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Genomic tools in legume breeding programs: status and perspectives

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Genomic tools have emerged as efficient and robust methods to enhance genetic gain in crop breeding programs; their use has been fast in staple cereals and high value crops, but limited in most of the legume crops. Legumes are an important source of proteins and micronutrients for humans and provide ...

Genomic tools have emerged as efficient and robust methods to enhance genetic gain in crop breeding programs; their use has been fast in staple cereals and high value crops, but limited in most of the legume crops. Legumes are an important source of proteins and micronutrients for humans and provide protein-rich fodder for livestock. They are valued for their nutritional value as well as symbiotic nitrogen fixation. But, the yields of legumes are generally low as they are often cultivated in marginal environments and low adoption of improved varieties. Consequently, legumes face more adverse challenges of climate change. New improved legume varieties with tolerance to abiotic and biotic stress are urgently needed to plug the yield losses, and those with enhanced quality contribute to nutritional security. The use of genomic tools in legume breeding programs can enhance the efficiency of delivery of trait specific legume varieties and thus contribute to enhanced productivity of legumes, and nutritional security.
Given the low research trust, some legumes were referred to as ‘orphan’ crops, although not anymore. Last decade was eventful for several legume breeding programs with respect to development and deployment of genomic tools. Linkage maps were published, mapping populations were developed, and marker-trait associations were identified paving way to use of genomic tools in legume breeding programs. In recent years, genomes of several legume species like soybean, pigeonpea, chickpea, common bean and mungbean were sequenced and that of other legumes are being deciphered. Improved legume varieties, bred using marker-assisted selection (MAS) and marker-assisted backcrossing (MABC), are under different stages of yield evaluations and a few of them were already released for cultivation. Attempts are in progress to use marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches. Precision breeding using genomic tools and modern breeding approaches has been rewarding in several legumes, particularly for resistance to diseases and enhanced nutritional quality. However, deployment of genomic tools is variable in different legumes depending on availability of genomic resources, human capacities and infrastructure. With this background, an attempt is made to review the status of available genomic tools in different legumes, their use in legume breeding programs, perspectives, and possibly cross-learning between legumes.
The review covers ten legume crops, besides crosscutting articles on emerging genomic tools, genetic resources and Bioinformatics for legumes breeding. The review on each crop is expected to cover the following broad areas, but not necessarily limited to this, and authors are encouraged to choose their unique structure for presenting the review.
1. Economic importance, growing regions, nutritional value
2. Linkage groups, breeding behavior, wild species
3. Target traits (production, stress tolerance, nutritional etc. and achievements through conventional breeding with examples)
4. Available genomic resources (linkage maps, populations, marker-trait associations, genome wide association studies, etc.)
5. The use of genomic tools in breeding programs with examples (MAS, MABC, MARS, and new alleles from wild species and others)
6. Perspectives (target traits for improvement using genomic tools, gene pyramiding, GS, GBS, SNPs, others)
7. Summary


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