Browsing by Author "Thudi, Mahendar"

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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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    Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)
    (Springer, 2014) Varshney, Rajeev K.; Mir, Reyazul Rouf; Bhatia, Sabhyata; Thudi, Mahendar; Hu, Yuqin; Azam, Sarwar; Zhang, Yong; Jaganathan, Deepa; You, Frank M.; Gao, Jinliang; Riera-Lizarazu, Oscar; Luo, Ming-Cheng
    Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance "QTL-hotspot" region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement.