title: Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization: a case study from southern China.
abstract: Whole-genome re-sequencing of weedy rice from southern China reveals that weedy rice can originate from hybridization of domesticated indica and japonica rice. Weedy rice (Oryza sativa f. spontanea Rosh.), which harbors phenotypes of both wild and domesticated rice, has become one of the most notorious weeds in rice fields worldwide. While its formation is poorly understood, massive amounts of rice genomic data may provide new insights into this issue. In this study, we determined genomes of three weedy rice samples from the lower Yangtze region, China, and investigated their phylogenetics, population structure and chromosomal admixture patterns. The phylogenetic tree and principle component analysis based on 46,005 SNPs with 126 other Oryza accessions suggested that the three weedy rice accessions were intermediate between japonica and indica rice. An ancestry inference study further demonstrated that weedy rice had two dominant genomic components (temperate japonica and indica). This strongly suggests that weedy rice originated from indica-japonica hybridization. Furthermore, 22,443 novel fixed single nucleotide polymorphisms were detected in the weedy genomes and could have been generated after indica-japonica hybridization for environmental adaptation.
authors.affiliation: Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China, lefroyqiu@foxmail.com.
authors.forename: Jie
authors.initials: J
authors.lastname: Qiu
authors.forename: Jinwen
authors.initials: J
authors.lastname: Zhu
authors.forename: Fei
authors.initials: F
authors.lastname: Fu
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.forename: Weidi
authors.initials: W
authors.lastname: Wang
authors.forename: Linfeng
authors.initials: L
authors.lastname: Mao
authors.forename: Zhangxiang
authors.initials: Z
authors.lastname: Lin
authors.forename: Li
authors.initials: L
authors.lastname: Chen
authors.forename: Haiqiang
authors.initials: H
authors.lastname: Zhang
authors.forename: Longbiao
authors.initials: L
authors.lastname: Guo
authors.forename: Shen
authors.initials: S
authors.lastname: Qiang
authors.forename: Yongliang
authors.initials: Y
authors.lastname: Lu
authors.forename: Longjiang
authors.initials: L
authors.lastname: Fan
mesh_terms: D000383:Agriculture; D000483:Alleles; D002681:China; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D017343:Genes, Plant; D005828:Genetics, Population; D018745:Genome, Plant; D006824:Hybridization, Genetic; D012275:Oryza / Q000235:genetics*; D010641:Phenotype; D057685:Plant Weeds / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA