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Uncovering the genomic regions underlying grain iron and zinc content using genome-wide association mapping in finger millet

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Abstract

Finger millet, being rich source of essential minerals like iron and zinc, is an ideal model to identify candidate genes contributing to high grain iron content (GIC) and zinc content (GZC) in plants. Hence, finger millet diversity panel comprised of 202 genotypes was evaluated in two geographical locations and found to have a wide variation for GIC and GZC. A genome-wide association study using 2977 single nucleotide polymorphism (SNP) markers identified reliable marker–trait associations (MTAs). The use of general linear model (GLM) and mixed linear model (MLM) approaches revealed 5 and 8 common MTAs linked to GIC and GZC, respectively, for both Almora and Pantnagar locations, with a high level of significance (P < 0.01). However, 12 significant MTAs were found to be linked with GIC for Pantnagar location alone. The MTAs were associated with specific genes that produce ferritin (Fer1), iron-regulated transporter-like protein (IRT2), and yellow stripe-like 2 proteins (YSL2). These genes are likely linked to GIC variation in finger millet. Additionally, the variation in GZC in finger millet was connected to genes that encode zinc transporters, namely ZIP1 protein (ZIP1) and ZTP29-like protein (ZTP29). Compared to low GIC and GZC genotypes, high GIC and GZC genotypes exhibited greater relative expression of these genes.

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Acknowledgements

The authors acknowledge G.B. Pant University of Agriculture and Technology, Pantnagar, and ICAR-VPKAS, Almora, for providing all the necessary facilities.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

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Author notes

  1. Ajay Kumar Chandra and Dinesh Chandra Joshi contributed equally.

Authors and Affiliations

  1. Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, 263145, India

    Ajay Kumar Chandra, Dinesh Pandey, Apoorv Tiwari, Divya Sharma, Kavita Gururani & Anil Kumar

  2. Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India

    Ajay Kumar Chandra

  3. Crop Improvement Division, Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India

    Salej Sood

  4. ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, 263601, India

    Dinesh Chandra Joshi

  5. Department of Computer Science and Information Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, 211007, India

    Apoorv Tiwari

  6. Department of Botany, Delhi University, North Campus, Delhi, 110007, India

    Divya Sharma

  7. Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, 284003, India

    Anil Kumar

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  1. Ajay Kumar Chandra
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Contributions

DP, AK, and SS conceptualized the research work. AKC, DS and KG performed lab experiments, analysed results and wrote the first draft of manuscript. SS, DCJ and DS did field experiments. AT, SS and AKC have statistically analysed the data. AKC, DP, SS and DCJ contributed to critical revision of the draft and finalization of the manuscript for publication.

Corresponding authors

Correspondence to Dinesh Pandey, Salej Sood or Anil Kumar.

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Chandra, A.K., Pandey, D., Sood, S. et al. Uncovering the genomic regions underlying grain iron and zinc content using genome-wide association mapping in finger millet. 3 Biotech 14, 47 (2024). https://doi.org/10.1007/s13205-023-03889-1

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