| Two hundred and twenty-two functional gene fragments with uniform distribution among rice genome were sequenced in representative wide rice and cultivated rice which including 20 landraces,22 male sterile lines and 35 restorer lines, for the study of single nuleotide polymorphisms (SNPs) and population differentiation between them. Use the SNPs marker, it would be helpful to reveal the molecular mechanism during domestication and breeding,at the same time,it can provide a basis for screening genes with important agronomic traits. The main results are as follows:1. As a result,1418 polymorphism sites were obtained in total of 113,775bp DNA sequence.900 transitions,509 transversion and 9 tri-state sites were found in all the 1418 single-base changes and Ts/Tv was 1.77:1, which was consistent with the theoretical ratio 2:1. A total of 1265 SNPs were found in wide rice with the SNPs frequency θ and π were 3.05×10-3 and 2.38×10-3 respectively,a total of 422 SNPs were found in landraces with the SNPs frequency 0 and π were 1.05×10-3 and 1.09×10-3 respectively, a total of 402 SNPs were found in male sterile lines with the SNPs frequency θ and π were 0.97×10-3 and 1.00×10-3 respectively, meanwhile a total of 437 SNPs were found in restorer lines with the SNPs frequency 0 and π were 1.08×10-3 and 1.07×10-3 respectively. We fide that it is obvious difference between wide rice and cultivated rice,but it is no obvious difference between landraces, male sterile lines and restorer lines.The most Minor SNPs frequency is 10% in both populations and the number of SNPs tends to reduce as the Minor SNPs frequency increase. But the number of SNPs with low Minor SNPs frequency (≤10%) is more in wide rice.On the whole, the genetic diversity of indica reduced greatly during domestication,which 0 and% were 34% and 46% respectively with wide rice. Genetic diversity was a slight change in breeding,but it reduced no obviously.2. Compare the frequency distribution of chromosome 12 in four groups, higher SNP frequency on chromosomes 12 and lower SNP frequency on chromosomes 1 and 3 and nonrandomly distributed SNPs on all the rice chromosomes. We also can found that genetic diversity was significantly reduced during domestication, while it was not the same trend during breeding.3. There were 208 gene sites found SNPs in 228 indica functional genes.Take the ratio with landraces and wide rice,when πin/πw<0.333,it was 110 sites. Then Gst> 0.3 and Fst> 0.3, we can filter out 16 genes which they may be very important during domestication, at the same time,there are two significant deviation from the neutral model.4. By AMOVA analysis based on all SNPs in four groups,it found that the biggest variation was between wild rice and restorer lines (difference between the groups was 33.11%, the total population of 66.89%); while it was smallest difference in male sterile lines and restorer lines (difference between the groups was 13.16%, the total population of 86.84%).The results of clustering analysis was the same as the AMOVA analysis. |
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