Indica-Japonica Component Analysis Of Main Hybrid Rice In Southern China

Heterosis is the result of interaction between the hybrid gene, and its genetic basis is the genetic differences between the parents. Crossbred F1of indica-japonica subspecies has a strong biological advantage, but the low pollen sterility and low seed setting percentage lead to low economic yield. Although the wide compatibility gene have improved the pollen sterility of crossbred F1of indica-japonica subspecies and have significantly improved the seed seeting percentage, but so far, the really high-yielding combination used in production has not been bred by typical indica-japonica subspecies. The most successful application is breeding some indica rice which posses some japonica gene, to increasing the genetic difference of hybrid rice parents, and enhancing the potential of heterosis. The sterile lines PeiAi-64is the most prominent representative. In recent years, the production of the southern indica hybrid rice has improved gradually, which is closely connected with application of breeding techniques. However, the genetic difference and proportion of japonica alleles incorporated in the genome of rice germplasm cultivated in southern China is unknown. The development of DNA molecular markers have provided a novel approach to address this question. In the present study, we used single nucleotide polymorphisms (SNP) markers to analyze the genetic difference on the main parents of indica hybrid rice in the southern China, and screening subspecies-specific SNP markers with typical indica variety and typical japonica variety. By using subspecies-specific SNP markers, we determined the proportion of japonica alleles in the indica cultivars, and thus provide a theoretical basis for parent selection of hybrid rice breeding in the future. The main results were as follows:(1) In the present study, we screened out2102Indica-Japonica specific markers from5420SNP markers, and use them to analyze the indica-japonica component of46indica cultivars in whole genome and its distribution on the chromosome. The results showed that all the46indica cultivars contain certain japonica kinship in whole genome, and vary from0.0087to0.2815, the highest is the sterile line PeiAi-64, the lowest is male parent YueZongZhan. The rank order of the groups from the maximum to minimum frequency of japonica alleles was semilate sterile lines> semilate male parents> early sterile lines> early male parents The distribution of japonica pedigree on early indica sterile line is more concentrated, which mainly distributed in chromosome2, but most varieties in indica sterile lines contain high japonica pedigree in multiple chromosomes, and the japonica alles distributing on different varieties has significant difference. Both the sterile line PeiAi64and H6244have high japonica component, but the distribution of japonica alleles on chromosome vary widely. The frequency of japonica alleles of sterile line PeiAi64on chromosomes7and12was significantly higher than indica alleles,while sterile line H6244posessed japonica alleles very low, but H6244posessed a significantly higher frequency of japonica alleles than indica alleles on chromosome9, while PeiAi64possessed a lower japonica alleles than indica alleles on this chromosome. The abundant japonica SNP loci on sterile lines PeiAi64and H6244, and its relationship with the heterosis remains to be further discussed.(2) Using5420SNPs markes analyze the genetic differences on main parents of hybred rice in southern China, the result show that the genetic difference between sterile line with male parents larger than those among sterile lines as well as among male parents, furthermore, the sterile lines were clustered separately from the male parents which are grown widely for production, which means that large genetic differences between sterile lines and male parents is the foundation of heterosis. The study also reveals that the genetic difference between the sterile lines and male parents among semilate indica rice larger than those among early indica rice, which closely related to the seletion of parents in early indica rice breeding most comes from conventional early rice along the Yangtze river basin, and the selection of parents in semilate indica rice derive from a wealth of sources. All the results showed that SNP molecular marker technique is an effective method for analysis of rice genetic differences, which can be used for genetic relationship of unknown materials, and the division of heterotic group.