Browsing by Author "Chitikineni, Annapurna"

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    A chickpea genetic variation map based on the sequencing of 3,366 genomes
    (Springer Nature Publishing AG, 2021) Varshney, 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; Wettberg, Eric von; Datta, Swapan K; Yang, Huanming; Nguyen, Henry T; Wang, Jian; Siddique, Kadambot H M; Mohapatra, Trilochan; Bennetzen, Jeffrey L; Xu, Xun; Liu, Xin
    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.
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    The genome sequence of segmental allotetraploid peanut Arachis hypogaea
    (Springer Nature Publishing AG, 2019) Bertioli, David J.; Jenkins, Jerry; Clevenger, Josh; Dudchenko, Olga; Gao, Dongying; Seijo, Guillermo; Leal-Bertioli, Soraya C. M.; Ren, Longhui; Farmer, Andrew D.; Pandey, Manish K.; Samoluk, Sergio S.; Abernathy, Brian; Agarwal, Gaurav; Ballén-Taborda, Carolina; Cameron, Connor; Campbell , Jacqueline; Chavarro, Carolina; Chitikineni, Annapurna; Chu, Ye; Dash, Sudhansu; Baidouri, Moaine El; Guo, Baozhu; Huang, Wei; Kim, Kyung Do; Korani, Walid; Lanciano, Sophie; Lui, Christopher G.; Mirouze, Marie; Moretzsohn, Márcio C.; Pham, Melanie; Shin, Jin Hee; Shirasawa, Kenta; Sinharoy, Senjuti; Sreedasyam, Avinash; Weeks, Nathan T.; Zhang, Xinyou; Zheng, Zheng; Sun, Ziqi; Froenicke, Lutz; Aiden, Erez L.; Michelmore, Richard; Varshney, Rajeev K.; Holbrook, C. Corley; Cannon, Ethalinda K. S.; Scheffler, Brian E.; Grimwood, Jane; Ozias-Akins, Peggy; Cannon, Steven B.; Jackson, Scott A.; Schmutz , Jeremy
    Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.