Genotyping By Molecular Markers Of Genes Related To Some Agronomic Traits And The Correlation Analysisin Rice Germplasms

Rice germplasm is the important material foundation for breeding, basic research theories, and rice biotechnology. In this study, eight genes, Wx( granular starch synthase gene), SSIIa(soluble starch synthase II), SSIIIa(soluble starch synthase III), Sbe1 and Sbe3(starch branching enzyme), GS3(the grain length), qSW5( the grain width) and Gn1a( the grain number per panicle), were genotyped by molecular markers that are developed by others and myself in 376 rice germplasms. The correlation analysis between genes and traits has been conducted and the database of genotypes was built. Results are as follows:For Wx gene, the molecular markers Wxb, WxHH, wx and the number of(AATT)n in the leading sequence were effective. While the molecular markers of Wxhp, Wxop, Wxin,Wxmq alleles were not. The rice amylose content and Wxb, Wx HH and the haplotypes composed by them were significantly correlated; the rice amylose content increased as the number of(AATT)n increased; and wx gene could be detected accurately in glutinous rice.The molecular markers of Sbe1 and Sbe3 gene were effective, four haplotypes composed by the genotypes had the significant correlation with the final viscosity but not the peak viscosity. So these two markers could be used to analyze the final viscosity of rice. The molecular markers of the three SNPs at site +2824, +3894 and +4424/4425 in SSIIa gene were effective. And the genotypes and haplotypes were significantly correlated with the calibrated pasting temperature. Meanwhile, the SNP at site +4424/4425 was significantly correlated with the amylose content. The molecular markers of the three SNPs at site+4117, +4898 and +5727 in SSIIIa gene were effective. And the SNP at site +5727 was significantly correlated with the peak viscosity. The SNP at site +4898 was significantly correlated with the final viscosity. The SNP at site +4117 was significantly correlated with the calibrated pasting temperature. However, these three SNPs had no significant correlation with the amylose content. For the GS3 gene, the two molecular markers for the SNP C/A in Exon 2 and the SSR(AT)n in Intron 4, respectively, were effective, and the SSR(TCC)n in Exon 5 was invalid. The SNP A/C in Exon 2 was significantly correlated with the grain length, also was significantly correlated with the japonica rice grain weight,but not the indica grain weight. The(AT)n repetition in Intron 4 had no significant correlation with neither the grain length nor the weight. Therefore, the dCAPS marker for the SNP in Exon 2 could be used to explain the characteristics of the rice grain length. For the qSW5 gene, the STS marker developed by the InDel among different rice varieties was effective and significantly correlated with the rice grain width. Therefore, the STS molecular marker can be used to analyze the rice grain width. For the Gn1 a gene, the STS marker that developed the 16 bp deletion in the 5' untranslated region was effective.