A chickpea genetic variation map based on the sequencing of 3,366 genomes

Varshney, R K and Roorkiwal, M and Sun, S and Bajaj, P and Chitikineni, A and Thudi, M and Singh, N P and Du, X and Upadhyaya, H D and Khan, A W and Wang, Y and Garg, V and Fan, G and Cowling, W A and Crossa, J and Gentzbittel, L and Voss-Fels, K P and Valluri, V K and Sinha, P and Singh, V K and Ben, C and Rathore, A and Punna, R and Singh, M K and Tar’an, B and Bharadwaj, C and Yasin, M and Pithia, M S and Singh, S and Soren, K R and Kudapa, H and Jarquín, D and Cubry, P and Hickey, L T and Dixit, G P and Thuillet, A and Hamwieh, A and Kumar, S and Deokar, A A and Chaturvedi, S K and Francis, A and Howard, R and Chattopadhyay, D and Edwards, D and Lyons, E and Vigouroux, Y and Hayes, B J and Wettberg, E v and Datta, S K and Yang, H and Nguyen, H T and Wang, J and Siddique, K H M and Mohapatra, T and Bennetzen, J L and Xu, X and Liu, X (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, 599. pp. 622-627. ISSN 1476-4687

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Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Item Type: Article
Divisions: Center of Excellence in Genomics and Systems Biology
Uncontrolled Keywords: Chickpea, Genetic variation map, 3,366 genomes
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Others > Food Security
Depositing User: Mr Nagaraju T
Date Deposited: 11 Jul 2023 06:29
Last Modified: 11 Jul 2023 06:29
URI: http://oar.icrisat.org/id/eprint/12132
Official URL: https://www.nature.com/articles/s41586-021-04066-1
Acknowledgement: R.K.V. acknowledges funding support in part from the Department of Agriculture and Farmers’ Welfare, Ministry of Agriculture and Farmers’ Welfare; Department of Biotechnology, Ministry of Science and Technology under the Indo- Australian Biotechnology Fund, Government of India, and the Bill & Melinda Gates Foundation; X.L. acknowledges the National Key R&D Program of China (2019YFC1711000), the Shenzhen Municipal Government of China (JCYJ20170817145512476) and the Guangdong Provincial Key Laboratory of Genome Read and Write (2017B030301011); E.L. thanks the National Science Foundation for funding CyVerse work (DBI-0735191, DBI-1265383 and DBI-1743442); and R.K.V. and W.A.C. thank B. Kinghorn for providing access to MateSel software and for help with OCS in this paper. We also thank S. Abbo and M. W. Bevan for their inputs while we were preparing the manuscript; M. Caccamo for constructive criticism and suggestions to improve the quality of the manuscript; and DivSeek International Network and its members, especially S. McCouch for useful discussions related to ‘The 3000 Chickpea Genome Sequencing Initiative’.
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