenging, as they need to provide sustainable food and healthful nutrition for populations, and, at the same time, must be environmentally friendly and resilient to climate change. The global community is projected to face increasing food crises due to changing dietary styles and the rising population, which is set to reach almost 10 billion people by 2050 [ 4 ]). The challenge ahead is determining how to reduce the use of limiting resources (water, energy, and agricultural land) for intensive agriculture, ensuring sufficient production of food ( Figure 1 ). Taking even the most conservative estimates, food production needs to double in the coming 30 years to meet the basic demands of the growing population [ 5 ]. Despite these challenges, there is growing evidence that food security and adequate nutrition for the global population can be achieved using climate-smart, sustainable agricultural practices, while reducing the negative impacts of agriculture on the environment, particularly greenhouse gas emissions [ 6 ].

Food systems are increasingly vulnerable due to human pressures on natural ecosystems and the climate: The challenge ahead. * World Resource Institute (WRI)’s 2023 report. Available online: https://research.wri.org/wrr-food (accessed on 22 January 2024); ** Statista Energy Consumption Worldwide from 2000 to 2019, with a forecast until 2050, by Energy Source. Available online: https://www.statista.com/statistics/222066/projected-global-energy-consumption-by-source/ (accessed on 22 January 2024); *** Mahpul IN, Mohamad AH, Mazalan MF, Razak A, Rasyidee A (2021) Population, food security, nutrition and sustainable development. Available online: https://www.un.org/development/desa/dpad/publication/un-desa-policy-brief-102-population-food-security-nutrition-and-sustainable-development/ (accessed on 22 January 2024) [ 4 ].

Plant biotechnology is seen as the breakthrough technology that can help to meet this challenge in this next phase of plant breeding. Plant biotechnologies that aid in developing new varieties and individual traits within existing plant varieties include cell and tissue manipulation, marker-assisted selection, transgenic technologies, genomics, and molecular breeding. Cell and tissue culture technologies provide a range of applications in the creation, conservation, and utilization of the genetic variability in crops, such as in vitro pollination and embryo rescue for distant hybridization, the production of haploids and doubled haploids, polyploid breeding, in vitro mutagenesis, somaclonal variation, in vitro selection, germplasm preservation (in vitro for medium-term and cryopreservation for long-term), protoplast fusion for producing somatic hybrids, and gene manipulation for producing transgenic crops or the newly emerging techniques that allow for the generation of gene-edited plants.

High-resolution genetic analysis has allowed physical mapping and positional gene cloning for traits of interest, while molecular markers allow for the characterization of germplasm and finding duplicates and gaps in collections [ 2 ]. They are becoming indispensable in some breeding programs when used for the early culling of unwanted material in perennial crops such as in the case of culling male vines early in hybrid populations, screening in kiwifruit for marker-assisted selection [ 7 , 8 ], the development of saturated linkage maps, and pyramiding genes in introgressive breeding [ 9 , 10 ]. Despite the strict laws governing genetically modified crops, transgenic varieties of maize, soybean, rapeseed, cotton, tomato, potato, papaya, etc., occupy over 190 million hectares across 26 countries, grown by 17 million farmers, bringing in both economic and environmental benefits and, at the same time, some social controversy [ 6 ]. The many tools that plant biotechnology provides for crop improvement for developing resilient food systems while conserving the environment are shown in Figure 2 . These aspects have been addressed in the 17 papers published in this Special Issue titled ‘Plant Biotechnology and Crop Improvement’. There have been four general review papers covering different biotechnologies and thirteen original research contributions focusing on different crop groups, including tropical and temperate cereal, legume, root and tuber, fruit, ornamental, and industrial crops. With 44,000 views and 86 citations at the time of writing, this Special Issue has attracted much attention across the scientific community as expected, considering the relevance of the topic to the current challenges in global food production.

The many aspects of the contribution of biotechnology towards crop improvement for resilient food systems while also contributing to environmental protection.

This Special Issue also contains methodology development for plant genetic transformation through the use of an easy selection marker for discriminating transformed plants from escapes. The reviews in this Special Issue look at specific trait improvements such as stress resistance using gene-editing technologies and manipulation of phytohormone metabolism, as well as exploring if a second “quantum-leap” in food production is possible using these technologies. Another review describes the contribution of genomics to our understanding of crop evolution. With a wide array of applications of plant biotechnology to crop improvement available, the research papers addressed several of these technologies in extensively cultivated crops such as wheat, barley, bean, and potato, as well as in underutilized crops with high potential such as tef and prickly pear. The technologies applied to improve crops in these papers include somaclonal variation, induced mutagenesis, in vitro polyploidization, embryo rescue, and gene editing. Several papers describe the use of genomics, transcriptome analysis, molecular markers, and metabolic profiling to assist in selection in breeding programs and monitoring of transgenic plants.

The possibility of modifying phytohormone metabolism and signaling is a promising direction of research aimed at the improvement of crop productivity and stress tolerance. In her review, Nowicka (contribution 1) summarizes the state-of-the-art research concerning the modulation of phytohormone content aimed at the stimulation of plant growth and the improvement of stress tolerance. In particular, the roles of auxins, cytokinins, gibberellins, brassinosteroids, abscisic acid, ethylene, jasmonic acid, and their derivatives are analyzed. The author hypothesizes that modification of this signaling at various levels, from elements of signaling cascades, through transcription factors to miRNAs, is a very promising direction of genetic engineering of crop plants aimed at improving the resilience of plants.

Remarkable progress in genome-editing technologies has been achieved over the past 10 years and have begun to show extraordinary utility to develop crop varieties with superior qualities, or those that can tolerate adverse environmental conditions. In their review, Hamdan et al. (contribution 2) provide a detailed analysis of the genome-editing technologies that have been expertly applied to improve important agronomic traits, especially yield, quality, and stress resistance of the most important crops. In particular, the review focuses on the Clustered Regularly Interspaced Palindromic Repeats (CRISPR/Cas) system, which has been the focus in recent years as a revolutionary genome-editing tool used for various crops. The authors discuss the current developments and future applications of genome-editing technologies for developing crops that can help in mitigating the impacts of climate change on agriculture with notes on future perspectives. A bibliographic analysis is also presented covering CRISPR-related papers published from 2012 to 2021 (10 years) to identify trends and potential in CRISPR/Cas-related plant research. The authors conclude that combining conventional and more innovative technologies in agriculture would be the key to optimizing crop improvement beyond the limitations of traditional agricultural practices. A more pessimistic view is provided in a review carried out by Buzdin et al. (contribution 3), reporting that, according to estimates, global crop yields must double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this “quantum-leap” in improvements in crop yield, we must respect environmental constraints and, at the same time, reduce the impact of agriculture on the environment. The authors support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Finally, in their review, Zhao et al. (contribution 4) analyze how recent advances in genomics have revolutionized our understanding of crop domestication. The authors summarize cutting-edge research on crop domestication by presenting the main methodologies and analyze the prospects for both targeted re-domestication and de novo domestication of wild species.

