Genome-wide Association Studies For Grain And Panicle Traits In Rice

Rice is one of the most important food crops in the world.The yield and quality of rice have a great impact on human living standards.The grain traits of rice mainly include grain length,grain width,length/width ratio,etc.,which are quantitative traits and are controlled by different genetic systems such as embryo,endosperm and maternal plants,are important traits affecting rice yield and quality.Elucidating the genetic regulation mechanism of rice grain shape is valuable to improve the yield and quality of rice.Genome-wide association analysis is an analytical method that has recently begun to be applied in plant quantitative traits research and plant breeding.It identifies the relationship between a trait within a population and a genetic marker or candidate gene based on linkage disequilibrium.In this study,phenotypic measurements of rice grain and panicle traits are carried out to screen elite varieties of granules,and a genome-wide association analysis(GWAS)is used to excavate and control grain type or panicle loci for later rice breeding and research.The main results of this study are as follows:1.A total of 413 sequenced rice varieties originated from the world are used after planting and harvesting screening,rice grain type gene identification is carried out with grain length and grain weight as indicators,and the results shows that rice in japonica and indica populations has extensive genetic variation and diversity among varieties.Some rice varieties with ideal grain shape are identified,such as NSFTV271,NSFTV376,NSFTV270,NSFTV87 and NSFTV264.The rice varieties with ideal panicle traits includes NSFTV139,NSFTV150,NSFTV178,etc.2.The GWAS analysis of rice grain shape is carried out by using the effective mixed model(EMMAX).The site containing two or more consecutive SNPs was defined as a grain type locus.The results showed that after the phenotypic analysis in 2015,7 rice grain type loci(qGW5,D61,GS3,qGL6,qTGW3,qTGW6,qTGW10).After 2016 phenotypic analysis,a total of 12 rice grain type loci(qGW5,qGW8.2,qGW12.2,qGL2,qGS3,SRS3,qGS5,qGL7,qGL9,q TGW3,q TGW6,qTGW10,qTGW11)were detected.Compared with previous reports,the multiple loci mapped in this study are similar to the physical locations of previously reported rice grain-type regulatory genes.Meanwhile,only one rice panicle length locus(PL4)was detected with the phenotypic observation in 2018.3.The above-mentioned loci containing>30 consecutive SNPs associated with the grain shape,and the loci detected both in 2015 and 2016 are regarded as key sites of rice grain type.The results showed that three key loci for grain traits were identified and the candidate genes were predicted for one key site of qTGW10.4.The candidate genes LOC_Os10g38700 and LOC_Os10g38850 located on chromosome 10 were suggested as candidate genes for qTGW10.RT-qPCR analysis suggested that LOC_Os10g38850 expression was involved in panicle development.The candidate gene LOC_Os4g08170 located on chromosome 4 were assigned as the candidate gene for PL4.The ideal rice grain and panicle traits resources selected by this study and the key loci for rice grain and panicle traits identified by GWAS can provide theoretical and material basis for rice high-yield and high-quality variety breeding.