Genomic and phenotypic characterization of finger millet indicates a complex diversification history
Abstract 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...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2024-03-01
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| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20392 |
| _version_ | 1797253800409432064 |
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| author | Jon Bančič Damaris A. Odeny Henry F. Ojulong Samuel M. Josiah Jaap Buntjer R. Chris Gaynor Stephen P. Hoad Gregor Gorjanc Ian K. Dawson |
| author_facet | Jon Bančič Damaris A. Odeny Henry F. Ojulong Samuel M. Josiah Jaap Buntjer R. Chris Gaynor Stephen P. Hoad Gregor Gorjanc Ian K. Dawson |
| author_sort | Jon Bančič |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-04-24T21:39:49Z |
| format | Article |
| id | doaj.art-ca17d067eabe4f1d84da08c14a9d7fb0 |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-04-24T21:39:49Z |
| publishDate | 2024-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-ca17d067eabe4f1d84da08c14a9d7fb02024-03-21T11:34:18ZengWileyThe Plant Genome1940-33722024-03-01171n/an/a10.1002/tpg2.20392Genomic and phenotypic characterization of finger millet indicates a complex diversification historyJon Bančič0Damaris A. Odeny1Henry F. Ojulong2Samuel M. Josiah3Jaap Buntjer4R. Chris Gaynor5Stephen P. Hoad6Gregor Gorjanc7Ian K. Dawson8The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Research Centre Midlothian UKInternational Crops Research Institute for the Semi‐Arid Tropics ICRAF House Gigiri Nairobi KenyaInternational Crops Research Institute for the Semi‐Arid Tropics ICRAF House Gigiri Nairobi KenyaDepartment of Horticulture University of Georgia Athens Georgia USAThe Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Research Centre Midlothian UKThe Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Research Centre Midlothian UKScotland's Rural College (SRUC) Kings Buildings Edinburgh UKThe Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh, Easter Bush Research Centre Midlothian UKScotland's Rural College (SRUC) Kings Buildings Edinburgh UKAbstract 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.https://doi.org/10.1002/tpg2.20392 |
| spellingShingle | Jon Bančič Damaris A. Odeny Henry F. Ojulong Samuel M. Josiah Jaap Buntjer R. Chris Gaynor Stephen P. Hoad Gregor Gorjanc Ian K. Dawson Genomic and phenotypic characterization of finger millet indicates a complex diversification history The Plant Genome |
| title | Genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| title_full | Genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| title_fullStr | Genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| title_full_unstemmed | Genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| title_short | Genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| title_sort | genomic and phenotypic characterization of finger millet indicates a complex diversification history |
| url | https://doi.org/10.1002/tpg2.20392 |
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