2. Cereal Crops

Dramatic increases in rice and wheat yields were achieved during the ‘Green Revolution’, where dwarfing genes were transferred to adapted cultivars through crossbreeding. The ‘Green Revolution’, with its high-input and technology-dependent approach, has been able to feed the growing world population in recent decades. It ensured food security, particularly in developing nations. However, long-term impacts are now evident: degraded soils, reduced groundwater levels, contaminated and salinized water bodies, and reduced biodiversity. Furthermore, high crop yields cannot be sustained without increased fertilizer use [ 6 , 11 , 12 , 13 ]. Traditional crossbreeding is straightforward when selecting for morphological traits that are easy to observe in field, such as height, grain size, color, and leaf shape, etc. The main change in rice and wheat achieved during the “Green Revolution” is dwarfing, resulting in greater partitioning of photosynthates in grains and better fertilizer response, without lodging. Hence, it was not difficult to identify dwarf plants in the segregating populations. However, traits such as nutritional quality, disease, and abiotic stress resistance are not easy to select visually in segregating populations under field conditions where breeders encounter many variables. Lab-based approaches to increase genetic variability or to genetically modify and select desirable genotypes are therefore required.

Over the past few decades, biotechnology has made significant contributions to cereal crop improvement by enhancing yield, nutritional content, biotic and abiotic stress tolerance, herbicide tolerance, and many other valuable traits. It has also played a crucial role in promoting environmental sustainability and has had positive economic impacts on agriculture. For example, the introduction of perennial cereals can alleviate many problems of annual monocultures [ 6 , 11 , 12 , 13 ]. Thinopyrum spp. is the most sought-after perennial grain in hybridization programs with wheat as it hybridizes freely with Triticum , producing fertile progeny [ 13 ], and perennial selections have outperformed the standard wheat cultivars in grain protein and mineral nutrient contents [ 14 ]. Yet, with genomic tools, selection for perennial growth and other quality traits would be easier and faster [ 13 ]. Thus, intermediate wheatgrass has been used in sequencing and marker-assisted recurrent selection [ 15 ], and a high-quality genetic map is now available online [ 16 ]. With these developments, breeding perennial wheat for large-scale cultivation will be possible.

Similarly, perennial rice (PR) will be the start of a second ‘Green Revolution’ as the data from 15,333 ha of perennial rice grown by 44,752 small holder farmers in southern China demonstrate [ 17 ]. The parents for the breeding program to develop PR were ‘RD23’, a cultivar of Oryza sativa ssp. indica , and a rhizomatous and perennial African species, O. longistaminata . Embryo rescue (a tissue-culture-based biotechnological intervention) of F 1 facilitated overcoming incompatibility and resulted in the foundation material for developing the commercialized PR. PR produced similar yields to annual rice over a period of four years, with eight harvests from a single planting. Farmers prefer PR due to 58.1% labor savings and 49.2% savings on inputs every growth cycle. Higher organic carbon and nitrogen accumulation in soils and improved soil water retention are other advantages [ 17 ]. Attempts to develop perennial rye using perennial wild rye Secale montanum L. [ 13 ] and perennial maize using tetraploid maize ( Zea mays 2n = 4x = 40), tetraploid Tripsacum dactyloides (2n = 4x = 72), and tetraploid Z. perennis (2n = 4x = 40) [ 18 ] are underway.

Many other biotechnological interventions are possible in the development and selection of climate-resilient cereals. For example, Kruglova and Zinatullina [ 19 ] describe many examples of in vitro selection for drought, simulating water deficiency in culture media. They suggest using embryos at a certain developmental stage, when they are autonomous. In vitro selection for iron toxicity [ 20 ], aluminum toxicity [ 21 ], nickel, and NaCl toxicity tolerance [ 22 ] has been demonstrated in cereal crops. In vitro mutation induction and selection have also been demonstrated in many cereals [ 23 ]. More targeted mutations can be used in crop improvement thanks to the development of techniques such as Targeting Induced Local Lesions in Genomes (TILLING), as well as the latest gene-editing techniques. For example, Acevedo-Garcia et al. [ 24 ] developed bread wheat cultivars resistant to powdery mildew by TILLING. The first genome-editing tools were Zinc Finger Nucleases (ZFN) and Transcription Activator-Like Effector Nucleases (TALENs), but, later, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Crispr associated protein (Cas) became the most widely used genome-editing tool due to its high editing efficiency, multiplex capability, and ease of use. Gene editing has enabled researchers to increase grain number and size in rice, and grain weight and yield in wheat. Powdery mildew resistance in wheat and resistance to Xanthomonas in rice have also been achieved using gene-editing technologies [ 25 ].

Wheat, barley, and tef are among the cereal crops covered in this Special Issue. In wheat breeding, crested wheatgrass Agropyron cristatum is considered a potential donor of valuable traits for abiotic (cold, drought, and salinity) and biotic (leaf rust, stripe rust, and powdery mildew) resistance. Crested wheatgrass belongs to the tribe Triticeae to which wheat also belongs and similar to Triticum has polyploid series with a basic chromosome number x = 7, but with the basic genome P. Agropyron is in the tertiary gene pool in the context of wheat breeding, and phylogenetically more distantly related than those in the primary and secondary gene pools of wheat. Fortunately, previous genetic studies have revealed that synteny is conserved between wheat and the P genome. Being a perennial species widely used in temperate regions for grazing beef and dairy cattle, it is also a candidate for transforming wheat into a perennial crop in futuristic sustainable agricultural systems [ 26 ]. In hybrids of these two species, chromosome recombination is key to transferring beneficial alleles from crested wheatgrass to wheat. Using in situ hybridization, a technique used to locate specific genomic DNA sequences within chromosomes, Prieto et al. (contribution 5) analyzed chromosome associations during meiosis in Triticum aestivum lines carrying chromosome introgressions of breeding interest (5P and 6P) in two sets of progenies: those with and without the Ph1 locus located in the long arm of chromosome 5B of wheat, known to genetically control chromosome pairing and recombination. The authors did not find homoeologous chromosome pairing either in the presence or absence of the Ph1 locus, indicating that this locus does not influence chromosome pairing between the two species.

