Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers

M. Roorkiwal; E.J. von Wettberg; H.D. Upadhyaya; E. Warschefsky; A. Rathore; R.K. Varshney

doi:10.1371/journal.pone.0102016

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Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers

Journal article

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Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers

M. Roorkiwal, E.J. von Wettberg, H.D. Upadhyaya, E. Warschefsky, A. Rathore and R.K. Varshney

PLoS ONE, Vol.9(7), Art. e102016

2014

DOI: https://doi.org/10.1371/journal.pone.0102016

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Abstract

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.

Details

Title: Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DArT markers
Authors/Creators: M. Roorkiwal (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
E.J. von Wettberg (Author/Creator) - Fairchild Tropical Botanic Garden
H.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
E. Warschefsky (Author/Creator) - Fairchild Tropical Botanic Garden
A. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: PLoS ONE, Vol.9(7), Art. e102016
Publisher: Public Library of Science
Identifiers: 991005542907207891
Copyright: © 2021 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Plant Sciences
ESI research areas: Plant & Animal Science