Genome-wide association mapping of nutritional traits for designing superior chickpea varieties

Roorkiwal, M and Bhandari, A and Barmukh, R and Bajaj, P and Valluri, V K and Chitikineni, A and Pandey, S and Chellapilla, B and Siddique, K H M and Varshney, R K (2022) Genome-wide association mapping of nutritional traits for designing superior chickpea varieties. Frontiers in Plant Science (TSI), 13. 01-17. ISSN 1664-462X

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Micronutrient malnutrition is a serious concern in many parts of the world; therefore, enhancing crop nutrient content is an important challenge. Chickpea (Cicer arietinum L.), a major food legume crop worldwide, is a vital source of protein and minerals in the vegetarian diet. This study evaluated a diverse set of 258 chickpea germplasm accessions for 12 key nutritional traits. A significant variation was observed for several nutritional traits, including crude protein (16.56–24.64/100 g), β-Carotene (0.003–0.104 mg/100 g), calcium (60.69–176.55 mg/100 g), and folate (0.413–6.537 mg/kg). These data, combined with the available whole-genome sequencing data for 318,644 SNPs, were used in genome-wide association studies comprising single-locus and multi-locus models. We also explored the effect of varying the minor allele frequency (MAF) levels and heterozygosity. We identified 62 significant marker-trait associations (MTAs) explaining up to 28.63% of the phenotypic variance (PV), of which nine were localized within genes regulating G protein-coupled receptor signaling pathway, proteasome assembly, intracellular signal transduction, and oxidation–reduction process, among others. The significant effect MTAs were located primarily on Ca1, Ca3, Ca4, and Ca6. Importantly, varying the level of heterozygosity was found to significantly affect the detection of associations contributing to traits of interest. We further identified seven promising accessions (ICC10399, ICC1392, ICC1710, ICC2263, ICC1431, ICC4182, and ICC16915) with superior agronomic performance and high nutritional content as potential donors for developing nutrient-rich, high-yielding chickpea varieties. Validation of the significant MTAs with higher PV could identify factors controlling the nutrient acquisition and facilitate the design of biofortified chickpeas for the future.

Item Type: Article
Divisions: Center of Excellence in Genomics and Systems Biology
Uncontrolled Keywords: biofortification, micronutrient, malnutrition, trait-mapping, genomics, GWAS
Subjects: Others > Biofortification
Mandate crops > Chickpea
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 16 Nov 2023 04:22
Last Modified: 16 Nov 2023 04:31
Official URL:
Acknowledgement: RKV is grateful to Bill & Melinda Gates Foundation, United States (Grant No OPP1114827), and Department of Biotechnology, Ministry of Science & Technology, Government of India for supporting this research in parts. The authors thank due to the Science & Engineering Research Board (SERB) of Department of Science & Technology (DST), Government of India for providing the J C Bose National Fellowship (SB/S9/Z-13/2019) to RKV, MR, and SP, and the Department of Science and Technology, Government of India for providing funding support through the INSPIRE Faculty Scheme, Early Career Research Award—SERB and SERB-NPDF (PDF/2016/003379), respectively.
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