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

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dc.creatorVarshney, Rajeev K.
dc.creatorRoorkiwal, Manish
dc.creatorSun, Shuai
dc.creatorBajaj, Prasad
dc.creatorChitikineni, Annapurna
dc.creatorThudi, Mahendar
dc.creatorSingh, Narendra P.
dc.creatorDu, Xiao
dc.creatorUpadhyaya, Hari D.
dc.creatorKhan, Aamir W.
dc.creatorWang, Yue
dc.creatorGarg, Vanika
dc.creatorFan, Guangyi
dc.creatorCowling, Wallace A.
dc.creatorCrossa, José
dc.creatorGentzbittel, Laurent
dc.creatorVoss-Fels, Kai Peter
dc.creatorValluri, Vinod Kumar
dc.creatorSinha, Pallavi
dc.creatorSingh, Vikas K.
dc.creatorBen, Cécile
dc.creatorRathore, Abhishek
dc.creatorPunna, Ramu
dc.creatorSingh, Muneendra K.
dc.creatorTar’an, Bunyamin
dc.creatorBharadwaj, Chellapilla
dc.creatorYasin, Mohammad
dc.creatorPithia, Motisagar S.
dc.creatorSingh, Servejeet
dc.creatorSoren, Khela Ram
dc.creatorKudapa, Himabindu
dc.creatorJarquín, Diego
dc.creatorCubry, Philippe
dc.creatorHickey, Lee T.
dc.creatorDixit, Girish Prasad
dc.creatorThuillet, Anne-Céline
dc.creatorHamwieh, Aladdin
dc.creatorKumar, Shiv
dc.creatorDeokar, Amit A.
dc.creatorChaturvedi, Sushil K.
dc.creatorFrancis, Aleena
dc.creatorHoward, Réka
dc.creatorChattopadhyay, Debasis
dc.creatorEdwards, David
dc.creatorLyons, Eric
dc.creatorVigouroux, Yves
dc.creatorHayes, Ben J.
dc.creatorvon Wettberg, Eric
dc.creatorDatta, Swapan K.
dc.creatorYang, Huanming
dc.creatorNguyen, Henry T.
dc.creatorWang, Jian
dc.creatorSiddique, Kadambot H. M.
dc.creatorMohapatra, Trilochan
dc.creatorBennetzen, Jeffrey L.
dc.creatorXu, Xun
dc.creatorLiu, Xin
dc.date2021-11-25
dc.date2024-12-19T12:53:31Z
dc.date2024-12-19T12:53:31Z
dc.date.accessioned2026-06-27T04:10:59Z
dc.descriptionZero 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.
dc.identifierhttps://hdl.handle.net/10568/164163
dc.identifier.urihttp://hdl.handle.net/123456789/24248
dc.languageen
dc.publisherSpringer
dc.rightsOpen Access
dc.sourceVarshney, Rajeev K.; Roorkiwal, Manish; Sun, Shuai; Bajaj, Prasad; Chitikineni, Annapurna; Thudi, Mahendar; Singh, Narendra P.; Du, Xiao; Upadhyaya, Hari D.; Khan, Aamir W.; Wang, Yue; Garg, Vanika; Fan, Guangyi; Cowling, Wallace A.; Crossa, José; Gentzbittel, Laurent; Voss-Fels, Kai Peter; Valluri, Vinod Kumar; Sinha, Pallavi; Singh, Vikas K.; Ben, Cécile; Rathore, Abhishek; Punna, Ramu; Singh, Muneendra K.; Tar’an, Bunyamin; Bharadwaj, Chellapilla; Yasin, Mohammad; Pithia, Motisagar S.; Singh, Servejeet; Soren, Khela Ram; Kudapa, Himabindu; Jarquín, Diego; Cubry, Philippe; Hickey, Lee T.; Dixit, Girish Prasad; Thuillet, Anne-Céline; Hamwieh, Aladdin; Kumar, Shiv; Deokar, Amit A.; Chaturvedi, Sushil K.; Francis, Aleena; Howard, Réka; Chattopadhyay, Debasis; Edwards, David; Lyons, Eric; Vigouroux, Yves; Hayes, Ben J.; von Wettberg, Eric; Datta, Swapan K.; Yang, Huanming; Nguyen, Henry T.; Wang, Jian; Siddique, Kadambot H. M.; Mohapatra, Trilochan; Bennetzen, Jeffrey L.; Xu, Xun and Liu, Xin. 2021. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature, Volume 599 no. 7886 p. 622-627
dc.titleA chickpea genetic variation map based on the sequencing of 3,366 genomes
dc.typeJournal Article

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Instituto Internacional de Investigación del Arroz (IRRI)