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ToolsHiggins, Janet, Santos, Bruno, Khanh, Tran Dang, Trung, Khuat Huu, Duong, Tran Duy, Doai, Nguyen Thi Phuong, Khoa, Nguyen Truong, Ha, Dang Thi Thanh, Diep, Nguyen Thuy, Dung, Kieu Thi, Phi, Cong Nguyen, Thuy, Tran Thi, Tuan, Nguyen Thanh, Tran, Hoang Dung, Trung, Nguyen Thanh, Giang, Hoang Thi, Nhung, Ta Kim, Tran, Cuong Duy, Lang, Son Vi, Nghia, La Tuan, Van Giang, Nguyen, Xuan, Tran Dang, Hall, Anthony, Dyer, Sarah, Ham, Le Huy, Caccamo, Mario and De Vega, Jose J. (2021) Resequencing of 672 native rice accessions to explore genetic diversity and trait associations in Vietnam. Rice, 14. ISSN 1939-8425
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Abstract
Background: Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems. This genetic diversity constitutes a highly valuable resource at a time when the highest rice production areas in the low-lying Mekong and Red River Deltas are enduring increasing threats from climate changes, particularly in rainfall and temperature patterns. Results: We analysed 672 Vietnamese rice genomes, 616 newly sequenced, that encompass the range of rice varieties grown in the diverse ecosystems found throughout Vietnam. We described four Japonica and five Indica subpopulations within Vietnam likely adapted to the region of origin. We compared the population structure and genetic diversity of these Vietnamese rice genomes to the 3000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had very low shared ancestry with accessions from any other subpopulation and were previously overlooked as admixtures. We scored phenotypic measurements for nineteen traits and identified 453 unique genotype-phenotype significant associations comprising twenty-one QTLs (quantitative trait loci). The strongest associations were observed for grain size traits, while weaker associations were observed for a range of characteristics, including panicle length, heading date and leaf width. Conclusions: We showed how the rice diversity within Vietnam relates to the wider Asian rice diversity by using a number of approaches to provide a clear picture of the novel diversity present within Vietnam, mainly around the Indica-5 subpopulation. Our results highlight differences in genome composition and trait associations among traditional Vietnamese rice accessions, which are likely the product of adaption to multiple environmental conditions and regional preferences in a very diverse country. Our results highlighted traits and their associated genomic regions that are a potential source of novel loci and alleles to breed a new generation of low input sustainable and climate resilient rice.
| Item Type: | Article |
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| Additional Information: | Availability of Data and Materials: All sequence data used in this manuscript have been deposited as study PRJEB36631 in the European Nucleotide Archive. Funding: 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. |
| Uncontrolled Keywords: | adaptation,breeding,genetic diversity,gwas,landraces,qtl,rice,agronomy and crop science,soil science,plant science ,/dk/atira/pure/subjectarea/asjc/1100/1102 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 21 Aug 2025 15:30 |
| Last Modified: | 21 Aug 2025 15:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/100201 |
| DOI: | 10.1186/s12284-021-00481-0 |
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