Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Bančič, J and Odeny, D A and Ojulong, H F and Josiah, S M and Buntjer, J and Gaynor, R C and Hoad, S P and Gorjanc, G (2023) Genomic and phenotypic characterization of finger millet indicates a complex diversification history. The Plant Genome (TSI). pp. 1-17. ISSN 1940-3372

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Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.

Item Type: Article
Divisions: Research Program : East & Southern Africa
Uncontrolled Keywords: phenotypic characterization, Genetics, finger millet
Subjects: Mandate crops > Millets > Finger Millet
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 29 Feb 2024 09:41
Last Modified: 29 Feb 2024 09:42
Official URL:
Acknowledgement: The authors are thankful for helpful comments from Rajiv Sharma and our much-valued late colleague Ian Mackay, and technical assistance from Ann Murithi and Erick Owuor Mikwa. We also thank Peter Bradbury for adding a bespoke filtering option in TASSEL for removing SNPs with a heterozygosity level greater than 2pq x (1 - F). Jon Bančič was funded by Scotland's Rural College through a PhD studentship Research Excellence Grant.
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