Genetic Basis Underlying The Correlations Among Growth Duration And Yield Traits Revealed By GWAS And Identification Of New Genes Related To Panicle Number In Rice(Oryza Sativa L.)

Rice is one staple food crop.Yield improvement of rice is essential to the world food security.Yield is the complex trait determined by many yield components and by their interactions with environment.In order to enrich the theoretical basis and gene resources for improvement of yield,it is significant to identify more genes related to yield factors and analyze the genetic basis underlying the correlations among yield factors and their interaction with environment.Here,we carried out genome wide association studies(GWAS)of panicle number using the highly diverse and representative mini core collection(MCC)and expanded mini core collection(EMCC),and high-quality single nucleotide polymorphism(SNPs).Our study investigated the genetic basis of panicle number,verified the new candidate genes regulating panicle number,and revealed the genetic basis underlying the correlations among heading date(HD),panicle number per plant(PN),grain number per panicle(GNP)and kilo-grain weight(KGW).The main results are as follows:Using 12 datasets of PN phenotyped under two environments in full,indica and japonica population of MCC and EMCC,we detected 138 quantitative trait loci(QTLs)based on GWAS.Among them,56 QTLs can be detected in at least two of 12 data sets,23 ones were environment-stable,and 11 ones can be detected in both subspecies.The distribution of different alleles in landrace varieties and improved varieties showed that alleles with small effect in stable QTLs were preferred to be used in the breeding,and the QTLs with the effect of three or more than three PN were not intensively used.The candidate genes in seven important QTLs were identified by an integrated strategy including the analyses on haplotype,Ho-LAMap,pathway,expression pattern and T-DNA mutants.This helped to decrease the candidate gene number of qPN2-1 and qPN7-1 to 14 and 10 respectively,verify one cloned gene OsARF25,and identify two new candidate genes(ETR3 and GR).ETR3 belongs to the same gene family with ETR2 which was cloned and was characterized as regulating panicle number of rice.GR encodes a gibberellin receptor and regulates the panicle number,plant height,panicle length and secondary branch number.We investigated HD,PN,GNP and KGW of MCC in both long-day and short-day environments.There were clear positive correlations between heading date and grain number per panicle,negative correlation between grain number per panicle and panicle number,as well as different degrees of correlation among other traits in different subspecies and environments.Based on GWAS of four traits,we detected 46 pleiotropic QTLs,in which 47 pleiotropic genes in 15 pleiotropic quantitative trait loci(pQTLs),18 pleiotropic genes containing pleiotropic SNP in 8 pQTLs,27 pQTLs with LD r2 higher than 0.2.And 39 pairs of interactive genes from 8 metabolic pathways.The numbers of pleiotropic SNPs/genes,pleiotropic QTLs or interactive genes among different traits represented high correspondence with the strength of their phenotypic correlations.Thus,the correlation among traits should attribute to three genetic bases including the pleiotropy,LD hitchhiking effect and gene interaction.The contribution of three genetic bases on trait correlation from strong to weak were pleiotropic gene,interactive gene and pleiotropic QTL with LD.Distribution of SNP or haplotypes within QTLs related to three genetic bases in landrace varieties and improved varieties revealed that:selection for pGenes or iGenes needed to focus on the genotypes with weak effects when two traits showed disadvantageous negative correlations or on genotypes with strong effect when two traits had advantageous positive correlations;in pQTLs,genotypes with disadvantageous negative correlations were developed by breaking the linkage between two genes controlling different traits,except for the selection of genotypes with weak effect.In summary,on the one hand,we investigated the genetic basis of panicle number,evaluated the breeding value of QTLs with different effects,and identified the genes of panicle number.They will provide theoretical guidance and gene resources for cloning of new gene and genetic improvement of varieties.On the other hand,our research depicted the genetic basis of the correlation among four agronomic traits,as will promote harmonious and high efficient improvement of important agronomic traits and breed improvement efficiently.