Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea

Soren, K R and Madugula, P and Kumar, N and Barmukh, R and Sengar, M S and Bharadwaj, C and Sharma, P C and Singh, S and Bhandari, A and Singh, J and Sanwal, S K and Pal, M and Sneha Priya, P R and Mann, A and Sagurthi, S R and Shanmugavadivel, P S and Siddique, K H M and Singh, N P and Roorkiwal, M and Varshney, R K (2020) Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom®CicerSNP Array in Chickpea. International Journal of Molecular Sciences (TSI), 21 (14). pp. 1-17. ISSN 1422-0067

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Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom®CicerSNP array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords: Chickpea, Salinity, Quantitative trait loci, Stress susceptibility index (SSI), Stress tolerance index (STI), Candidate genes
Subjects: Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Arun S
Date Deposited: 05 Sep 2020 09:27
Last Modified: 06 Sep 2020 08:33
Official URL:
Acknowledgement: M.R. and R.K.V. thank the Department of Science and Technology, Government of India for providing funding support through the INSPIRE Faculty Scheme and Early Career Research Award—SERB and the JC Bose Fellowship, respectively. R.B. acknowledges funding support from the Council of Scientific and Industrial Research (CSIR), India for the award of research fellowship. The work reported in this article was undertaken as part of the CGIAR Research Program on Grain Legumes and Dryland Cereals. ICRISAT is a member of the CGIAR Consortium.
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