Toward the sequence-based breeding in legumes in the post-genome sequencing era

Varshney, R K and Pandey, M K and Bohra, A and Singh, V K and Thudi, M and Saxena, R K (2019) Toward the sequence-based breeding in legumes in the post-genome sequencing era. Theoretical and Applied Genetics (TSI), 132 (3). pp. 797-816. ISSN 0040-5752

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Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4–6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers’ fields.

Item Type: Article
Divisions: Research Program : Genetic Gains
Uncontrolled Keywords: breeding programs, legume crops, chickpea, pigeonpea, groundnut, genomic tools and technologies, next-generation sequencing technologies, seed systems, improved varieties, genome sequences, genetic gains, sequence‑based breeding, speed breeding, genetic diversity, molecular breeding, trait mapping, genetic populations, genome re‑sequencing
Subjects: Others > Food Production
Others > Plant Breeding
Mandate crops > Chickpea
Mandate crops > Pigeonpea
Mandate crops > Groundnut
Others > Food Legumes
Others > Genetics and Genomics
Others > Food Security
Others > Legume Crops
Depositing User: Mr Ramesh K
Date Deposited: 21 Jun 2019 06:13
Last Modified: 21 Jun 2019 06:13
Official URL:
Acknowledgement: The authors are thankful to the Bill and Melinda Gates Foundation (Tropical Legumes I, II and III), United States Agency for International Development (USAID), and MARS-Wrigley of USA; Indian Council of Agricultural Research (ICAR)-National Agricultural Science Funds (NASF), and Department of Biotechnology (DBT) of Government of India and World Bank-assisted Karnataka Watershed Development Project-II (KWDP-II) funded by Government of Karnataka (GoK), India. Authors would like to thank all their colleagues and collaborators at ICRISAT and other organizations for useful discussions about genomics applications in crop improvement. The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC). ICRISAT is a member of the CGIAR.
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