Resequencing of 672 native rice accessions to explore genetic diversity and trait associations along 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 3,000 genomes of Asian cultivated rice. The named Indica-5 (I5) subpopulation was expanded in Vietnam and contained lowland Indica accessions, which had with 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: 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 sustainable and resilient rice.

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

“…We used a well-tested method, named XP-CLR, to identify distorted allele frequency patterns in contiguous SNP sites that cannot be explained by random drift. To identify regions under selection, we leveraged the strong population structure recently described in Vietnam (Higgins et al 2021), which comprised five Indica and four Japonica subpopulations of native rice accessions adapted to variable geography and latitude range. We observed a stronger signature of selection in the Indica subtypes than in the Japonica subtypes, which may reflect the higher diversity within the Indica subtypes in Vietnam.…”

“…We observed a stronger signature of selection in the Indica subtypes than in the Japonica subtypes, which may reflect the higher diversity within the Indica subtypes in Vietnam. Taking into consideration the size and diversity in each subpopulation (Higgins et al 2021), the whole-genome XP-CLR score was lower in the larger subpopulations (I1 and J1) and the subpopulations with the lower diversity.…”

“…We utilized a set of 2,027,294 SNPs for the 426 Indica samples and 1,125,716 SNPs for the 211 Japonica samples. Detailed information for each sample is available in Higgins et al (2021). A summary of the number and source of each subpopulation is available in Table 1 (47 Indica samples and 9 Japonica samples native to Vietnam were obtained from the 3K RGP project).…”

“…A summary of the number and source of each subpopulation is available in Table 1 (47 Indica samples and 9 Japonica samples native to Vietnam were obtained from the 3K RGP project). The putative effects of the bi-allelic SNPs (low, medium and high effects) on the genome were determined using SnpEff (Cingolani et al 2012) as detailed in Higgins et al (2021) and the pre-built release 7.0 annotation from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/).…”

“…This diversity constitutes a largely untapped and highly valuable genetic resource for local and international breeding programs (Khanh et al 2021). Vietnamese rice shows a strong population structure, which is captured within five Indica and four Japonica subpopulations that we have recently described (Higgins et al 2021). These subpopulations were characterised in relation to the fifteen subpopulations of Asian rice described by the rice 3,000 rice genomes project (3K RGP) (Zhou et al 2020).…”