Hệ thống quản lý khoa học - Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam

Tên bài báo:	Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam (Lượt xem: )
Tên tạp chí:	Rice
Tạp chí thuộc:	Tạp chí KH quốc tế ISI
Chỉ số IF/H:	4.595
Năm xuất bản:	2021
Nước xuất bản:	Mỹ
Tác giả thuộc Học viện:	TS. Nguyễn Thanh Tuấn
Các tác giả bài báo:	Janet Higgins1, Bruno Santos2, Tran Dang Khanh3,4, Khuat Huu Trung3, Tran Duy Duong3, Nguyen Thi Phuong Doai3, Nguyen Truong Khoa3, Dang Thi Thanh Ha3, Nguyen Thuy Diep3, Kieu Thi Dung3, Cong Nguyen Phi3, Tran Thi Thuy3, Nguyen Thanh Tuan4, Hoang Dung Tran5, Nguyen Thanh Trung6,7, Hoang Thi Giang3, Ta Kim Nhung3, Cuong Duy Tran3, Son Vi Lang3, La Tuan Nghia8, Nguyen Van Giang4, Tran Dang Xuan9, Anthony Hall1, Sarah Dyer2, Le Huy Ham3, Mario Caccamo2 and Jose J. De Vega1*
Tóm tắt bài báo:	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
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