Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.)
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...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/173018 |
| _version_ | 1855517864044265472 |
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| author | Vetriventhan, Mani Upadhyaya, Hari D. Deshpande, Santosh Johnson, Matthew S. Wallace, Jason G. Victor, Allan Naresh, D. Rayaprolu, Laavanya Singh, Kuldeep Mayes, Sean |
| author_browse | Deshpande, Santosh Johnson, Matthew S. Mayes, Sean Naresh, D. Rayaprolu, Laavanya Singh, Kuldeep Upadhyaya, Hari D. Vetriventhan, Mani Victor, Allan Wallace, Jason G. |
| author_facet | Vetriventhan, Mani Upadhyaya, Hari D. Deshpande, Santosh Johnson, Matthew S. Wallace, Jason G. Victor, Allan Naresh, D. Rayaprolu, Laavanya Singh, Kuldeep Mayes, Sean |
| author_sort | Vetriventhan, Mani |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. |
| format | Journal Article |
| id | CGSpace173018 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| record_format | dspace |
| spelling | CGSpace1730182025-10-26T12:51:34Z 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 proso millet agronomic characters nutritive value agrobiodiversity nutrition genomes 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. 2024-06-13 2025-02-13T12:55:59Z 2025-02-13T12:55:59Z Journal Article https://hdl.handle.net/10568/173018 en Open Access application/pdf Vetriventhan, Mani; Upadhyaya,Hari D.; Deshpande, Santosh; Johnson, Matthew S.; Wallace, Jason G.; Victor, Allan; Naresh, D.; Rayaprolu, Laavanya; Singh, Kuldeep; Mayes, Sean. 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, no. 1 (2024): 21920. |
| spellingShingle | proso millet agronomic characters nutritive value agrobiodiversity nutrition genomes Vetriventhan, Mani Upadhyaya, Hari D. Deshpande, Santosh Johnson, Matthew S. Wallace, Jason G. Victor, Allan Naresh, D. Rayaprolu, Laavanya Singh, Kuldeep Mayes, Sean Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title | Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title_full | Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title_fullStr | Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title_full_unstemmed | Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title_short | Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.) |
| title_sort | genome wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet panicum miliaceum l |
| topic | proso millet agronomic characters nutritive value agrobiodiversity nutrition genomes |
| url | https://hdl.handle.net/10568/173018 |
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