The second cereal featured in this Special Issue is barley. Co-evolution of Hordeum vulgare and the fungus Blumeria graminis (D.C.) Golovin ex Speer, f. sp. hordei Em. Marchal ( Bgh ), causing powdery mildew is well studied and recorded, with more than 70 resistance genes. Most of the cultivated winter barley varieties carry one or more of these genes in different combinations, and this information can be used to authenticate accessions in a collection. Using sets of five single-plant progenies (SPPs) per accession from 172 winter barley accessions belonging to the core collection of Czeck gene bank, Dreiseitl and Nesvadba (contribution 6) tested 53 isolates of the pathogen for virulence/avirulence. While the majority of the accessions showed a single phenotype for resistance in their five SPPs, 78 (45.7%) accessions had more than one phenotype indicating heterogeneity in their seed stocks. With defined powdery mildew resistance genes in the SSPs, these accessions can be used with confidence in barley breeding for powdery mildew resistance. The third cereal featured in this Special Issue is the ancient grain tef ( Eragrostis tef (Zucc.) Trotter), an underutilized cereal from Ethiopian highlands with outstanding nutritional value and more resilient than traditional cereals under marginal conditions. With no gluten epitopes, it is recommended for people suffering from celiac disease; hence, it is gaining increased attention around the globe. In this Special Issue, Numan et al. (contribution 7) describe the use of in vitro culture and mutagenesis to improve disease and lodging resistance, as well as the use of molecular markers for selection in tef. They conclude by discussing the potential of genome-editing technologies in tef improvement.

3. Pulse Crops

Pulses constitute an integral part of cropping systems and provide low-cost proteins in diets as well as essential micronutrients. They are the primary source of proteins in vegetarian and vegan diets as well as in the diets of the majority of the population in many developing countries where protein malnutrition is widespread. They improve soil through biological nitrogen fixation, helping to reduce nitrogen fertilizer requirements of the pulse crop, as well as for the next non-legume crop in cropping systems. The value of pulses was highlighted by declaring 2016 as the year of pulses at the 68th United Nations General Assembly (UNGA) with Food and Agriculture Organization (FAO) facilitating its implementation with the participation of Governments and various other stakeholders [ 27 ]. Recognizing the potential of pulses to achieve the 2030 Agenda for Sustainable Development, the UNGA designated 10 February 2023 as World Pulse Day [ 28 ]. Additionally, legumes are an important component of animal feed.

Conventional breeding of leguminous crops has been based on the selection for agronomic traits in the vegetative and reproductive phases that have distinct heritability values. One of the main features for mechanized cultivation of legumes is their transformation from an indeterminate growth habit to a determinate growth habit, facilitating synchronous flowering, pod maturation, and resistance to lodging. Soybean yields have increased globally from around 1130 kg ha −1 in the early 1960s to the current 2800 kg ha −1 , with the yields in the three top soybean-producing countries (USA, Brazil, and Argentina) recording 3200–3300 kg ha −1 [ 29 ]. The breeding of determinate cultivars is a major factor for such yield increases and the expansion of the production area through mechanization. The determinate trait is recessive and monogenically inherited, with the heterozygous individuals showing semi-determinate growth [ 30 , 31 ]. Determinate growth habits have been bred into many other leguminous crops used for seeds, such as pea, chickpea, pigeon pea [ 31 , 32 ], mung bean, black gram [ 33 ], grass pea, and cowpea [ 34 ]. Many of the first determinate cultivars were bred by mutation induction [ 35 ] and not through traditional crossbreeding.

Pulses were regarded as ‘orphan crops’ until recently due to lesser attention given to them compared to cereals. However, many of the pulse crops have now become ‘mainstream crops’, with draft genomes of many of them completed in the past decade [ 36 , 37 , 38 , 39 ] improving the efficiency of breeding efforts. Next-generation sequencing technologies have enabled the deployment of modern genomic tools, including a range of molecular markers associated with many agronomic traits, and disease and abiotic stress tolerances [ 40 ].

Beans, chickpeas, and peas are the most well-known and widely consumed pulses in the world [ 28 ], and two of these are featured in this Special Issue. Common beans ( Phaseolus vulgaris ) were introduced to Ethiopia in the 16th century, and farmers have selected varieties adapted to the local climate and soils over centuries. Their wide genetic diversity, particularly their tolerance to biotic and abiotic stress, has been incorporated in selections developed by the National Common Bean Improvement Program in Ethiopia. Tigist et al. (contribution 8) used 144 genotypes in a multilocation study to understand the variation in 15 agro-morphological traits. Multivariate analysis revealed six principal components. Based on agro-morphological traits, the clustering patterns were according to seed size with considerable genetic variation for the studied characters. The study revealed several accessions with distinct advantages in terms of agro-morphological traits and adaptability suitable for further improvement in the breeding program.

