Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)

Article


Fayaz, Humara, Tyagi, Sandhya, Wani, Aijaz A., Pandey, Renu, Akhtar, Sabina, Bhat, Mohd Ashraf, Chitikineni, Annapurna, Varshney, Rajeev Kumar, Thudi, Mahendar, Kumar, Upendra and Mir, Reyazul Rouf. 2022. "Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-14487-1
Article Title

Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.)

ERA Journal ID201487
Article CategoryArticle
AuthorsFayaz, Humara, Tyagi, Sandhya, Wani, Aijaz A., Pandey, Renu, Akhtar, Sabina, Bhat, Mohd Ashraf, Chitikineni, Annapurna, Varshney, Rajeev Kumar, Thudi, Mahendar, Kumar, Upendra and Mir, Reyazul Rouf
Journal TitleScientific Reports
Journal Citation12 (1)
Article Number11357
Number of Pages14
Year2022
PublisherNature Publishing Group
ISSN2045-2322
Digital Object Identifier (DOI)https://doi.org/10.1038/s41598-022-14487-1
Web Address (URL)https://www.nature.com/articles/s41598-022-14487-1
Abstract

Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.

Keywordschickpea; seed nutrient density; genotypes
Byline AffiliationsSher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), India
University of Kashmir, India
Indian Agricultural Research Institute, India
American University in the Emirates, UAE
International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India
Murdoch University
Dr. Rajendra Prasad Central Agricultural University, India
University of Southern Queensland
Chaudhary Charan Singh Haryana Agricultural University, India
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