Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.)

    Vetriventhan, M and Upadhyaya, H D and Deshpande, S P and Johnson, M S and Wallace, J G and Victor, A and Naresh, D and Rayaprolu, L and Singh, K and Mayes, S (2024) Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.). Scientific Reports (TSI), 14. pp. 1-17. ISSN 2045-2322

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    Abstract

    Proso millet is an important but under-researched and underutilized crop with the potential to become a future smart crop because of its climate-resilient features and high nutrient content. Assessing diversity and marker-trait associations are essential to support the genomics-assisted improvement of proso millet. This study aimed to assess the population structure and diversity of a proso millet diversity panel and identify marker-trait associations for agronomic and grain nutrient traits. In this study, genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping raw genotyping-by-sequencing (GBS) data onto the proso millet genome, resulting in 5621 quality-filtered SNPs in 160 diverse accessions. The modified Roger's Distance assessment indicated an average distance of 0.268 among accessions, with the race miliaceum exhibiting the highest diversity and ovatum the lowest. Proso millet germplasm diversity was structured according to geographic centers of origin and domestication. Genome-wide association mapping identified 40 marker-trait associations (MTAs), including 34 MTAs for agronomic traits and 6 for grain nutrients; 20 of these MTAs were located within genes. Favourable alleles and phenotypic values were estimated for all MTAs. This study provides valuable insights into the population structure and diversity of proso millet, identified marker-trait associations, and reported favourable alleles and their phenotypic values for supporting genomics-assisted improvement efforts in proso millet.

    Item Type: Article
    Divisions: Genebank
    Global Research Program - Accelerated Crop Improvement
    CRP: UNSPECIFIED
    Uncontrolled Keywords: Proso millet, Genome-wide association mapping, Agronomic traits, Grain nutrients, Marker-traits associations, Diversity, Population structure
    Subjects: Mandate crops > Millets
    Others > Genetics and Genomics
    Depositing User: Mr Nagaraju T
    Date Deposited: 23 Sep 2024 06:25
    Last Modified: 23 Sep 2024 06:25
    URI: http://oar.icrisat.org/id/eprint/12821
    Official URL: https://www.nature.com/articles/s41598-024-72319-w
    Projects: UNSPECIFIED
    Funders: UNSPECIFIED
    Acknowledgement: This work was supported by NSF grants DBI-0820619 and IOS-1238014, ICRISAT, and the USDA–ARS. This work has been undertaken as part of the Global Research Program—Accelerated Crop Improvement, and CGIAR Genebank Platform.
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