Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)
Syed Sab, R. Lokesha, D. M. Mannur, Somasekhar, Kisan Jadhav, Bingi Pujari Mallikarjuna, C. Laxuman, Sharanbasappa Yeri, Vinod Kumar Valluri, Prasad Bajaj, Annapurna Chitikineni, Anilkumar Vemula, Abhishek Rathore, Rajeev K. Varshney, I. Shankergoud, Mahendar Thudi
Abstract
Biofortification through plant breeding is athe cost effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening of cultivars for micronutrient content and , identification of QTLs/genes and markers help in the development of biofortified varieties in chickpea (Cicer arietinum L.). With thean aim of identifying the genomic regions controlling the seed-Fe and Zn concentrations, the F2:3 population derived from athe cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for seed-Fe and Zn concentration. An intra-specific genetic linkage map comprising 839 SNPs spanning a total map distance of 1088.04 cM with an average marker density of 1.30 cM, was constructed. By integrating the linkage map data with the phenotypic data of the F2:3 population, a total of 11 QTLs were detected for seed -Fe concentration on CaLG03, CaLG04 and CaLG05, with phenotypic variation explained ranginged from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed -Zn concentration, 8 QTLs were identified on CaLG04, CaLG05 and CaLG08. The QTLs individually explained phenotypic variations ranginged between 5.7% (CaqZn8.1) and 13.7% (CaqZn4.1). Three QTLs for seed -Fe and Zn concentrations (CaqFe4.4,CaqFe4.5 and CaqZn4.1) were co-located in the “QTL-hotspot” region, on CaLG04, that harbours several drought tolerance- related QTLs. We identified genes in the QTL regions that encode iron-sulphur metabolism and zinc dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, zinc- induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers associated can be used infor marker-assisted selection tofor increaseing seed-Fe and Zn concentrations in agronomically superior chickpea varieties.