Chickpea ( Cicer arietinum ) is the second most consumed pulse after dry beans, and Australia is a major producer and exporter of this pulse. Among all the continents, Australia is the second driest continent after Antarctica; hence, the drought resistance of crops is a top priority in breeding programs. In both Australia and India (the largest producer of chickpea), chickpea is sown on residual summer moisture and left to grow in progressively depleting soil water, finally maturing under terminal drought. There are many traits associated with drought tolerance, such as root biomass and some leaf anatomical and physiological features. Early maturity is a drought escape strategy in crops such as chickpea sown on residual moisture. There is intensive ongoing work in identifying molecular markers for marker-assisted selection for drought tolerance in chickpea, and a quantitative trait loci (QTL) hotspot region for this trait has been found. The variety ‘Geletu’ with a high yield and drought tolerance was released in 2019 through a backcrossing program to introgress drought tolerance from accession ICC4958 to a high yielding Indian cultivar ‘JG11’, using this hotspot as a selection marker in a backcross breeding program [ 41 ]. However, other more innovative methods for screening populations for drought tolerance in the early growth stages would further accelerate breeding. In their paper in this Special Issue, Purdy et al. (contribution 9) went a step further and identified metabolites in young, watered seedlings of chickpea that can be prognostically used to predict seed numbers in mature plants under terminal drought. Among the yield components of annual crops, it is the seed number, not the seed size (weight) that is sacrificed under abiotic stress, drought in particular (contribution 9) [ 42 , 43 ]. Hence, identifying metabolites that can be used as indicators of seed number under terminal drought later in the life cycle would help in selecting drought-tolerant segregants early on in breeding populations. In chickpea, pinitol, sucrose (negative correlation with seed number), and gamma-aminobutyric acid (positive correlation) can be used to predict high or low seed numbers under these conditions (contribution 9). This is the first instance where a predictive marker was identified for screening drought tolerance that could be used by breeders to identify genotypes that perform well under adverse conditions, without having to expose them to drought.

4. Root and Tuber Crops

Almost all root and tuber crops are traditionally propagated vegetatively, and most are either sterile or partially sterile (cassava and yam); moreover, flowering is irregular and asynchronous (cassava), or crops do not flower at all (aroids such as Colocasia ) [ 44 ]. Therefore, these crops are ideal candidates for improvement through in vitro-based biotechnological approaches. Potato [ 45 ] and sweet potato [ 46 ] have been improved through hybridization and selection; therefore, modern genomics tools are invaluable in improving the efficiency of breeding.

As tuber and root crops are an important source of carbohydrates in many impoverished communities around the world, attention has been focused on improving their mineral and vitamin contents because hidden hunger resulting from their deficiencies is prevalent in these communities, with an estimated two billion people affected [ 47 ]. About 800 million people use cassava ( Manihot esculenta Crantz—Euphorbiaceae) as their staple food, and one third of the sub-Saharan population depends on cassava for over 50% of their caloric intake [ 48 ]. Breeding for increased mineral nutrition in cassava is hampered by the lack of genetic variation for these traits [ 49 ]; hence, transgenic approaches have been tested. For example, the overexpression of a gene for vacuolar iron sequestration, AtV1T1 , resulted in altered partitioning of iron, with an iron content that was three to seven times higher in storage roots in transgenic plants compared to the wild type in field trials. The coexpression of a mutant Arabidopsis thaliana iron transporter IRT1 and A. thaliana ferritin ( FER1 ) produced transgenic cassava plants that accumulated iron levels that were 7–18 times higher and zinc levels that were 3–10 times higher, providing 40–50% of estimated average requirements (EAR) of iron and 60–70% of EAR of zinc for 1–6-year-old children and nonlactating, nonpregnant West African women [ 50 ]. In recent developments in the genomics of cassava, a haplotype-resolved diploid genome of an African landrace cassava (‘TMEB 117’) has been sequenced to a high level of accuracy providing valuable insights into the heterozygous genome of cassava and its resistance to African cassava mosaic virus [ 51 ].

Cassava mosaic disease (CMD), caused by a group of at least eight geminiviruses transmitted by white fly Bemisia tabaci and through infected planting material, is the most devastating disease of cassava in Africa and the Indian subcontinent. With an annual estimated economic loss of USD1.9–2.7 billion, it is considered the most damaging plant virus disease in the world [ 52 ]. The newly emerged cassava brown streak disease (CBSD) caused by two species of ipomoviruses, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), also transmitted by white fly, has become a serious threat to millions of subsistence farmers in Eastern and Central Africa. RNAi-based technology can be deployed for the simultaneous management of multiple viruses using hairpin probes with sequences from several viruses. This approach was used by Beyene et al. [ 53 ] to develop transgenic plants of the popular African cultivar ‘TME204’, expressing an inverted repeat construct derived from coat protein sequences from CBSV and UCBSV fused in tandem. The resulting transgenic plants showed robust resistance to both viruses while retaining the desirable agronomic characteristics of the cultivar preferred by Ugandan farmers, ‘TME204’ [ 53 ]. CBSD-tolerant GM cassava was approved for cultivation in Kenya in 2020 [ 54 ]. Although the disease resistance and safety of the cultivar has been tested, the release is still surrounded by skepticism and criticism [ 55 ]. A non-GM approach to mutation induction has also been attempted to develop mutants with a tolerance for CMD and CBSD. Field trials conducted in different agro-ecological regions in Kenya have revealed that the three mutants have better tolerance to these diseases than their respective parents [ 56 ]. On the other hand, an attempt to increase β carotene content by co-expression of transgenes for deoxy-d-xylulose-5-phosphate synthase and bacterial phytoene synthase in cassava resulted in reduced dry matter and starch content, despite a 15–20-fold increase in carotenoids [ 57 ].

Sweet potato ( Ipomoea batatas (L.) Lam—Convolvulaceae) is the other most important root and tuber crop cultivated worldwide, ranking seventh overall in terms of production [ 57 ] and having considerable potential to reduce the Global Hunger Index, particularly in sub-Saharan Africa, the Pacific Islands, and parts of Asia [ 58 ]. Hexaploidy and self- and cross-incompatibility in sweet potato introduce difficulties in using both traditional breeding and genomic approaches for their improvement. Nevertheless, in recent times, next-generation sequencing, high-throughput genotyping, and phenotyping technologies have been applied to this crop, providing genomic tools and resources for its genetic improvement. The available genomic resources, databases, bioinformatic tools, and the current reference genome of sweet potato were recently reviewed by Yan et al. [ 46 ]. The improvement of sweet potato can now be fast-tracked thanks to the availability of efficient Agrobacterium transformation systems based on embryogenic suspension cultures [ 59 ] and via direct organogenesis using petiole explants [ 60 ], enabling, for example, the development of transgenic sweet potato with herbicide tolerance [ 61 ]. Biolistic transformation has also been successfully developed for this species [ 62 ]. Sweet potato feathery mottle virus (SPFMV), a Potyvirus in the family Potyviridae , is a devastating virus for sweet potato growers worldwide. Using the electroporation method of transformation, Okada et al. [ 63 ] introduced an expression vector harboring the coat protein of SPFMV and hygromycin phosphotransferase genes driven by cauliflower mosaic virus 35 S promoter into a popular sweet potato variety, ‘Chikei 682-11’. Greenhouse testing of three independent transformants showed resistance to both primary and secondary infection by the virus, confirming the possibility of using coat-protein-mediated resistance to SPFMV [ 63 ].

