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	The power of inbreeding: ngs-based gwas of rice reveals convergent evolution during rice domestication
	Wang, Hongru1,2,3; Xu, Xun4; Vieira, Filipe Garrett5; Xiao, Yunhua1,2,3; Li, Zhikang6; Wang, Jun3; Nielsen, Rasmus7; Chu, Chengcai1,2
刊名	Molecular plant
	2016-07-06
卷号	9期号:7页码:975-985
关键词	Inbreeding Gwas Rice Pericarp color
ISSN号	1674-2052
DOI	10.1016/j.molp.2016.04.018
通讯作者	Wang, jun(wangj@genomics.org.cn) ; Nielsen, rasmus(rasmus_nielsen@berkeley.edu) ; Chu, chengcai(ccchu@genetics.ac.cn)
英文摘要	Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in humans, due to the availability of large reference panels for genotype imputation. however, it is unclear whether this strategy can be utilized in other species without reference panels. using simulations, we show that this approach is even more relevant in inbred species such as rice (oryza sativa l.), which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. we sequenced 203 rice varieties with well-characterized phenotypes from the united states department of agriculture rice mini-core collection at an average depth of 1.53 and used the data for mapping three traits. for the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal snps in the major-effect loci. for the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. although known loci can explain color variation in the varieties of two main subspecies of asian domesticated rice, japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
WOS关键词	GENOME-WIDE ASSOCIATION ; GENERATION SEQUENCING DATA ; BIOCHEMICAL INSIGHTS ; POPULATION-GENETICS ; NATURAL VARIATION ; AGRONOMIC TRAITS ; ORYZA-SATIVA ; WAXY GENE ; DISCOVERY ; PROTEIN
WOS研究方向	Biochemistry & Molecular Biology ; Plant Sciences
WOS类目	Biochemistry & Molecular Biology ; Plant Sciences
语种	英语
出版者	CELL PRESS
WOS记录号	WOS:000379655800004
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2374682
专题	中国科学院大学
通讯作者	Wang, Jun; Nielsen, Rasmus; Chu, Chengcai
作者单位	1.Chinese Acad Sci, State Key Lab Plant Genom, Beijing 100101, Peoples R China 2.Chinese Acad Sci, Inst Genet & Dev Biol, Natl Ctr Plant Gene Res Beijing, Beijing 100101, Peoples R China 3.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100101, Peoples R China 4.BGI Shenzhen, Shenzhen 518083, Peoples R China 5.Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark 6.Chinese Acad Agr Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Inst Crop Sci, 12 South Zhong Guan Cun St, Beijing 100081, Peoples R China 7.Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA
推荐引用方式 GB/T 7714	Wang, Hongru,Xu, Xun,Vieira, Filipe Garrett,et al. The power of inbreeding: ngs-based gwas of rice reveals convergent evolution during rice domestication[J]. Molecular plant,2016,9(7):975-985.
APA	Wang, Hongru.,Xu, Xun.,Vieira, Filipe Garrett.,Xiao, Yunhua.,Li, Zhikang.,...&Chu, Chengcai.(2016).The power of inbreeding: ngs-based gwas of rice reveals convergent evolution during rice domestication.Molecular plant,9(7),975-985.
MLA	Wang, Hongru,et al."The power of inbreeding: ngs-based gwas of rice reveals convergent evolution during rice domestication".Molecular plant 9.7(2016):975-985.

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