Next generation sequencing (NGS) technologies are being used to generate whole genome sequences for a wide range of crop species. When combined with precise phenotyping methods, these technologies ...provide a powerful and rapid tool for identifying the genetic basis of agriculturally important traits and for predicting the breeding value of individuals in a plant breeding population. Here we summarize current trends and future prospects for utilizing NGS-based technologies to develop crops with improved trait performance and increase the efficiency of modern plant breeding. It is our hope that the application of NGS technologies to plant breeding will help us to meet the challenge of feeding a growing world population.
•Summarized the current status of genomic-assisted breeding in three legumes.•Highlighted the progress in development of genomics resources in three legumes.•Presented future prospects of ...translational genomics for crop improvement.
Legume crops such as chickpea, pigeonpea and groundnut, mostly grown in marginal environments, are the major source of nutrition and protein to the human population in Asia and Sub-Saharan Africa. These crops, however, have a low productivity, mainly due to their exposure to several biotic and abiotic stresses in the marginal environments. Until 2005, these crops had limited genomics resources and molecular breeding was very challenging. During the last decade (2005–2015), ICRISAT led demand-driven innovations in genome science and translated the massive genome information in breeding. For instance, large-scale genomic resources including draft genome assemblies, comprehensive genetic and physical maps, thousands of SSR markers, millions of SNPs, several high-throughput as well as low cost marker genotyping platforms have been developed in these crops. After mapping several breeding related traits, several success stories of translational genomics have become available in these legumes. These include development of superior lines with enhanced drought tolerance in chickpea, enhanced and pyramided resistance to Fusarium wilt and Ascochyta blight in chickpea, enhanced resistance to leaf rust in groundnut, improved oil quality in groundnut and utilization of markers for assessing purity of hybrids/parental lines in pigeonpea. Some of these stories together with future prospects have been discussed.
Over the past decade, genomics-assisted breeding (GAB) has been instrumental in harnessing the potential of modern genome resources and characterizing and exploiting allelic variation for germplasm ...enhancement and cultivar development. Sustaining GAB in the future (GAB 2.0) will rely upon a suite of new approaches that fast-track targeted manipulation of allelic variation for creating novel diversity and facilitate their rapid and efficient incorporation in crop improvement programs. Genomic breeding strategies that optimize crop genomes with accumulation of beneficial alleles and purging of deleterious alleles will be indispensable for designing future crops. In coming decades, GAB 2.0 is expected to play a crucial role in breeding more climate-smart crop cultivars with higher nutritional value in a cost-effective and timely manner.
Availability of reference genomes and genome-wide surveys on comprehensive diversity panels pave the way to associate the allelic variation with phenotypes.Methods are now available to evaluate the genetic worth of the vast genetic resources archived in gene banks and streamline application of these resources in crop improvement programs.Precise genome editing technologies in concert with enhanced trait architectures enable innovative solutions to engineer complex trait variation.High-throughput phenotyping methods are beginning to alleviate the challenge of accurate, precise, and large-scale measurements of plant performance.Optimized speed breeding protocols remain crucial to accelerating breeding advance when applied with genomic breeding approaches.Sustaining gains from genomic breeding seeks fast-tracking exploitation of the minor effect alleles, accumulation of favorable alleles, and purging of deleterious alleles.
There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 ...different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of ...quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genome-wide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre- and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.
Plants are extensively well-thought-out as the main source for nourishing natural life on earth. In the natural environment, plants have to face several stresses, mainly heat stress (HS), chilling ...stress (CS) and freezing stress (FS) due to adverse climate fluctuations. These stresses are considered as a major threat for sustainable agriculture by hindering plant growth and development, causing damage, ultimately leading to yield losses worldwide and counteracting to achieve the goal of "zero hunger" proposed by the Food and Agricultural Organization (FAO) of the United Nations. Notably, this is primarily because of the numerous inequities happening at the cellular, molecular and/or physiological levels, especially during plant developmental stages under temperature stress. Plants counter to temperature stress via a complex phenomenon including variations at different developmental stages that comprise modifications in physiological and biochemical processes, gene expression and differences in the levels of metabolites and proteins. During the last decade, omics approaches have revolutionized how plant biologists explore stress-responsive mechanisms and pathways, driven by current scientific developments. However, investigations are still required to explore numerous features of temperature stress responses in plants to create a complete idea in the arena of stress signaling. Therefore, this review highlights the recent advances in the utilization of omics approaches to understand stress adaptation and tolerance mechanisms. Additionally, how to overcome persisting knowledge gaps. Shortly, the combination of integrated omics, genome editing, and speed breeding can revolutionize modern agricultural production to feed millions worldwide in order to accomplish the goal of "zero hunger."
Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and ...genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding.
In recent years, the global climate has changed, resulting in drastic fluctuations in rainfall patterns and increasing temperature. Sudden climate changes can cause significant economic losses to countries worldwide.
Genetic improvement of several economically important crops during the 20th century using phenotypic, pedigree, and performance data was very successful. However, signs of grain yield stagnation in some crops, especially in drought-stressed and semi-arid regions, are evident.
Genomic selection offers the opportunity to increase grain production in less time. International Maize and Wheat Improvement Center (CIMMYT) maize breeding research in Sub-Saharan Africa, India, and Mexico has shown that genomic selection can reduce the breeding interval cycle to at least half the conventional time and produces lines that, in hybrid combinations, significantly increase grain yield performance over that of commercial checks.
Public and private investment in crop genomic selection research should increase to successfully develop in less time germplasm that is adapted to sudden climate change.
Summary
Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of ...high‐yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host–pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani–rice pathosystem research with gap analysis are provided.
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