Potato, cassava, and sweet potato, the three most important root and tuber crops worldwide, are featured in this Special Issue. Traditional hybridization-based potato breeding is cumbersome due to the tetraploid nature of cultivated potato ( Solanum tuberosum ) and its narrow genetic base. Starch content on a fresh and dry weight basis is an important breeding objective in potato breeding. Despite the common use of in vitro-produced microtubers in commercial production and germplasm conservation of potato, in vitro techniques remain in limited use as research tools for understanding the biochemical and molecular bases of the physiology of tubers or in breeding. Traits such as dormancy [ 64 , 65 ], cold-induced sweetening [ 66 ], and salinity tolerance [ 67 ] have been shown to be amenable to examination when using this system. In their paper published in this Special Issue, Adley et al. (contribution 10) used callus cultures to induce somaclonal variation in the variety ‘Lady Rosetta’ and screened 105 regenerants for starch content. They isolated a somaclonal variant with 42% and 61% higher fresh and dry weights, respectively. This somaclone had a 10% and 75% higher starch content based on the dry weight and average content per plant, respectively, compared to ‘Lady Rosetta’. Molecular analysis using real-time PCR of the new variant named ‘Ros 119’ demonstrated upregulation of six starch-synthesis genes (contribution 10).

Cassava ( Manihot esculenta Crantz) is the third largest source of food carbohydrates in the tropics after rice and maize. It is one of the most drought-tolerant food crops; hence, it is the staple crop in the poorest and most remote areas in Africa. With great variation in climatic conditions in the tropics, particularly with regard to rainfall and temperature, cultivars with stable high yields across environments are required, especially in large countries with varying climates. In this Special Issue, Amelework et al. (contribution 11) report the results of testing 11 advanced selections of cassava in six sites across South Africa. They analyzed of genotype and environment, and the effects of their interaction on fresh root yield (FRY) and dry matter content (DMC). The results revealed that the variation in percentage due to genotype x environment interaction was highest for FRY, whereas genotypic variation was the main contributor to the total variation in DMC. The authors identified two genotypes providing high DMC and FRY across all environments, and three sites that are representative of the variation in climatic conditions, suitable for variety evaluation and breeding.

Sweet potato ( Ipomoea batatas (L.) Lam.) is a valuable source of carbohydrates, vitamins, fibers, and minerals, and is considered one of the most important crops in both tropical and subtropical climates. Cylas formicarius (Fabricius) and West Indian sweet potato weevil ( Euscepes postfasciatus (Fairmaire)) are the most damaging pests of sweet potato in many continents including Central and South America, the South Pacific, and Japan. In the first comprehensive gene expression analysis during weevil infection in the resistant ‘Kyushu No 166’ cultivar published in this Special Issue, Nokihara et al. (contribution 12) show that genes related to phosphorylation, metabolic, and cellular processes, as well as terpenoid-related genes responsible for producing plant-derived juvenile hormones, are upregulated.

5. Industrial Crops

The only plantation crop that sustainably supplies natural rubber for aviation and other industries, as well as domestic uses, is the Pará rubber tree ( Hevea brasiliensis ); this tree originated in the Amazon, but was domesticated in Asia. As a result of domestication in a distant continent, Pará rubber tree populations have a very narrow genetic base in cultivation and are prone to many diseases. With 3–4 years from seed planting to flowering, 6–7 years to start tapping for rubber, and another 5–10 years required to assess yield, traditional breeding is a difficult and prolonged process. It takes, on average, three decades to complete the entire cycle of selection and release of new clones for planting. Therefore, marker-assisted selection and genetic transformation can accelerate breeding. Somatic embryo-based transformation has been developed for Hevea , and the advances made in this area have been discussed in detail in a recent review by Wang et al. [ 68 ]. The first draft of the H. brasiliensis genome was reported by Rahman et al. [ 69 ] in 2013. Their results indicated that 78% of the genome comprised repetitive DNA and 12.7% of the gene models unique to Hevea . Key genes associated with rubber biosynthesis, disease resistance, and allergenicity were identified [ 69 ]. Genome assembly of the popular rubber clone ‘RRIM 600’ revealed an expansion in the number of rubber-biosynthesis-related genes and their high expression in latex, explaining its high rubber yield [ 70 ]. This was further confirmed in the report by Tang et al. [ 71 ], who demonstrated the expansion of the REF/SRPP (rubber elongation factor/small rubber particle protein) gene family and its divergence. Using a high-density single-nucleotide polymorphism (SNP)-based map, Pootakham et al. [ 72 ] were able to anchor about two thirds of protein-coding genes into 18 linkage groups of the H. brasiliensis ‘BPM 24’ clone. Comparative analysis of the intragenomic homeologous synteny provided evidence for the presence of paleotetraploidy in the species. Chao et al. [ 73 ] demonstrated the relationship of increase in rubber yields during the domestication process with the increase in the number of laticifer rings and its high correlation with HbPSK5 encoding the small-peptide hormone phytosulfokine—a key domestication gene of rubber. Thus, through genomic studies, our understanding of the expression of different traits of agronomic interest in rubber trees has increased. In a recent review, Priyadarshan [ 74 ] discussed the possible application of molecular markers to rubber plants in their juvenile phase to select for traits expressed after maturity using genomic selection. These studies will no doubt accelerate the breeding of new rubber clones with desired traits and improve the efficiency of breeding as well.

