| DNA sequence diversity and the differentiation of Indica and Japonica werestudied with Cheng's six diagnostic characters, SSR and SNPs in morphological andDNA sequence level to learn the population structure of rice and the utilization ofcomparative genomics and heterosis of subspecies. The main results are as follows:1. DNA sequence diversity of rice landraces of Indica and JaponicaGene diversity of the SSR randomly distributed on the 12 chromosomes of ricewere analyzed. The average gene number was 3.6 and 4.2 in Indica and Japonica,and the average gene diversity was 0.373 and 0.434 respectively, indicating thatJaponica harbors more gene diversity than Indica. And among all the variation foundin the rice landraces we studied, 27.8% was due to the differentiation of Indiea andJaponica.Sixty two DNA fragments, in total of 38,507bp, were successfully sequenced inall of the 58 rice accessions. 234 and 214 SNPs were found respectively in indicaand japonica and the SNPs frequency (θ) are 1.52×10-3and (π) 1.28×10-3 in indicaand (θ) are 1.45×10-3and (π) 1.23×10-3 in japonica, and the average gene diversitywas 0.154 and 0.146 respectively in indica and japonica, indicating that indicaharbors more gene diversity than japonica. And among all the variation found in therice landraces we studied, 58.1% was due to the differentiation of Indica andJaponica.One hundred and ninety two and One hundred and sixty eight haplotypes werediscovered in indica and japonica and the haplotype diversity index (H) was 0.341and 0.231 respectively in indica and japonica, indicating that indica harbors moregene diversity than japonica. And among all the variation found in the rice landraceswe studied, 44.7% was due to the differentiation of Indica and Japonica.The correlation of the allele frequency of indica and japonica was finally computed with SSR, SNPs and haplotypes, which show that the correlation was notsignificant, indicating that significant differences were subject to exist betweenindica and japonica.2. Classification and differentiation of indica and japonicaSeventy five, one hundred and forty eight and fifty indica and japonica specificalleles distributing on 12 chromosomes of rice were obtained respectively in 262SSR alleles, 311 SNPs alleles and 283 haplotypes, in which more than 50% wereshown to be associated with the differentiation of indica and japonica. It is indicatedthat the differentiation of indica and japonica was initiated in multiple loci and thedifferentiation of each locus was not synchronous which implyed both specific andnon-specific alleles and genes would be expected to exist in rice genome.The goodness of fit of the TDj value conducted by specific alleles of SSR,SNPs and haplotype was above 93%, and the goodness of fit of the cladogram andthe classification of rice landraces of indica and japonica studied with molecularmarkers was up to 98%, which suggest the classification of indica and japonica wasreliable with both morphological characters and molecular markers. |
