Gebreyohannes, A and Shimelis, H and Gimode, D M and Gandham, P and Valluri, V K and Nida, H and Moenga, S M and Ojiewo, C O and Kilian, B and Odeny, D A (2025) Genetic structure of Ethiopian finger millet landraces and genome-wide association mapping for agronomic and nutritional traits. Theoretical and Applied Genetics (TSI), 138. pp. 1-25. ISSN 0040-5752
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Abstract
Finger millet (Eleusine coracana subsp. coracana) (2n = 4x = 36) remains one of the most important millets in East Africa (EA), where it was most likely domesticated along the highlands of Ethiopia and Uganda. The goal of the current study was to understand the population structure of the Ethiopian finger millet landraces and identify quantitative trait nucleotides (QTNs) and haplotypes associated with agronomic and nutritional traits. In a field evaluation across three environments, 448 genotypes were assessed for days to flowering (DTF), days to maturity (DTM), thousand seed weight (TSW), grain yield (GY), stay-green score (STG), and drought score (DrtSc). The harvested grain was analyzed for Fe and Zn contents. A subset of 391 genotypes was skim-sequenced, generating 24,112 high-quality SNPs that were employed for population structure, association mapping, and haplotype analysis. Seventy marker-trait associations were detected including 15 major QTNs with more than 30% phenotypic variance explained (PVE) for all traits except STG and GY. Pleiotropic major QTNs were identified for DTM/DTF and Fe/Zn on chromosomes 9B and 2B, respectively. Haplotype analysis of major QTNs identified 54 significant haplotype blocks and 2 additional haplotypes for a multidrug ABC transporter gene family like protein on chromosome 4A that was associated with PTH. Favorable haplotypes from pleiotropic DTM/DTF and Fe/Zn QTNs were present in 13 and 12 genotypes respectively, majority from Tigray region. Two genotypes from Tigray and one from Amhara harbored favorable haplotypes for DTM/DTF and Fe/Zn. These findings provide invaluable insights for targeted breeding to enhance finger millet resilience, nutritional profile, and yield.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : East & Southern Africa |
| CRP: | UNSPECIFIED |
| Uncontrolled Keywords: | finger millet, genome-wide association mapping, agronomy, nutritional traits |
| Subjects: | Mandate crops > Millets > Finger Millet Others > Genetics and Genomics |
| Depositing User: | Mr Nagaraju T |
| Date Deposited: | 05 Jun 2025 08:39 |
| Last Modified: | 05 Jun 2025 08:39 |
| URI: | http://oar.icrisat.org/id/eprint/13128 |
| Official URL: | https://link.springer.com/article/10.1007/s00122-0... |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | This research was financially supported by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) through the ‘Harnessing Opportunities for Productivity Enhancement (HOPE II) for Sorghum and Millets in Sub-Saharan Africa’ project (grant number OPP1198373) and CIMMYT Dryland Crops' AVISA projects (OPP1198373), both funded by the Bill and Melinda Gates Foundation (BMGF). Additionally, ICRISAT provided support for the genotyping research work through the project “Safeguarding crop diversity for food security: Pre-breeding complemented with Innovative Finance” (TWCF0400), funded by the Templeton World Charity Foundation, Inc. (TWCF) and managed by the Global Crop Diversity Trust. The authors gratefully acknowledge the Ethiopian Institute of Agricultural Research, Melkassa Agricultural Research Center (Ethiopia) and the University of KwaZulu-Natal for their in-kind support and for facilitating the first author’s research and study leave |
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