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Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea ( Cicer arietinum L.)

  • Sab, Syed1, 2
  • Lokesha, Ramappa1
  • Mannur, D. M.1
  • Somasekhar,1
  • Jadhav, Kisan1
  • Mallikarjuna, Bingi Pujari2
  • C, Laxuman3
  • Yeri, Sharanbasappa3
  • Valluri, Vinod2
  • Bajaj, Prasad2
  • Chitikineni, Annapurna2
  • Vemula, AnilKumar2
  • Rathore, Abhishek2
  • Varshney, Rajeev Kumar2
  • Shankergoud, I.1
  • Thudi, Mahendar2
  • 1 Department of Genetics and Plant Breeding, University of Agricultural Sciences - Raichur (UAS-R), Raichur , (India)
  • 2 Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad , (India)
  • 3 Zonal Agricultural Research Station, University of Agricultural Sciences - Raichur, Kalaburagi , (India)
Published Article
Frontiers in Nutrition
Frontiers Media SA
Publication Date
Oct 15, 2020
DOI: 10.3389/fnut.2020.559120
PMCID: PMC7588353
PubMed Central


Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea ( Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 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 ranging from 7.2% ( CaqFe3.4 ) to 13.4% ( CaqFe4.2 ). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% ( CaqZn8.1 ) and 13.7% ( CaqZn4.3 ). Three QTLs for seed Fe and Zn concentrations ( CaqFe4.4, CaqFe4.5 , and CaqZn4.1 ) were colocated in the “ QTL-hotspot ” region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties.

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