title: The genetic diversity and structure of indica rice in China as detected by single nucleotide polymorphism analysis.
abstract: BACKGROUND
  Rice (Oryza sativa L.) is the staple food of more than half of the world's population. The identification of genetic diversity in local varieties of rice compared with that of improved or introduced varieties is important in breeding elite varieties for sustainable agriculture. Array-based single nucleotide polymorphism (SNP) detection is a useful technique for such studies and breeding applications.
  
  
  RESULTS
  We developed a 5291-SNP genome-wide array and used it to genotype 471 indica rice accessions in China using Illumina's Infinium technology. Local, introduced, and improved rice varieties were clustered into three sub-groups, with some overlapping shown in principal component analysis and neighbor-joining tree, also confirmed by model-based structure. A minor allele frequency ≥ 0.2 was observed in 72% of polymorphic SNPs in local rice varieties, which was higher than that in other sub-groups. Local rice varieties also had the highest mean polymorphism information content (PIC) and genetic diversity. Analysis of molecular variance showed that 90.61% of genetic variation was a result of differences within sub-groups.
  
  
  CONCLUSIONS
  Our results revealed that SNP analysis clustered local varieties, introduced varieties, and improved varieties into three clear sub-groups. The distribution of parameter PIC values on sub-group genomes revealed that genetic differentiation among them might not be on a genome-wide scale, but rather on selected loci or chromosomal intervals. The result of Gene Ontology enrichment analysis showed that genes nearby those selected SNPs associated different molecular functions or various traits among sub-groups.
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Xu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yuan
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Shan
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Hanyong
authors.initials: H
authors.lastname: Yu
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Yiping
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
authors.forename: Yaolong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. weixinghua@caas.cn.
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
authors.affiliation: State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. liximing@caas.cn.
authors.forename: Ximing
authors.initials: X
authors.lastname: Li
mesh_terms: D002681:China; D032461:Chromosomes, Plant / Q000235:genetics; D005787:Gene Frequency; D018745:Genome, Plant; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide
keywords: Array; Genetic diversity; Rice (Oryza sativa L.); Single nucleotide polymorphism (SNP); Structure