Excellent Allelic Variation Of Starch Synthesis Related Genes And Association Analysis Of Eating Quality Traits In Rice Cultivars

Rice is one of the most important food crops in our country.Currently,the main objective of rice breeding is to improve yield and grain quality.However,the genetic distance and genetic diversity are becoming narrow due to the long-term and orientatial breeding strategy.So the study of genetic diversity of rice cultivars will clearly understand their genetic background,help choose rational hybrid combinations.In addition,there are exists large amounts of gene loci and allelic variation associated with rice grain quality traits in rice germplasms.Therefore,it is of great importance to discover the associated loci with rice grain traits using the association analysis strategy.In this research,88 indica rice varieties and 184 japonica rice varieties were chosen from abroad and different provinces of China.Functional markers of 18 genes related to starch synthesis and 164 SSR markers were used to identify the genetic diversity and population structure of these rice materials.And then the association analysis of rice eating quality traits were executed seperately in indica and japonica varieties.The main results were as follows:1.11 eating quality traits of AC,ASV,GC and RVA profiles were determinated in 88 indica population and 12 traits of palatability,AC,ASV,GC and RVA profiles were measured in 184 japonica population.The results indicate that there was significant variation in each trait,either in indica or in japonica population.2.Functional markers of 18 genes related to starch synthesis and 164 SSR markers were screened for the genetic diversity analysis.inindica population,727 alleles were detected with allele number ranging from 2 to 9,average allele number of 3.67.Gene diversity index varied from 0.044 to 0.818,with an average value of 0.446 and the polymorphism information content(PIC)ranged from 0.043 to 0.793 with the average of 0.400.In japonica population,628 alleles were detected with alleles ranging from 2 to 6 and the average of allele number of 3.17.Gene diversity index ranged from 0.011 to 0.766 with the average of 0.273.The polymorphism information content(PIC)ranged from 0.0108 to 0.727 with an average of 0.244.3.Cluster analysis and population structure were executed using PowerMark3.2 and Structure2.3 software.In Indica population,there were four categories based on the result of cluster analysis and three groups,some of which is consistent with the cluster analysis.Burma X023 and X027,Bangladesh varieties DHALA,Dvl,SHADA,Cambodia 41580,41583,41586,41594 and Fujian yajiaoshu et al indica rice varieties can be as a parent indica and configuration of cross combination,rich domestic indica germplasm genetic diversity.In 184 japonica population,the japonica rice varieties and domestic rice and japonica varieties between genetic similarity are high,narrow genetic basis,so in domestic rice breeding should make great efforts to introduce new germplasm as japonica parents will help broaden the genetic base of parents in promoting the emergence of a variety of types of recombinant hybrid offspring.4.According to the results of association analysis of rice eating quality traits,51 and 30 loci were identified in Indica and japonica population,respectively.The association loci were quite different between Japonica and indica populations.In indica population,there were 10 loci associated with eight eating quality traits of GT,GC,CPV,PKV,SBV,CSV,BDV,PET collocated with Wx gene.Three loci associated with GC and PKV were collocated with SSII-3 gene.Whereas,in japonica population,4 loci associated with BDV,AC,and PET collocated with Wx gene and one locus associated with GT(ASV)collocated with SSII-3 gene.In the middle of chromosome 3,we found multiple loci related to eating quality traits indicating that there might be important candidate genetic factors controlling rice eating quality in this area.Besides these loci,4 and 5 other loci from indica and japonica populations were consistent with the previous reports by comparing with the reported associated or QTL mapping loci.The additional loci were the new loci found in the present study.These associated loci obtained in this study and their corresponding carrier varieties will provide valuable references for improvement of rice grain quality of Indica and japonica varieties.