Effects Of Starch Synthesis-related Genes Polymorphism On Glutinous Rice Quality

Rice is one of the most important crops as it provides the staple food for nearly half of the world's population,and its high yield and good quality are two key targets for rice production.Due to the successful utilization of the semi-dwarf gene and heterosis technology,rice yield has been dramatically improved over the past several decades.However,the quality of rice still cannot meet the increasing demands of consumers.Improvements in grain quality still remains a major problem and it is controlled by quantitative trait loci(QTLs)and influenced by environmental change.Despite a great deal of research effort,only a small number of relevant genes have been identified thus far.The genetic mechanism of rice quality remains unclear.Most researches on rice grain quality have been conducted on non-glutinous rice,only a few on glutinous rice.Therefore,we need to reveal the genetic basis of eating and cooking quality,and to provide the foundation for its quality improvement.QTL mapping is an important method to detect functional sites of rice genome.However,this technique cannot find the genetic effects of minor genes,nor can it explain the complex interaction effects between genes.Association analysis is a powerful tool for studying genetic loci involved in the inheritance of complex traits,and it has been successfully exploited in plant molecular genetics.In this study,63 glutinous rice materials were used to identify the genotypes of 17 starch synthesis-related genes and determine their physicochemical indexes,RVA profile characteristics,thermal characteristics and retrogradation characteristics.41 pairs of SSR primers were used to analyze the population structure to exclude false associations.Association analysis was used to clarify the influence of each gene and its interaction on the quality of glutinous rice,so as to provide theoretical basis for the quality breeding and breeding of glutinous rice.The main results were as follows:1.Rice qualities of 63 glutinous rice varieties differed significantly,and the correlation between many quality traits was significant at 0.05 or 0.01 level.They were regulated by some genes together.2.A total of 127 alleles were detected by using 41 pairs of SSR primers in 63 glutinous materials,with an average of 3.1 per locus.There were abundant polymorphism of RM markers in the germplasm resources.Clustering analysis showed that the tested rice materials could be divided into two groups: Indica and Japonica.The population structure analysis showed that the optimum subgroup number was two.Most of the cultivars had a relatively pure genetic background,and a few parts with the mixed background.This might be related to the intersubspecific hybridization between Indica and Japonica during the long-term acclimation of rice.3.Results of association analysis showed that eight genes were associated with the variation of gel consistency(GC).The genetic effects of ISA,SSIV-2,SBE3,SSII-1,PUL,SBE4,SSII-3 and SBE1 decreased sequentially.The genetic mechanism of GC needs to be verified by further experiments.4.A total of six starch synthesis-related genes were involved in the regulation of the RVA profile characteristics,SSII-3,PUL,SSI,SBE4,SSIV-1and SBE3.Each characteristic value was affected by at least two genes.Except for the setback value,the PUL was associated with other five viscosity characteristics,indicating that PUL was the most significant gene affecting the viscosity characteristics of RVA profile in glutinous rice.The pasting temperature and peak time were affected by the SSII-3 and SSI genes together.5.The results of association analysis showed that the peak width at half height(PWH)of glutinous rice was only affected by SSII-3 and the change of enthalpy was only affected by SSI.The other thermal and regenerative characteristics were influenced by both SSII-3 and SSI genes.We found that the correlation between each trait and SSII-3 was significantly greater than that of SSI gene if comparing the corresponding F values of genes.It implied that SSII-3 was a major gene controlling thermal and retrogradation.6.There were extensive interactions among the starch synthesis-related genes.Except for setback value,PWH and enthalpy,significant interactions were detected in other traits.This showed the complexity of the genetic mechanism of starch quality in glutinous rice.The breeding is still difficult by marker-assisted selection and the genetic mechanism of the starch quality of glutinous rice needs to be further studied.