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

Thudi, M and Upadhyaya, H D and Rathore, A and Gaur, P M and Krishnamurthy, L and Roorkiwal, M and Nayak, S N and Chaturvedi, S K and Basu, P S and Ganga Rao, N V P R and Fikre, A and Kimurto, P and Sharma, P C and Sheshashayee, M S and Tobita, S and Kashiwagi, J and Ito, O and Killian, A and Varshney, R K (2014) Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches. PLoS ONE, 9 (5). e96758. ISSN 1932-6203

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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.

Item Type: Article
Divisions: RP-Grain Legumes
CRP: CGIAR Research Program on Grain Legumes
Uncontrolled Keywords: Drought, Heat Tolerance, abiotic stress, biotic stress, Mapping, Chickpea
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Siva Shankar
Date Deposited: 14 May 2014 06:17
Last Modified: 15 May 2014 03:03
URI: http://oar.icrisat.org/id/eprint/7995
Official URL: http://dx.doi.org/10.1371/journal.pone.0096758
Projects: Tropical Legumes I (TLI- Objective 4: Chickpea)
Funders: Bill & Melinda Gates Foundation (BMGF)
Acknowledgement: UNSPECIFIED
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