Development And Application Of Functional Markers For Rice Grain-related Gene Variant Loci

Rice is one of the most important staple food crops and a primary food source in our country. It is an important way to increase rice yield and improve quality by innovating on breeding methods to breed rice new varieties. In recent years, with the continuous development of molecular biology and genomics, molecular breeding as the supplement of conventional breeding is innovated and improved constantly.Rice grain shape is closely related to rice yield and quality. Carrying out a research on the related genes of rice grain shape has important theoretical significance and practical value to rice genetic improvement. As a fairly complex traits, rice grain shape involves many of genes(enzyme).In this study, five important rice grain shape genes GW8、GS5、GW5、GS3 and qGL3 were selected as the research object. Based on an online public database of target gene sequence alignment, the five gene sequence variation information were analyzed and 9 functional molecular markers were developed. Using the nine markers and grain character index data(Grain Length, Grain Width, Grain Thickness, Length-Width Ratio and Thousand Kernel Weight) of rice micro core collections, the effects of the haplotype of target gene and different allelic variation on the rice grain traits were analyzed. The study has important guidance value to rice molecular design breeding.The main results of this study are as follows:1、In this article,294 rice micro core collections, which is rich in genetic variation, were used as research population. Rice Grain Length, Grain Width, Grain Thickness, Length-Width Ratio and Thousand Kernel Weight in this native population are similar normal distribution.2、In the rice micro core collections, the number of functional mutation loci of GW8, GS5, GW5, GS3 and qGL3 which were detected in this study were 3,2,1,2 and 1, respectively.3、The t test showed that the 9 variable loci had different effects on rice grain traits. Nine mutation loci of GW8, GW5, GS3, GS5 and qGL3 were detected which contain two rare locus, a 13bp deletions in exon-5(5955bp) of GS3 gene, and a single A base mutation in exon-1(4332bp) of qGL3 gene.4、Each mutation loci of GW8 and GW5 gene had a extremely significant effect on rice Grain Length, Grain Width, Grain Thickness, Length-Width Ratio; Two mutation loci of GS5 gene had a significant effect on rice Grain Length, Grain Width, Grain Thickness, Length-Width Ratio; Each mutation loci of GW8, GW5 and GS5 gene had no significant effect on Thousand Kernel Weight. An A/C mutation in exon-2(2252bp) of GS3 genehad a extremely significant effect on Grain Length, Grain Width, Grain Thickness, Length-Width Ratio and no effect on Thousand Kernel Weight; A 13bp InDels mutation in exon-5(5955bp) of GS3 genehad a extremely significant effect on Grain Width, Length-Width Ratio, Thousand Kernel Weight and significant effect on Grain Length, Grain Thickness. An A/C mutation in exon-1(4332bp) of qGL3 gene had a extremely significant effect on Grain Width, Grain Thickness, Length-Width Ratio, Thousand Kernel Weight and no effect on Grain Length.5、Different haplotypes of GW8, GS3 and GS5 gene had different effects on rice grain traits:Each haplotype of GW8 gene had a extremely significant effect on the Grain Length, Grain Width, Grain Thickness, Length-Width Ratio and no effect on Thousand Kernel Weight in rice micro core collections; Different haplotypes of GS5 gene had a significant effect on rice grain length in rice micro core collections; Two haplotypes of GS3 gene had a extremely significant effect on rice Grain Length, Grain Width, Grain Thickness, Length-Width Ratio and no effect on Thousand Kernel Weight in rice micro core collections. GW8 and GS3 gene each have a rare haplotype in rice micro core collections.6、In this study, nine function molecular markers were used to identify the genotypes of the 65 japonica rice varieties in Jiangsu province which is authorized in recent seven years. the results showed that the genetic variations and haplotypes of the 65 japonica rice varieties in the target genes are single. The aboved results pay the way to improve breeding in rice grain shape in Jiangsu province...