Single Nucleotide Polymorphisms In Oryza Rufipogon Griff.

Oryza rufipogon Griff. has received wide attention because of its valuable wild germplasm source.Twenty four DNA fragments randomly distributed on each arm of the 12 chromosomes of rice, in total of 18,989bp, were successfully sequenced in 22 Oryza rufipogon accessions. 152 SNPs were found with transformation accounting for 60.5% and transition for 39.5%, in which rare SNPs accounted for 59.21%.The SNPs frequency (θ) in Oryza rufipogon was 2.54×10^-3 and (π) 2.35×10^-3, and the SNPs frequency in noncoding regions between genes was far more than that in coding regions which is close to that of noncoding regions in genes.A total of 172 haplotypes were identified with average haplotype diversity equal to 0.5944. And the haplotype diversity of accessions in Guangdong province is close to that in Guangxi province, which is lower that in Hainan province.Most accessions from Hainan province, all accessions from Dongxiang Jiangxi province and those from Guangdong province appeared to be in three distinct groups in the UPMGA cladogram which indicated that the diversification of Oryza rufipogon has something to do with the geographical distribution.The frequency and distribution of SNPs in the same sites in Oryza rufipogon and cultivated rice were also discussed in present research, which suggested DNA variation of Oryza rufipogon was greater than that of cultivated rice due to the loss of variation during the evolution process.