title: Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.
abstract: Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 × raw data coverage. We investigated genome-wide variation patterns in rice and obtained 6.5 million high-quality single nucleotide polymorphisms (SNPs) after excluding sites with missing data in any accession. Using these population SNP data, we identified thousands of genes with significantly lower diversity in cultivated but not wild rice, which represent candidate regions selected during domestication. Some of these variants are associated with important biological features, whereas others have yet to be functionally characterized. The molecular markers we have identified should be valuable for breeding and for identifying agronomically important genes in rice.
authors.affiliation: CAS-Max Planck Junior Research Group on Evolutionary Genomics, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China.
authors.forename: Xun
authors.initials: X
authors.lastname: Xu
authors.forename: Xin
authors.initials: X
authors.lastname: Liu
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
authors.forename: Fengyi
authors.initials: F
authors.lastname: Hu
authors.forename: Xin
authors.initials: X
authors.lastname: Li
authors.forename: Yang
authors.initials: Y
authors.lastname: Dong
authors.forename: Ryan N
authors.initials: RN
authors.lastname: Gutenkunst
authors.forename: Lin
authors.initials: L
authors.lastname: Fang
authors.forename: Lei
authors.initials: L
authors.lastname: Huang
authors.forename: Jingxiang
authors.initials: J
authors.lastname: Li
authors.forename: Weiming
authors.initials: W
authors.lastname: He
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Zheng
authors.forename: Fumin
authors.initials: F
authors.lastname: Zhang
authors.forename: Yingrui
authors.initials: Y
authors.lastname: Li
authors.forename: Chang
authors.initials: C
authors.lastname: Yu
authors.forename: Karsten
authors.initials: K
authors.lastname: Kristiansen
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Mark
authors.initials: M
authors.lastname: Wright
authors.forename: Susan
authors.initials: S
authors.lastname: McCouch
authors.forename: Rasmus
authors.initials: R
authors.lastname: Nielsen
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
mesh_terms: D001947:Breeding; D002874:Chromosome Mapping; D019143:Evolution, Molecular; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D015810:Linkage Disequilibrium; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011153:Population; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D005819:Genetic Markers