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Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica)

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Abstract

Key message

A total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker–trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits.

Abstract

Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker–trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.

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Data availability

The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

MP acknowledges the financial support received through the National Bioscience Award (2015) from Department of Biotechnology (DBT), Government of India. VJ [CSIR-IHBT publication number is 5445] and VG acknowledge the DST-INSPIRE Faculty Awards received from Department of Science and Technology, Ministry of Science and Technology, Government of India. VJ also thank the Science and Engineering Research Board (SERB) for the Early Career Research Award. The authors are thankful to DBT-eLibrary Consortium (DeLCON) for providing access to E−resources.

Funding

Department of Science and Technology (DST) for the INSPIRE faculty award (File no. DST/INSPIRE/04/2016/001189).

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Authors and Affiliations

  1. Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India

    Vandana Jaiswal & Vijay Gahlaut

  2. National Institute of Plant Genome Research, New Delhi, India

    Tirthankar Bandyopadhyay, Roshan Kumar Singh & Manoj Prasad

  3. Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, India

    Vijay Gahlaut

  4. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India

    Mehanathan Muthamilarasan & Manoj Prasad

  5. Department of Genetics, University of Delhi South Campus, New Delhi, India

    Manoj Prasad

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  1. Vandana Jaiswal
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  2. Tirthankar Bandyopadhyay
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  3. Roshan Kumar Singh
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  4. Vijay Gahlaut
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  5. Mehanathan Muthamilarasan
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  6. Manoj Prasad
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Contributions

MP and VJ conceived and designed the experiments. VJ, TB, RKS, and VG performed the experiments. VJ and VG analysed the results. VJ and MM wrote the manuscript. MP approved the final version of the manuscript.

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Correspondence to Vandana Jaiswal or Manoj Prasad.

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Communicated by Om Parkash Parkash Dhankher.

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Jaiswal, V., Bandyopadhyay, T., Singh, R.K. et al. Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica). Plant Cell Rep 43, 6 (2024). https://doi.org/10.1007/s00299-023-03127-1

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