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

Rice

Ta Kim Nhung¹  Cong Nguyen Phi¹  Tran Thi Thuy¹  Nguyen Truong Khoa¹  Dang Thi Thanh Ha¹  Hoang Thi Giang¹  Nguyen Thi Phuong Doai¹  Son Vi Lang¹  Nguyen Thuy Diep¹  Tran Duy Duong¹  Khuat Huu Trung¹  Cuong Duy Tran¹  Kieu Thi Dung¹  Le Huy Ham¹  Tran Dang Khanh²  Janet Higgins³  Jose J. De Vega³  Anthony Hall³  Hoang Dung Tran⁴  Nguyen Thanh Trung⁵  Tran Dang Xuan⁶  Mario Caccamo⁷  Bruno Santos⁷  Sarah Dyer⁷  La Tuan Nghia⁸  Nguyen Thanh Tuan⁹  Nguyen Van Giang⁹ 

[1] Agriculture Genetics Institute (AGI), Hanoi, Vietnam;Agriculture Genetics Institute (AGI), Hanoi, Vietnam;Vietnam National University of Agriculture, 131000, Hanoi, Vietnam;Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK;Faculty of Biotechnology, Nguyen Tat Thanh University, 72820, Ho Chi Minh, Vietnam;Faculty of Pharmacy, Duy Tan University, 550000, Da Nang, Vietnam;Institute of Research and Development, Duy Tan University, 550000, Da Nang, Vietnam;Graduate School of Advanced Science and Engineering, Hiroshima University, 739-8529, Hiroshima, Japan;NIAB, 93 Lawrence Weaver Road, CB3 0LE, Cambridge, UK;Plant Resource Center, An Khanh, Hoai Duc, 152900, Hanoi, Vietnam;Vietnam National University of Agriculture, 131000, Hanoi, Vietnam;

关键词: Rice;    Breeding;    Adaptation;    QTL;    Genetic diversity;    GWAS;    Landraces;   

DOI  :  10.1186/s12284-021-00481-0

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY