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Higgins, Janet, Santos, Bruno, Khanh, Tran Dang, Trung, Khuat Huu, Duong, Tran Duy, Doai, Nguyen Thi Phuong, Hall, Anthony 
ORCID: https://orcid.org/0000-0002-1806-020X, Dyer, Sarah, Ham, Le Huy, Caccamo, Mario and De Vega, Jose
(2022)
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.
Evolutionary Applications, 15 (7).
pp. 1141-1161.
ISSN 1752-4563
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Abstract
Vietnam harnesses a rich diversity of rice landraces adapted to a range of conditions, which constitute a largely untapped source of diversity for the continuous improvement of cultivars. We previously identified a strong population structure in Vietnamese rice, which is captured in five Indica and four Japonica subpopulations, including an outlying Indica-5 group. Here, we leveraged that strong differentiation and 672 native rice genomes to identify genomic regions and genes putatively selected during the breeding of rice in Vietnam. We identified significant distorted patterns in allele frequency (XP-CLR) and population differentiation scores (FST) resulting from differential selective pressures between native subpopulations, and later annotated them with QTLs previously identified by GWAS in the same panel. We particularly focussed on the outlying Indica-5 subpopulation because of its likely novelty and differential evolution, where we annotated 52 selected regions, which represented 8.1% of the rice genome. We annotated the 4576 genes in these regions and selected 65 candidate genes as promising breeding targets, several of which harboured alleles with nonsynonymous substitutions. Our results highlight genomic differences between traditional Vietnamese landraces, which are likely the product of adaption to multiple environmental conditions and regional culinary preferences in a very diverse country. We also verified the applicability of this genome scanning approach to identify potential regions harbouring novel loci and alleles to breed a new generation of sustainable and resilient rice.
| Item Type: | Article |
|---|---|
| Additional Information: | Data Availability Statement: All sequence data used in this manuscript have been deposited as study PRJEB36631 in the European Nucleotide Archive. Plant accessions were obtained from the Vietnamese National Genebank in compliance with the national laws and international treaties. A research collaboration was developed with scientists from the countries providing genetic samples, all collaborators are included as co-authors, the results of the research have been shared with the provider stakeholders and the broader national and international scientific community. Funding Information: The author(s) acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation; this research was funded by the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work package BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation); and BBSRC’s grants BB/N013735/1 (Newton Fund), and the Newton Fund Institutional Links (Project 172732508), which is managed by the British Council. All sequence data used in this manuscript have been deposited as study PRJEB36631 in the European Nucleotide Archive. Biological materials are available from the Vietnamese National Genebank. |
| Uncontrolled Keywords: | allele mining,genome scan,landraces,rice,selection,ecology, evolution, behavior and systematics,genetics,agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/1100/1105 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 22 Oct 2024 13:30 |
| Last Modified: | 12 Nov 2024 14:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97109 |
| DOI: | 10.1111/eva.13433 |
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