title: Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China.
abstract: As a weed of rice paddy fields, weedy rice has spread worldwide. In northern China, the expansion of weedy rice has been rapid over the past two decades. Its evolutionary history and adaptive mechanisms are poorly understood. Evolutionary relationships between northern weedy rice and rice cultivars were analyzed using presumed neutral markers sampled across the rice genome. Genes involved in rice domestication were evaluated for their potential roles in weedy rice adaptation. Seed longevity, a critical trait of weedy rice, was examined in an F(2)  population derived from a cross between weedy rice and a rice cultivar to evaluate weedy rice adaptation and the potential effect of candidate genes. Weedy rice in northern China was not derived directly from closely related wild Oryza species or from the introgression of indica subspecies. Introgression with local cultivars, coupled with selection that maintained weedy identity, shaped the evolution of weedy rice in northern China. Weedy rice is a unique system with which to investigate how weedy plants adapt to an agricultural environment. Our finding that extensive introgression from local cultivars, combined with the continuing ability to maintain weedy genes, is characteristic of weedy rice in northern China provides a clue for the field control of weedy rice.
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Sun
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
authors.forename: Qian
authors.initials: Q
authors.lastname: Qian
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Dian-Rong
authors.initials: DR
authors.lastname: Ma
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Zheng-Jin
authors.initials: ZJ
authors.lastname: Xu
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Dan
authors.initials: D
authors.lastname: Liu
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Hong-Bo
authors.initials: HB
authors.lastname: Du
authors.affiliation: Key Laboratory of Northeast Rice Biology and Breeding, Ministry of Agriculture, and Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education, Rice Research Institute, Shenyang Agricultural University, Dongling Road 120, Shenyang, 110866, China.
authors.forename: Wen-Fu
authors.initials: WF
authors.lastname: Chen
mesh_terms: D000220:Adaptation, Biological; D000483:Alleles; D002681:China; D018556:Crops, Agricultural / Q000235:genetics; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D005787:Gene Frequency; D017343:Genes, Plant; D056426:Genetic Loci; D005819:Genetic Markers; D018745:Genome, Plant; D018525:Germination; D006239:Haplotypes; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D057445:Plant Dormancy; D057685:Plant Weeds / Q000145:classification / Q000235:genetics*; D012639:Seeds / Q000235:genetics; D012641:Selection, Genetic; D013997:Time Factors
chemical_list: D005819:Genetic Markers