Genetic dissection and identification of candidate genes for salinity tolerance using axiom®cicerSNP array in chickpea

Khela Ram Soren, Praveen Madugula, Neeraj Kumar, Rutwik Barmukh, Menu Singh Sengar, Chellapilla Bharadwaj, Parbodh Chander Sharma, Sarvjeet Singh, Aditi Bhandari, Jogendra Singh, Satish Kumar Sanwal, Madan Pal, P. R. Sneha Priya, Anita Mann, Someswar Rao Sagurthi, P. S. Shanmugavadivel, Kadambot H.M. Siddique, Narendra Pratap Singh, Manish Roorkiwal, Rajeev K. Varshney

Research output: Contribution to journalArticle


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.

Original languageEnglish
Article number5058
Pages (from-to)1-17
Number of pages17
JournalInternational Journal of Molecular Sciences
Issue number14
Publication statusPublished - 2 Jul 2020

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