Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

M. Thudi; H.D. Upadhyaya; A. Rathore; P.M. Gaur; L. Krishnamurthy; M. Roorkiwal; S.N. Nayak; S.K. Chaturvedi; P.S. Basu; N.V.P.R. Gangarao; A. Fikre; P. Kimurto; P.C. Sharma; M.S. Sheshashayee; S. Tobita; J. Kashiwagi; O. Ito; A. Killian; R.K. Varshney

doi:10.1371/journal.pone.0096758

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Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

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Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

M. Thudi, H.D. Upadhyaya, A. Rathore, P.M. Gaur, L. Krishnamurthy, M. Roorkiwal, S.N. Nayak, S.K. Chaturvedi, P.S. Basu, N.V.P.R. Gangarao, …

PLoS ONE, Vol.9(5), Art. e96758

2014

DOI: https://doi.org/10.1371/journal.pone.0096758

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Abstract

To understand the genetic basis of tolerance to drought and heat stresses in chickpea, a comprehensive association mapping approach has been undertaken. Phenotypic data were generated on the reference set (300 accessions, including 211 mini-core collection accessions) for drought tolerance related root traits, heat tolerance, yield and yield component traits from 1–7 seasons and 1–3 locations in India (Patancheru, Kanpur, Bangalore) and three locations in Africa (Nairobi, Egerton in Kenya and Debre Zeit in Ethiopia). Diversity Array Technology (DArT) markers equally distributed across chickpea genome were used to determine population structure and three sub-populations were identified using admixture model in STRUCTURE. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations (r2; when r2<0.20) was found to decay rapidly with the genetic distance of 5 cM. For establishing marker-trait associations (MTAs), both genome-wide and candidate gene-sequencing based association mapping approaches were conducted using 1,872 markers (1,072 DArTs, 651 single nucleotide polymorphisms [SNPs], 113 gene-based SNPs and 36 simple sequence repeats [SSRs]) and phenotyping data mentioned above employing mixed linear model (MLM) analysis with optimum compression with P3D method and kinship matrix. As a result, 312 significant MTAs were identified and a maximum number of MTAs (70) was identified for 100-seed weight. A total of 18 SNPs from 5 genes (ERECTA, 11 SNPs; ASR, 4 SNPs; DREB, 1 SNP; CAP2 promoter, 1 SNP and AMDH, 1SNP) were significantly associated with different traits. This study provides significant MTAs for drought and heat tolerance in chickpea that can be used, after validation, in molecular breeding for developing superior varieties with enhanced drought and heat tolerance.

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Title: Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches
Authors/Creators: M. Thudi (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
H.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Rathore (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
P.M. Gaur (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
L. Krishnamurthy (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
M. Roorkiwal (Author/Creator) - Guru Gobind Singh Indraprastha University
S.N. Nayak (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
S.K. Chaturvedi (Author/Creator) - Indian Institute of Pulses Research
P.S. Basu (Author/Creator) - Indian Institute of Pulses Research
N.V.P.R. Gangarao (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
A. Fikre (Author/Creator) - Ethiopian Institute of Agricultural Research
P. Kimurto (Author/Creator) - Egerton University
P.C. Sharma (Author/Creator) - Guru Gobind Singh Indraprastha University
M.S. Sheshashayee (Author/Creator) - University of Agricultural Sciences, Bangalore
S. Tobita (Author/Creator) - Japan International Research Center for Agricultural Sciences
J. Kashiwagi (Author/Creator) - Hokkaido University
O. Ito (Author/Creator) - United Nations University
A. Killian (Author/Creator) - Dart NeuroScience (United States)
R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
Publication Details: PLoS ONE, Vol.9(5), Art. e96758
Publisher: Public Library of Science
Identifiers: 991005542616307891
Copyright: © 2014 Thudi et al.
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