Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers

Roorkiwal, M and von Wettberg, E J and Upadhyaya, H D and Warschefsky, E and Rathore, A and Varshney, R K (2014) Exploring Germplasm Diversity to Understand the Domestication Process in Cicer spp. Using SNP and DArT Markers. PLoS ONE, 9 (7). pp. 1-10. ISSN 1932-6203

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To estimate genetic diversity within and between 10 interfertile Cicer species (94 genotypes) from the primary, secondary and tertiary gene pool, we analysed 5,257 DArT markers and 651 KASPar SNP markers. Based on successful allele calling in the tertiary gene pool, 2,763 DArT and 624 SNP markers that are polymorphic between genotypes from the gene pools were analyzed further. STRUCTURE analyses were consistent with 3 cultivated populations, representing kabuli, desi and pea-shaped seed types, with substantial admixture among these groups, while two wild populations were observed using DArT markers. AMOVA was used to partition variance among hierarchical sets of landraces and wild species at both the geographical and species level, with 61% of the variation found between species, and 39% within species. Molecular variance among the wild species was high (39%) compared to the variation present in cultivated material (10%). Observed heterozygosity was higher in wild species than the cultivated species for each linkage group. Our results support the Fertile Crescent both as the center of domestication and diversification of chickpea. The collection used in the present study covers all the three regions of historical chickpea cultivation, with the highest diversity in the Fertile Crescent region. 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 in the past.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 15 Jul 2014 03:51
Last Modified: 15 Jul 2014 03:53
URI: http://oar.icrisat.org/id/eprint/8206
Official URL: http://dx.doi.org/10.1371/journal.pone.0102016
Funders: Australian Indo Strategic Research Fund (AISRF) of Ministry of Science & Technology, CGIAR Generation Challenge Programme (GCP), Mexico
Acknowledgement: The authors confirm that all data underlying the findings are fully available without restriction. Relevant data are included within the paper and Supporting Information files. Genotyping data (DArT and SNP) used for the analysis are available on the CEG website at: http://www.icrisat.org/CEG/PublicDomain1​.html.
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