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

Vetriventhan, Mani; Upadhyaya, Hari D.; Deshpande, Santosh; Johnson, Matthew S.; Wallace, Jason G.; Victor, Allan; Naresh, D.; Rayaprolu, Laavanya; Singh, Kuldeep; Mayes, Sean

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.

Citation

Vetriventhan, M., Upadhyaya, H. D., Deshpande, S., Johnson, M. S., Wallace, J. G., Victor, A., Naresh, D., Rayaprolu, L., Singh, K., & 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, 14(1), Article 21920. https://doi.org/10.1038/s41598-024-72319-w

• Journal Article Type: Article
• Acceptance Date: Sep 5, 2024
• Online Publication Date: Sep 19, 2024
• Publication Date: Sep 19, 2024
• Deposit Date: Oct 1, 2024
• Publicly Available Date: Oct 2, 2024
• Journal: Scientific Reports
• Electronic ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 14
• Issue: 1
• Article Number: 21920
• DOI: https://doi.org/10.1038/s41598-024-72319-w
• Keywords: Proso millet; Genome-wide association mapping; Agronomic traits; Grain nutrients; Marker-traits associations; Diversity; Population structure
• Public URL: https://nottingham-repository.worktribe.com/output/40002553
• Publisher URL: https://www.nature.com/articles/s41598-024-72319-w
• Additional Information: Received: 13 July 2024; Accepted: 5 September 2024; First Online: 19 September 2024; : The authors declare no competing interests.