The three main diseases affecting rubber plantations worldwide are caused by Phytophthora spp. (causing shoot rot, abnormal leaf fall, patch canker, and black stripe diseases), Corynespora cassiicola (causing Corynospora leaf fall disease), and Colletotrichum spp. (causing Colletotrichum leaf fall disease). All these diseases reduce plant growth and latex yield, and are controlled using fungicides. Breeding for resistance using traditional hybridization and selection is practically impossible because of the high degree of heterozygosity in Pará rubber clones, thus requiring several backcrosses to introgress genes controlling disease resistance in this species with a long breeding cycle and the large land area required for screening such populations. Thus, early screening of breeding populations at the seedling stage can revolutionize breeding of this valuable species. Polymerase chain reaction (PCR) is a simple and rapid method that can detect nucleotide polymorphisms and sequence variation. When PCR reactions are conducted competitively in the presence of allele-specific primers to preferentially amplify only certain alleles, the variant is called allele-specific PCR (AS-PCR). Kompetitive Allele-Specific PCR (KASP) is a variant of AS-PCR modified for fluorescence-based detection of amplification results. In this Special Issue, Roy et al. (contribution 13) report the identification of 12 single nucleotide polymorphisms (SNPs) significantly associated with resistance against Phytophthora , Corynespora, and Colletotrichum in six linkage groups using an integrated linkage map of a F 1 progeny in an interspecific cross between H. brasiliensis (‘RRII 105’—susceptible parent) and H. benthamiana (‘F4542’—resistant parent) using 23,978 markers. To demonstrate the possible application of these findings in marker-assisted breeding of rubber for resistance to these diseases, the authors used KASP assays for all 12 SNPs that showed significant associations with the disease traits. When the KASP assays were applied to 178 ‘RRII’ 105 × ‘F4542’ F 1 progeny, the genotypes could be clearly separated on the basis of resistance. Four F 1 plants were found to carry favorable alleles from H. benthamiana for all the three disease traits. They also predicted 41 key genes within proximity to those SNPs that were previously reported to be associated with disease resistance. This is the first report of the development of molecular markers for the three diseases, and this work has the potential to fast-track the breeding of disease-resistant Pará rubber.

6. New Crops for Arid Regions

The impact of climate change on the agro-forestry systems and the adaptive capacity of plants and animals will be of strategic importance in the immediate future to ensure food security. Numerous evidence suggests that reduced water availability and rising temperatures associated with global warming will have a significant impact on agriculture in the future [ 75 ]. Water is an essential component of agricultural production. According to UN and FAO data, approximately 3000–5000 L of water are needed to meet the daily food requirement of a person [ 76 ]. Furthermore, in the Global Risks Report of the World Economic Forum, water crises are stated as the third most important global risk in terms of impact on humanity [ 77 ].

Climate change has caused an increase in average temperatures and an ever-increasing demand for water. Furthermore, given that the demand for food production is likely to increase in the future [ 78 ], the challenge of sustainably producing food and non-food resources with organisms adapted to new environmental conditions will become of strategic interest. The application of biotechnology to drought-resistant crops would be a long-term solution for the production of more food with less water in increasingly warmer environments. An important contribution to achieving this objective comes from the use of cacti, known for their minimum water requirement; they have been grown extensively in arid lands, for food, feeds, and medicinal and therapeutic uses [ 79 ]. Cacti utilize Crassulacean Acid Metabolism (CAM) for photosynthesis, a unique process in desert plants that opens their stomata only at night when the plant is relatively cool, so that less moisture is lost through transpiration. Among the most interesting species, Opuntia ficus-indica (commonly known as prickly pear) represents an archetypal constitutive CAM species. In this Special Issue, Carra et al. (contribution 14) describe the use of the in vitro rescue of zygotic embryos for the genetic improvement of O. ficus-indica . Prickly pear cactus is an important forage and food source in arid and semiarid ecosystems, and is the most important cactus species cultivated globally. Both fruits and seeds have shown important antioxidant and nutritional properties, and can be a potential source of functional and nutraceutical ingredients. This crop is one of the most promising in the face of new environmental conditions due to climate change which will increasingly reduce the availability of water. In fact, it is able to produce fruits even in conditions where other crops cannot survive. The high degree of apomixis in the species is a hindrance in plant breeding programs where genetic segregation is sought for the selection of superior genotypes. Therefore, the protocols described for in vitro embryo rescue open a pathway to increase the availability of zygotic seedlings in O. ficus-indica breeding programs through in ovule embryo culture.

7. Ornamental Crops

The economic importance of ornamental plants has been increasing significantly in many countries with international demand expanding rapidly, providing many benefits to nature and humans both in urban and peri-urban areas. Ornamental plants, including cut flowers, foliage, and live plants, showed a positive trend in export growth, which led to an aggregate world value of around EUR 18 billion in 2020 [ 80 ]. Ornamental plants, cultivated both in indoor and outdoor environments, can contribute to human health and wellbeing, and can ensure essential environmental services ( Figure 3 ), including the mitigation of the climate change, reduction in air and soil pollution, and providing food for habitants [ 81 , 82 ].

Ecosystem services and benefits obtained from ornamental plants in an urban and peri-urban area.

Ornamentals are a hugely diverse group of commercially significant plants that are grown and traded usually for decorative purposes, either as whole plants or for their parts. Among the ornamental plants, orchids have a special place due to their stunning displays of color and the shape of the flowers. Apart from their scientific fascination due to many unusual biological features, orchids account for a great part of the global floriculture trade. These are either traded as whole plants or cut flowers. Novelty is of great importance in the ornamental plant industry and many biotechnological approaches have applications in developing such novelties. In this Special Issue, such applications in two valuable orchid species of commercial importance have been described.

Polyploidy is much more pronounced in the plant kingdom than in the animal kingdom and has played a key role in plant evolution, species adaptation, and spread. Polyploids are more frequent among agricultural crops than in nature as they have many agronomic benefits such as larger size of organs, higher concentration of secondary metabolites, and better adaptation. Although polyploidization occurs in nature sporadically, in plant breeding it is artificially induced at higher frequencies. The development of new polyploid orchids often results in superior ornamental characteristics compared to their diploid counterparts. Orchids of the genus Cattleya are commercialized as hybrids. Although there are protocols for the polyploidization of Cattelya spp., there are no protocols for their interspecific or intergeneric hybrids, the widely commercialized types. In the current Special Issue, Vilcherrez-Atoche et al. (contribution 15) describe the use of in vitro cultured protocorms and seeds to induce polyploidy in Brassolaeliocattleya, a cross between three genera: Brassavola , Laelia , and Cattleya [ 83 ], using colchicine—an inhibitor of microtubule formation in the chromatic spindle resulting in the nondisjunction of chromosomes; this, in turn, results in the duplication of chromosomes within the nucleus. They report higher rates of polyploidization in protocorms and use flowcytometry to confirm the ploidy level in regenerants.

