Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm

Srungarapu, R and Mahendrakar, M D and Mohammad, L A and Chand, U and Jagarlamudi, V R and Kondamudi, K P and Kudapa, H and Samineni, S (2022) Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells (TSI), 11(15) (2457). pp. 1-21. ISSN 2073-4409

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Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.

Item Type: Article
Divisions: Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: chickpea reference set, grain Fe, Zn, protein, linkage disequilibrium, population structure, GWAS, FarmCPU and BLINK
Subjects: Mandate crops > Chickpea
Others > Germplasm
Depositing User: Mr Ramesh MNR
Date Deposited: 09 Aug 2022 08:15
Last Modified: 09 Aug 2022 08:15
Official URL:
Funders: The research is financially supported by the DBT, Government of India; ICAR, India; OIIPCRA, Government of Odisha, India.
Acknowledgement: Authors are thankful to all the team members involved in the entire field opera-tions, ICRISAT, Patancheru, India. We also would like to acknowledge Charles Renard Analytical Laboratory, ICRISAT for analyzing grain iron and zinc contents and RK labs Junagadh, Gujarat, India for grain protein content. Thanks to Acharya N.G. Ranga Agricultural University, Guntur, Andhra Pradesh, India for providing the fellowship during the research.
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