Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

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.

Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

“…Quick and accurate classification of rice germplasms into indica or japonica can provide essential information for parental selection strategies in rice breeding programs. Previously, most studies strongly agreed that the population structure of rice accessions ( Oryza sativa L.) could be classified into two main subgroups corresponding to indica or japonica [ 11 , 12 , 14 ]. However, a previous study detected 10 indica accessions classified together with the subgroup (SG2) as dominated by japonica accessions [ 3 ].…”

“…Despite the abundant genetic resources, a few reports have been published relating to Vietnamese rice landraces with traits of interest, such as flowering time [ 11 ], drought tolerance [ 12 ], and salinity tolerance [ 13 ]. Recently, the resequencing of 672 native rice accessions was performed to explore genetic diversity and trait associations using the genome-wide association study (GWAS) approach [ 14 ]. The results of these studies generally recognized that Vietnamese rice germplasm had a high level of genetic diversity, and that their population structure might correlate with geographic regions.…”

“…In this study, we used a new collection containing 79 rice landraces from northern Vietnam that satisfied the above conditions, 10 of which were used in a previous study by Higgins et al (2021) [ 14 ]. Our objectives were to systematically analyze the genetic variations and population structure of this collection, select an effective marker for classifying rice ( Oryza sativa L.) into indica or japonica subspecies, and identify the markers associated with various agro-morphological traits and emphasize the allele specificity, which are often ignored in GWAS studies.…”

Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province

“…To adapt to different environmental and developmental conditions, environmental factors and developmental signals will induce certain adjustments in genes, leading to changes in the final phenotype 6 . Many previous studies have focused on the environmental heterogeneity and wide distribution of varieties, exploring the impact of different geographical distances and environmental factors on genetic diversity 7 – 9 . Few studies, however, attempted to explain the influence of environmental and geographic factors on phenotypic polymorphism by epigenetic factors.…”

Genomic regions and candidate genes selected during the breeding of rice in Vietnam

“…(Tables 1 and 2; Higgins et al, 2021). These subpopulations were characterized in relation to the fifteen subpopulations of Asian rice described by the rice 3000 rice genomes project (3K RGP; Zhou et al, 2020).…”