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.
Highlights
Vietnam possesses a vast diversity of rice landraces due to its geographical situation, latitudinal range, and a variety of ecosystems
Five hundred eleven of the accessions were obtained from the PRC (Plant Resource Centre, Hanoi, Vietnam, http://csdl.prc.org.vn), together with their passport data, which shows that they were collected from all eight administrative regions of Vietnam (Table S1)
A total of 1174 Giga base-pairs (Gbps) of data was generated for the 616 samples representing an average sequencing depth of 30x for 36 “high coverage” samples and 3x for 580 “low coverage” samples (Table S1)
Summary
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, in rainfall and temperature patterns. In 2017, the total planted area of rice in Vietnam was 7.7 million hectares This includes 4.2 million hectares in the Mekong River Delta and 1.1 million hectares in the Red River Delta (GSO-Database 2017). In the Mekong River Delta, the damaging effects of salinisation and drought to rice production have increasingly manifested themselves in recent years (Parker et al 2019; Son et al 2018; Tran et al 2019; Yen et al 2019)
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