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Diversity analysis in chickpea germplasm using SNP and DArT markers
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Diversity analysis in chickpea germplasm using SNP and DArT markers

  1. Manish Roorkiwal1, Eric J von Wettberg2,3, Hari Upadhyaya1, R Varma Penmetsa4, Douglas R Cook4, Rajeev Varshney1,5,* To estimate genetic diversity within or between 10 Cicer species (94 accessions) covering the primary, secondary and tertiary gene pool we analyzed 5257 DArT markers and 651 KASPar SNP markers. However, allelic data for only 2763 DArT and 624 SNP markers that are polymorphic between accessions of primary and tertiary genepools were analyzed further to tackle ascertainment bias. STRUCTURE analyses showed 3 populations (kabuli, desi and pea shaped) with substantial admixture in the cultivated material, while two populations were observed among the wild species using DArT markers. Analysis of molecular variance (AMOVA) was used to partition variance among hierarchical sets of landraces and wild species at either geographical level or species level. 61% of the variation was found between species, and 39% within species. Molecular variance among the wild species was high (39%) as compared to cultivated (10%). We found widespread variation in linkage disequilibrium (LD) across the genome, with variation in patterns between the relatively homogenous domesticated and more diverse wild germplasm. Observed heterozygosity was higher in wild than cultivated for each linkage group. Our results confirm the Fertile Crescent both as the center of domestication and diversification of chickpea. Although the collection used in the present study has limitations for inferences about wild diversity, it still has higher diversity in the Fertile Crescent. Shared alleles between different gene pools suggest the possibility of gene flow among these species or incomplete lineage sorting and could indicate complicated patterns of divergence and fusion of wild chickpea taxa during the Pleistocene. Abstract Diversity analysis in chickpea germplasm using SNP and DArT markers Diverse Chickpea collection  96 chickpea accessions representing 10 Cicer species  68 cultivated chickpea and 28 wild chickpea accessions  28 wild accession covered 9 different wild species ranging from primary, secondary, tertiary gene pools (GP) and one accession was perennial  Based on the distribution, the germplasm was divided in three different clusters namely Geographical clusters 1International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; 2Florida International University, Florida, USA; 3Fairchild Tropical Botanic Garden, Florida, USA; 4University of California-Davis, Davis, CA, USA; 5CGIAR Generation Challenge Programme, c/o CIMMYT, Mexico DF, Mexico; *Address for correspondence: r.k.varshney@cgiar.org Collection sites of diversity panel KabuliDesi Pea Ter Sec Pri Perennial Wild Cultivated STRUCTURE analysis of cultivated chickpea STRUCTURE analysis of chickpea germplasm Among Pops 61% Within Pops 39% Molecular variance among cultivated and wild Among Pops 3% Within Pops 97% Among Pops 31% Within Pops 69% Molecular variance among cultivated in seed type Molecular variance among wilds in gene pools Secondary GPPrimary GP Tertiary GP 0 200 400 600 800 1000 No.ofDArT PIC value range Polymorhic DArT markers 0 40 80 120 160 200 No.ofSNP PIC value range Polymorphic SNP markers Polymorphism status of SNP & DArT markers  651 SNPs were used for KASPar genotyping, of which 624 were mapped LG (Hiremath et al. 2012 Plant Biotechnol J 10:716-732)  611 SNPs were polymorphic across the diverse collection  2763 were chosen for analysis our of total 5257 polymorphic DArT markers based on the presence of allele in tertiary gene pool  Both markers were highly polymorphich across the germplasm with the mean PIC value of 0.2313 (SNP) and 0.2214 (DArT) Coord.2 Coord. 1 Principal Coordinates Wild Cultivated Two major groups were identified by using Neighbor-joining tree and PCA among Cicer accessions Wild from primary gene pool were mixed with cultivated chickpea Only perennial accession was embedded among the wild from tertiary gene pool Financial support provided by CGIAR Generation Challenge Programme (GCP).Acknowledgements Genetic diversification analysis CaLG01 CaLG02 CaLG03 CaLG04 CaLG05 CaLG06 CaLG07 CaLG08 Whole genome SNP gene diversity in wild and cultivated Summary  Present study suggest the possibility of gene flow among these species or incomplete lineage sorting  Variation in linkage disequilibrium (LD) across the genome was observed showing different patterns between domesticated and wild germplasm  Higher heterozygosity was observed in wild than cultivated for each linkage group
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