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

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.

EKSPLORASI KEBERADAAN GENOTIPE POTENSIAL PADI LOKAL DI WILAYAH BARAT- SELATAN ACEH

The South-West Region of Aceh is one of the regions in the province of Aceh that is very rich in local rice diversity that needs to be identified and utilized as a source of genes in ssembling new superior varieties to support food security and sustainable agriculture. This study aims to determine the presence of potential local rice genotypes in the South-West Region of Aceh. This research was carried out in the South-West region of Aceh for potential local rice exploration. The survey results in the Aceh Barat-Selatan region have several potential genotypes of local rice in districts in the South-West Aceh region that are still cultivated by farmers in the south, while potential local gonotypes of rice in the South-West Aceh region, namely Aceh Jaya district: , Jantoeng, Sikleng, Ramos, Sijane, Dewi and Leukat Jeuram, West Aceh districts: Itam Tangke Lango, Head of Gidan Kinco, Lekat jero Lango, Sirendeh Semantuk Wayla and Bo Rayek Semantok Wayla. Nagan Raya Regency: Siputeh, Manyam U and Lekat Tuleng, Southwest Aceh Regency: Sigupai. South Aceh Regency: Sitandun, Silian. Simeulue Regency: Sambai and Pade Sialek. Keywords: Exploration, Local of Rice

Hidden Rice Diversity in the Guianas

Traditional crop varieties are an important source of genetic diversity for crop adaptation and modern breeding. Landraces of Asian (Oryza sativa) and African (Oryza glaberrima) rice have been well studied on the continents where they were domesticated. However, their history of cultivation in northern South America is poorly understood. Here we reveal the rice diversity that is maintained by Maroons, descendants of enslaved Africans who fled to the interior forests of the Guianas ca. 300 years ago. We interviewed subsistence farmers who practice shifting cultivation along the Maroni and Lawa rivers that form the natural border between French Guiana and Suriname, and used ethnobotanical and morphological methods to identify around 50 varieties, of which 15 were previously undocumented. The genetic origin of these varieties was explored using the Angiosperms-353 universal probe set. Despite the large distances between sites and relative inaccessibility of the area, phenotypic and genetic diversity did not display any geographic structure, which is consistent with knowledge of seed exchange among members of the same ethnolinguistic group. Although improved US cultivars were introduced in Maroon villages in the 1940s, these have not displaced the traditional landraces, which are cherished for their taste and nutritious qualities and for their importance in Maroon spiritual life. The unique agricultural and ritual practices of Maroons confirm their role as custodians of rice diversity, a role that is currently under threat from external pressures and encroaching globalization. We expect that the rice diversity uncovered in this study represents only a fraction of the total diversity in the Guianas and may constitute a large untapped resource that holds promise for future rice improvement. Further efforts to inventory and preserve these landraces will help to protect a precious cultural heritage and local food security.