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

Fayaz, H and Tyagi, S and Wani, A A and Pandey, R and Akhtar, S and Bhat, M A and Chitikineni, A and Varshney, R K and Thudi, M and Kumar, U and Mir, R R (2022) Genome‑wide association analysis to delineate high‑quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.). Scientific Reports, 12. 01-14. ISSN 2045-2322

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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.

Item Type:	Article
Divisions:	Others
CRP:	UNSPECIFIED
Uncontrolled Keywords:	Chickpea, seed micronutrient density, high‑quality SNPs
Subjects:	Mandate crops > Chickpea Others > Genetics and Genomics
Depositing User:	Mr Nagaraju T
Date Deposited:	08 Jun 2023 03:37
Last Modified:	08 Jun 2023 03:37
URI:	http://oar.icrisat.org/id/eprint/12105
Official URL:	https://www.nature.com/articles/s41598-022-14487-1
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	The authors are thankful to ICRISAT, Hyderabad, IIPR, Kanpur, NBPGR, and New Delhi for providing the germplasm for the present study. The authors are also thankful to the head Division of Genetics and Plant Breeding SKAUT-K for providing the necessary facilities during the course of the study. RRM is also thankful to various funding agencies, including the Science and Engineering Research Board (SERB), Department of Science and Technology (DST) and Department of Biotechnology (DBT), Government of India, for financial support. MT grateful to the SERB Government of India for financial support.
Links:	Google Scholar

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