Genome-wide Association Analysis Of Rice Leaf Angle Sensitivity To Br Of 533 Domestic And Foreign Rice Core Germplasm

Brassinosteroid(BR),is a kind of steroid hormones,which widely exists in the plant.As the sixth largest plant hormone which found in the last century,it plays an important role in the process of plant growth and development.In rice,Leaf Angle as one of the standard of ideal plant,is an important agronomic traits affecting rice yield,erect leaf can significantly improve the efficiency of photosynthesis and plant density to increase production.Therefore,the regulation of rice leaf angle of external factors,genetic factors,cytological and molecular mechanism research will provide rice molecular design breeding with molecular function module components,is great significance for high-yielding rice molecular design breeding,BR plays an important role in the formation process of leaf angle in rice.This study will use 533 rice germplasm materials come form China and abroad as the research object,using genome-wide SNP markers,including genes epistatic and the environment interaction effect model,sensitivity to rice leaf angle of BR traits genome-wide association analysis.Main results are as follows,(1)Through analysis statistics of phenotypic traits for leaf angle of the 505 rice germplasm resources,BR treatment significantly promoted leaf angle of the most rice germplasm enlarged.(2)Through respectively genome wide association analysis of the BR sensitivey of leaf angle for all population,Indica and Japonica,169 significantly related SNP markerswere detected.84 among All population,43 among Indica and 56 among Japonica.There are2 SNP markers repeatedly detected in All population and Indica,there are 12 SNP markers repeatedly detected in All population and Japonica,there is no SNP markers repeatedly detected in Indica and Japonica.Indica and Japonica rice leaf angle sensitivity to BR traits phenotypic have large genetic differences.(3)Further discussion to genome-wide association analysis(GWAS)results ofthe sensitivity of rice leaf angle in All population and Indica,there are 2 SNP markers were detected at the same time,13534966 and 19494269 are all in the rice chromosome1;Further discussion to genome-wide association analysis(GWAS)results ofthe sensitivity of rice leaf angle in All population and Japonica,there are 12 SNP markers were detected at the same time,they areall located on the rice chromosome 1;there was no SNP marker were detected in Indica population and Japonica at the same time.(4)There are 49 known genes related significantly SNPs detected in this study,there are 23 known genes related significantly SNPs detected in All population,including 15 known genes related significant SNP markers located in introns,four non-synonymous known genes related to significant SNP markers,three synonymous known genes related significant SNP markers and another one in 3 ’UTR region known genes related SNP marker significantly.For Indica population,the result of genome-wide association of leaf angle sensitivity to BR indicate that there are 13 known genes related significant SNP markers.Located on the known gene introns includes five known genes related SNP markers,four non-synonymous known genes related SNP markers and four synonymous known genes correlated significantly SNP markers.Sf0119494269 is located in the intron of Os01g35220,a predictive coding protein translocation subclass function area,this SNP marker was detected in all population and Indicaat the same time.Of Japonica leaf Angle of BR in the sensitivity analysis of genome-wide association detected significantly.For Japonica population,the result of genome-wide association of leaf angle sensitivity to BR indicate that there are 15 known genes related significant SNP markers,including seven known genes related significant SNP markers on the intron of reported genes,four non-synonymous known genes related significant SNP markers,synonymous two known genes related to significant SNP markers and 1 known genes related significant SNP marker located in 3 ’UTR region and a forecast for interruption termination codon function significantly related to known genes SNP marker。Among them,SNP marker sf0118771688 is located in a predicthas encoding one type of arabidopsis thaliana armadillo/beta-catenin-like repeat family protein function on Os01g34080,is detected in all groups and Japonica at the same time.(5)Through genome wide association analysis of All groups,we identified four non-synonymous SNPs significantly known genes about leaf Angle susceptibility to BR,respectively are sf1114565598,sf0519093641,sf0519056263 and sf1115976699.Use Rice Var Map website,through the analysis of genotype and phenotype,we supported some evidence for the four SNPs with leaf Angle susceptibility to BR phenotypic correlation,the boxplot has been further confirmed.(6)Through analysis these SNPs by the Rice Xpro Website,two candidate gene Os05g32710 and Os11g28530 were regulated by BR,and there are non-synonymous SNPs appeeared。The expression level are changed after BR treatment。Study assumes that the two genes take an important role in the regulation of rice leaf angle susceptibility to BR。Therefore,further research will be focus on the two genes,through further sequencing and function verification to analysis the two genes regulation effect.In this study,the genetic effect of rice leaf angle sensitivity to BR presents different inheritance patterns,the most significant SNPS detected by GWAS is closely associated w ith gene controlled target traits.In this study the SNP markers exploed in this study can b e used on rice plant improvement,and the genetic effect of the SNP markers are importan t genetic resource in the process of improvement of rice breeding.Future research will also focus on the gene Os05g32710 and Os11g28530 as candidate genes for deeper sequencing and functional verification work.