Dendrobium orchids are traded both as cut flowers and potted plants. They are among the top ten orchid taxa of commercial importance, with a wide variety of choices in flower color, texture, and shape, and a good vase life. However, two varieties account for 70% of the world trade, indicating a limited choice of varieties suited for the export market. Hence, there is an enormous potential for the right cultivars to break into the export market. However, compatibility barriers in intersectional crossing, negative genetic linkages in promising traits and prolonged juvenile phase and high mortality at hardening stages of in vitro cultures are barriers to improvement and commercialization of novel Dendrobiums. Induced mutations offer unique opportunities to improve elite cultivars by rectifying a defect such as late flowering, disease susceptibility or flower size [ 23 ]. The Dendrobium hybrid ‘Emma White’ is popular, but has a long juvenility after micropropagation. With the objective of developing an early flowering mutant of ‘Emma White’, Sherpa et al. (contribution 16) used gamma irradiation on protocorm-like bodies of this mutant and studied growth responses at different dosages and found optimal dose levels for producing high mutation rates with low mortality. By screening the mutant population, they were able to isolate a mutant with early flowering (294 days vs. 959 days in “Emma White’), demonstrating the value of in vitro mutagenesis in improving orchids.

8. Development of New Methodologies in Plant Biotechnology

Genetic transformation is a breakthrough biotechnology that has transformed agriculture in recent times, with 29 countries growing over 190.5 million ha of biotech crops. Although the number of countries is small, the impact of biotech crops is high, with most of North and South America, China, India, Australia, Indonesia, Vietnam, Myanmar, Pakistan, Bangladesh, the Philippines, and large countries in Africa (South Africa, Nigeria, Ethiopia, Kenya, Sudan, etc.) growing these crops. Thanks to improved traits such as insect resistance, growing these crops is more environmentally friendly, and the additional income from these crops is estimated at USD 225 billion for the 20-year period since 1996 thanks to the production of an additional 824 Mt of food, feed, and fiber [ 6 ]. Stable gene transformation systems and strong positive selection markers are imperative for developing transgenic plants. Co-cultivation of the host plant tissue in vitro along with Agrobacterium carrying the desired gene construct is the traditional method for transformation, and antibiotic- or herbicide-resistant genes inserted along with the desired gene/s are used as positive selection markers. Due to environmental and health concerns with such genes in plants, other markers such as β-glucuronidase or fluorescent protein markers are used, but they require destructive staining for former or expensive equipment to detect fluorescent cells for the latter option. Therefore, more robust and simple selection marker development for crop transformation is important. In this Special Issue, Lim et al. (contribution 17) report the development of a simple system for the selection of transgenic plants. They report the use of the R2R3 MYB transcription factor gene CaAN2 from chili pepper ( Capsicum annuum ) for use as a visible selection marker with successful selection in both transient assays and in stable transformation, using tobacco as the model system. Transgenic tobacco plants harboring the chili pepper CaAN2 readily promoted the accumulation of anthocyanin throughout the plant, allowing easy selection at the plant regeneration stage of the transformation experiment without the involvement of additional steps to identify the transgenic plants. The method has the potential to dramatically improve the efficiency of selection in plant genetic transformation, a key biotechnological approach for crop improvement.

Abbreviations

Author Contributions

Conceptualization, R.P. and F.C.; methodology, R.P. and F.C.; software, R.P. and F.C.; resources, R.P. and F.C.; writing—original draft preparation, R.P. and F.C.; writing—review and editing, R.P. and F.C.; visualization, R.P. and F.C. All authors have read and agreed to the published version of the manuscript.

Conflicts of Interest

The author declares no conflicts of interest.

List of Contributions

• Nowicka, B. Modifications of Phytohormone Metabolism Aimed at Stimulation of Plant Growth, Improving Their Productivity and Tolerance to Abiotic and Biotic Stress Factors. Plants 2022 , 11 , 3430.
• Hamdan, M.F.; Karlson, C.K.S.; Teoh, E.Y.; Lau, S.-E.; Tan, B.C. Genome Editing for Sustainable Crop Improvement and Mitigation of Biotic and Abiotic Stresses. Plants 2022 , 11 , 2625.
• Buzdin, A.V.; Patrushev, M.V.; Sverdlov, E.D. Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population? Plants 2021 , 10 , 1667.
• Zhao, Y.; Feng, M.; Paudel, D.; Islam, T.; Momotaz, A.; Luo, Z.; Zhao, Z.; Wei, N.; Li, S.; Xia, Q.; et al. Advances in Genomics Approaches Shed Light on Crop Domestication. Plants 2021 , 10 , 1571.
• Prieto, P.; Palomino, C.; Cifuentes, Z.; Cabrera, A. Analysis of chromosome associations during early meiosis in wheat lines carrying chromosome introgressions from Agropyron cristatum . Plants 2021 , 10 , 2292, https://doi.org/10.3390/plants10112292 .
• Dreiseitl, A.; Nesvadba, Z. Powdery mildew resistance genes in single-plant progenies derived from accessions of a winter barley core collection. Plants 2021 , 10 , 1988, https://doi.org/10.3390/plants10101988 .
• Numan, M.; Khan, A.L.; Asaf, S.; Salehin, M.; Beyene, G.; Tadele, Z.; Ligaba-Osena, A. From Traditional Breeding to Genome Editing for Boosting Productivity of the Ancient Grain Tef [Eragrostis tef (Zucc.) Trotter]. Plants 2021 , 10 , 628.
• Tigist, S.G.; Sibiya, J.; Amelework, A.; Keneni, G. Agromorphological and physiological performance of Ethiopian common bean ( Phaseolus vulgaris L.) Genotypes Under Different Agroecological Conditions. Plants 2023 , 12 , 2342, https://doi.org/10.3390/plants12122342 .
• Purdy, S.J.; Fuentes, D.; Ramamoorthy, P.; Nunn, C.; Kaiser, B.N.; Merchant, A. The metabolic profile of young, watered chickpea plants can be used as a biomarker to predict seed number under terminal drought. Plants 2023 , 12 , 2172.
• Adly, W.M.R.M.; Niedbała, G.; EL-Denary, M.E.; Mohamed, M.A.; Piekutowska, M.; Wojciechowski, T.; Abd El-Salam, E.-S.T.; Fouad, A.S. Somaclonal variation for genetic improvement of starch accumulation in potato ( Solanum tuberosum ) tubers. Plants 2023 , 12 , 232.
• Amelework, A.B.; Bairu, M.W.; Marx, R.; Laing, M.; Venter, S.L. Genotype x Environment Interaction and stability analysis of selected cassava cultivars in South Africa. Plants 2023 , 12 , 2490.
• Nokihara, K.; Okada, Y.; Ohata, S.; Monden, Y. Transcriptome analysis reveals key genes involved in weevil resistance in the hexaploid sweetpotato. Plants 2021 , 10 , 1535.
• Roy, C.B.; Goonetilleke, S.N.; Joseph, L.; Krishnan, A.; Saha, T.; Kilian, A.; Mather, D.E. Analysis of genetic diversity and resistance to foliar pathogens based on genotyping-by-sequencing of a para rubber diversity panel and progeny of an interspecific cross. Plants 2022 , 11 , 3418.
• Carra, A.; Catalano, C.; Pathirana, R.; Sajeva, M.; Inglese, P.; Motisi, A.; Carimi, F. Increased Zygote-Derived Plantlet Formation through In Vitro Rescue of Immature Embryos of Highly Apomictic Opuntia ficus-indica (Cactaceae). Plants 2023 , 12 , 2758.
• Vilcherrez-Atoche, J.A.; Silva, J.C.; Clarindo, W.R.; Mondin, M.; Cardoso, J.C. In Vitro Polyploidization of Brassolaeliocattleya Hybrid Orchid. Plants 2023 , 12 , 281.
• Sherpa, R.; Devadas, R.; Bolbhat, S.N.; Nikam, T.D.; Penna, S. Gamma Radiation Induced In-Vitro Mutagenesis and Isolation of Mutants for Early Flowering and Phytomorphological Variations in Dendrobium ‘Emma White’. Plants 2022 , 11 , 3168.
• Lim, S.-H.; Kim, D.-H.; Cho, M.-C.; Lee, J.-Y. Chili pepper AN2 ( CaAN2 ): A visible selection marker for nondestructive monitoring of transgenic plants. Plants 2022 , 11 , 820.

Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

• View all journals

Biotechnology articles from across Nature Portfolio

Biotechnology is a broad discipline in which biological processes, organisms, cells or cellular components are exploited to develop new technologies. New tools and products developed by biotechnologists are useful in research, agriculture, industry and the clinic.

Phage genome engineering with retrons

A method using retron recombineering for phage genome modification may facilitate access to therapeutic phages.

• Ilya Osterman
• Rotem Sorek

Mitochondrial transplants to treat mitochondrial dysfunction

A new approach to treating mitochondrial disorders is based on the transplantation of healthy mitochondria, and improves symptoms and survival in a mouse model of Leigh syndrome — a paediatric mitochondrial disease that is characterized by failure to thrive, lactic acidosis, and progressive degeneration.

• Alessandro Bitto

DNA nanoswitches pack an anti-cancer punch

A DNA origami nanodevice presents its hidden death ligand pattern in the acidic tumour microenvironment to kill cancerous cells, opening opportunities for effective and safe cancer therapy.

• Chenxiang Lin

Related Subjects

• Animal biotechnology
• Applied immunology
• Assay systems
• Biomaterials
• Biomimetics
• Cell delivery
• Environmental biotechnology
• Expression systems
• Functional genomics
• Gene delivery
• Gene therapy
• Industrial microbiology
• Metabolic engineering
• Metabolomics
• Molecular engineering
• Nanobiotechnology
• Nucleic-acid therapeutics
• Oligo delivery
• Peptide delivery
• Plant biotechnology
• Protein delivery
• Regenerative medicine
• Stem-cell biotechnology
• Tissue engineering

Latest Research and Reviews

Insights into the evaluation, influential factors and improvement strategies for poultry meat quality: a review

• Ke Yue (岳珂)
• Qin-qin Cao (曹芹芹)
• Shu-cheng Huang (黄淑成)

Photocatalytic and antibacterial activity properties of Ti surface treated by femtosecond laser–a prospective solution to peri-implant disease

• Adriana Barylyak
• Renata Wojnarowska-Nowak
• Joanna Kisała

Local administration of regulatory T cells promotes tissue healing

Regulatory T cells (Tregs) are known for suppressing inflammatory processes, but their full capacity for tissue regeneration is yet to be harnessed. Here, the authors demonstrate the efficiency of Tregs in facilitating tissue healing in mouse models of bone, muscle, and skin injury, with monocytes/macrophages and interleukin-10 playing a key mechanistic role in the process.

• Bhavana Nayer
• Jean L. Tan
• Mikaël M. Martino

Identification and knockout of a herbivore susceptibility gene enhances planthopper resistance and increases rice yield

Planthoppers are among the most destructive pests on rice. This study identified that a leucine-rich repeat protein OsLRR2 negatively regulates defence responses. Knockout of the encoding gene OsLRR2 enhances rice herbivore resistance and yield, which holds the potential to produce high-yielding rice varieties that are resistant to devastating pest insects.

• Yonggen Lou

DNA microbeads for spatio-temporally controlled morphogen release within organoids

Creating precise morphogen gradients for tissue engineering is challenging. Here the authors present mechanically tunable DNA hydrogel-based microbeads for light-controlled morphogen release in retinal organoids for better tissue mimicry.

• Cassian Afting
• Tobias Walther
• Kerstin Göpfrich

A flow cytometry method for quantitative measurement and molecular investigation of the adhesion of bacteria to yeast cells

• Marion Schiavone
• Adilya Dagkesamanskaya
• Jean Marie François

News and Comment

I make fake eyes for those who need them

As the only ocularist in Uganda, Franklin Wasswa produces customized prosthetic eyes for people who’ve lost their own to injury or disease.

• Linda Nordling

Molecular architecture of the human brain vasculature

• Elisa Floriddia

A biodegradable tent electrode

An article in Nature Electronics reports the development of a biodegradable, minimally invasive tent electrode for large-area cortex monitoring.

• Caroline Beyer

Cells as active crosslinkers in living materials

An article in Nature Materials reports a new method for generating macroscale living materials by using cells as active crosslinkers.

• Sadra Bakhshandeh

Quick links

• Explore articles by subject
• Guide to authors
• Editorial policies