Genetic Network Analysis And Verification Of Starch Synthesis Related Genes Under The Background Of Glutinous Rice

In the past several decades, the yield level of rice has been dramatically improved mainly as the result of genetic improvement, increasing harvest index by reducing plant height making use of the semidwarf gene sd-1, and utilization of heterosis by producing hybrids. With the improvement of people's living level, the requirement of rice with good quality has become higher and higher, especially in cooking and eating quality. Cooking and eating quality has been largely determined by four physical and chemical indexes, amylose content (AC), gel consistency (GC), and gelatinization temperature (GT) and rapid viscosity analyzer profile (RVA profile). Thus, it is necessary to understand the mechanisms underlying the rice starch biosynthesis, particularly the genetic basis of AC, GC, GT and RVA profile.We collected 118 waxy rice landraces for our research; and 17 starch synthesis related genes were selected to elucidate the putative genetic net work for starch synthesis. On the basis of the information of 17 starch synthesis related genes'sequences in 13 representative cultivars, a series of markers for each gene were developed; these developed markers were employed to detect the genotype of the 118 varieties. The starch physicochemical properties (including RVA profile and GC) of the 118 varieties were measured. Population structure was evaluated by Admixture Model and Linkage Model in"Structure"program based on the phenotypic information on 45 simple sequence repeats (SSRs) loci distributed on 12 chromosomes in rice genome. The result showed that the 118 varieties could be divided into two groups, matching well to the two subspecies groups of indica and japonica. The Q-values were determined by Admixture Model when the K was set to 2. Q values of each variety are used as the correction parameters in association analysis. In order to understand genetic effect of the starch synthesis related genes, genotypic data and quality data were used for association analysis by SAS9.0.In the present study, an indica cv Guichao 2 and a japonica cv Suyunuo were selected as materials, which differ dramatically in grain quality, to evaluate the genetic effects of SSII-3, SSIII-2 and PUL on grain quality. In order to precisely analyze their effects, the nearly iso-genic lines (NILs) for those three genes were developed through the molecular marker-based selection in the progeny of backcross population of Guichao 2×Suyunuo. Thus, the two sets of NILs, Suyunuo and Guichao 2 as recurrent parents, respectively, were subsequently employed for grain quality measurement (including RVA profile,GC and GT) and genetic analysis. The main results were summarized as following:1. The association analysis results showed that in the background of glutinous rice, PUL gene exhibits the most notable effect on RVA profile; including PKV, HPV, CPV, SBV, PaT and PeT. The RVA profile of NIL-PUL (Suyunuo as recurrent) showed significant differences in PKV, HPV, BDV, CPV and SBV.2. The results of association analysis and the NILs indicated that the gelatinization temperature of rice is mainly controlled by SSII-3 gene. Other genes, such as PUL and SSIII-2, also have the effects on GT.3 Previous studies indicated that BDV and SBV were highly correlated with eating quality, they were controlled by several genes. In our study, BDV was found to be mostly affected by AGPlar, ISA, SBE1, SSI, SSII-2 and SSIV-1. Meanwhile, twelve genes may involve in the control of SBV, which are AGPlar, AGPsma, GBSSII, ISA, PUL, SBE3, SBE4, SSI, SSII-1, SSII-2, SSIV-1 and SSIV-2. It is difficulty for the breeder to improve the grain quality by molecular marker-assisted breeding.4 PUL gene also contributes to the variation of gel consistency in some content, but the result can not validated by the NILs. Therefore, more efforts have to be put in the understanding the mechanisms of GC.5 The interaction among genes affect several characteristics of RVA profile, including BDV, PaT, PeT. Interaction between genes is not related with other physical and chemical quality parameters of starch.