The Genetic Diversity And Structure Of Indica Rice In China As Detected By Single Nucleotide Polymorphism Analysis

Rice(Oryza sativa L.) is the staple food for more than 3.5 billion people worldwide, which represents around half of the world’s population. Local varieties of rice have evolved from their wild progenitors under both natural and human selection, resulting in a high level of genetic diversity. They represent the main sources with which to undertake genetic improvement for the toleration of biotic and abiotic stress. Thus 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 and helpful to change the narrow genetic basis for breeding new varieties. Array-based single nucleotide polymorphism(SNP) detection is a useful technique for such studies and breeding applications. In this paper we developed a 5291-SNP genome-wide array and used it to genotype 471 indica rice accessions(including 285 local varieties, 94 introduced varieties and 92 improved varieties)in China using Illumina’s Infinium technology. The main results were as follows:1. Most SNPs are located in intergenic regions, while 42% are located in genic regions including untranslated regions, introns, and coding sequences. The gaps between 72.33% of SNPs are less than 75 kb, and that all gaps exceed 0.5 kb.2. 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.3. Local rice varieties also had the highest mean polymorphism information content(PIC) and genetic diversity. 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.4. Analysis of molecular variance showed that 90.61% of genetic variation was a result of differences within sub-groups.5. 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.6. The result of Gene Ontology(GO) enrichment analysis showed that genes nearby selected SNPs associated different molecular functions or various traits among sub-groups.7. 23, 24, 20, 21 nonoverlapping windows significant in the reduction of diversity were found by ROD values between introduced/local varieties, improved/local varieties, local/introduced varieties, and local/improved varieties, including 56, 47, 45, 40 genes respectively.