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

Creator: Varshney, R.K.
Creator: Roorkiwal, M.
Creator: Shuai Sun
Creator: Bajaj, P.
Creator: Annapurna Chitikineni
Creator: Thudi, M.
Creator: Singh, N.P.
Creator: Xiao Du
Creator: Upadhyaya, H.
Creator: Khan, A.W.
Creator: Yue Wang
Creator: Vanika Garg
Creator: Guangyi Fan
Creator: Cowling, W.A.
Creator: Crossa, J.
Creator: Gentzbittel, L.
Creator: Voss-Fels, K.P.
Creator: Valluri, V.K.
Creator: Sinha, P.
Creator: Singh, V.K.
Creator: Ben, C.
Creator: Abhishek Rathore
Creator: Punna, R.
Creator: Muneendra K. Singh
Creator: Tar’an, B.
Creator: Chellapilla Bharadwaj
Creator: Yasin, M.
Creator: Pithia, M.S.
Creator: Singh, S.
Creator: Soren, K.R.
Creator: Kudapa, H.
Creator: Jarquín, D.
Creator: Cubry, P.
Creator: Lee T. Hickey
Creator: Dixit, G.P.
Creator: Thuillet, A.C.
Creator: Hamwieh, A.
Creator: Kumar, S.
Creator: Deokar, A.
Creator: Chaturvedi, S.K.
Creator: Francis, A.
Creator: Howard, R.
Creator: Chattopadhyay, D.
Creator: Edwards, D.
Creator: Lyons, E.
Creator: Vigouroux, Y.
Creator: Hayes, B.J.
Creator: Von Wettberg, E.
Creator: Datta, S.K.
Creator: Huanming Yang
Creator: Nguyen, H.T.
Creator: Jian Wang
Creator: Siddique, K.H.M.
Creator: Mohapatra, T.
Creator: Bennetzen, J.L.
Creator: Xun Xu
Creator: Xin Liu
Year: 2021
Language: English
Publisher: Nature Publishing Group
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: London (United Kingdom)
Volume: In press
DOI: 10.1038/s41586-021-04066-1
Description: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) 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.
ISSN: 0028-0836
Journal: Nature

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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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