ArticleRice (New York, N.Y.)2021
Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam.
Article in Rice (New York, N.Y.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Genomic insights into the medieval cultivation history of influential high-yielding Asian rice.Scientific reports · 2026Article
- SSR_VibraProfiler: a Python package for accurate classification of varieties using SSRs with intra-variety specificity and inter-variety polymorphism.Plant methods · 2025Article
- Review
- Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages.Annals of botany · 2024Article
- Genetic Diversity and Breeding Signatures for Regional Indica Rice Improvement in Guangdong of Southern China.Rice (New York, N.Y.) · 2023Article
- Genomic regions and candidate genes selected during the breeding of rice in Vietnam.Evolutionary applications · 2022Article
- Fine-scale genetic structure of the rice landrace population in Japan.Molecular genetics and genomics : MGG · 2022Article
- Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province.Scientific reports · 2022Article
- Genetic Structure and Geographical Differentiation of Traditional Rice (Plants (Basel, Switzerland) · 2021Article
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27 authors.
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Abstract
backgroundVietnam 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.
resultsWe 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.
conclusionsWe 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.
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