Development Of Molecular Markers On Rice Starch Synthesis Related Genes And Genetic Network Analysis Of Starch Synthesis

Rice starch consists of amylose and amylopectin. Both the ratio of the two types of starch and the structure of amylopectin decide the rice qualities. Amylose is synthesized by granule-bound starch synthase (GBSS) encoded by Wx gene, while amylopectin is synthesized by a series of enzymes, including soluble starch synthases(SSS), starch branching enzymes(SBE) and starch debranching enzyme(DBE), each of which has different isoforms, so the pathway of amylopectin synthesis is very complex. Recently, there has been much knowledge accumulated about the regulation mechanism of Wx gene as well as its effect on rice quality. However, there have been few such reports on amylopectin. In this research, on the base of sequences of 18 genes related to starch synthesis in 13 typical varieties, totally 49 molecular markers (STS and CAPs) were developed at the site of In/Del or SNP mutation spreading all over the gene from promoter to 3'UTR region, 2~4 markers for each gene were developed. And these markers were verified through 13 sequenced varieties. Subsequently, these developed markers were employed to genotype 64 varieties from different ecotypes, and the potential of novel alleles mining was assessed for the 49 markers. Furthermore, the starch physicochemical properties (including AAC, GC and RVA profile) of the 60 varieties were measured. Based on the genotype and phenotype data of the 60 varieties, the function of each gene related to starch synthesis was analyzed through Bayesian algorithm, and the genetic network for starch synthesis was constructed. The main results were summarized as following: 1. In this study, based on the development of genomic sequencing technology and bioinformatic methods, 49 markers were developed for 18 starch-synthesizing genes (AGPsma, AGPiso, AGPlar, Wx, GBSSII, SSI, SSII1, SSII2, SSII3, SSIII1, SSIII2,SSIV1, SSIV2, Sbe1, Sbe3, Sbe4, Pul, Isa). Haplotype analysis was done on each gene loci, and several new haplotypes were detected in 10 gene loci(AGPiso, AGPlar, Wx, SSI, SSII2, SSII3, SSIII1, Sbe1, Sbe4, Pul)in 64 varieties, in which pul gene had the most new ones. Furthermore, the new haplotype were mainly found in Indian rice (Aman, Bulu, Dular, et al.) and American rice ( Lemont, Cpslo17, et al.)2. Based on statistic analysis of 49 genotype data and 10 quality data in 60 varieties, linear model was established, and Bayesian algorithm was applied to estimate genetic function of each allele variation on the 10 quality traits including main genetic effects and interaction effects. 12 markers were detected to show high estimated value of main genetic effects on starch physicochemical properties, and 22 markers were detected to interact each other on the qualities, including the interaction among genes encoding different starch-synthesizing enzymes and genes encoding same starch-synthesizing enzyme.