Genome-Wide Association Analysis Of Panicle Length And Candidate Gene Validation In Rice

A lot of attention has been paid to improve crop production during plant breeding.The rice yield is closely related with panicle traits.The panicle length,which has been widely studied during breeding practice,takes important part of rice panicle traits.However,limited variations are identified in rice panicle length when compared with wild rice.Therefore,new genes related to panicle length are required for further improving of rice production.The panicle length in rice is a complex quantitative trait and is susceptible to environment.The genome wide association study(GWAS),which scans genetic variation information in a genome-wide scale,is not only suitable for traits controlled by a single gene but also can be better used to analyze complex characters.In this study,panicle length of 627 varieties in Hangzhou and Hainan were analyzed by GWAS,using mixed linear model(MLM)at-lg P>6,based on SNPS markers from 627 resequencing varieties.Then candidate genes were validated using bioinformatics and chromosome segment substitution lines(CSSL).These results are as follows:1.Panicle length showed difference in phenotype according to different light environment.The panicle length under long-day environment(Hangzhou)was longer than that under short-day environment(Hainan).Different environment also affected the GWAS analysis results of panicle length.The GWAS peak level identified in short-day environment was absent in short-day environment.However,when the population structure under short-day environment was separated into indica and japonica,the position represented.The result indicated that simplified group structure analysis can be used when the traits were complex or vulnerable to environment.2.According to the functional annotation and expression analysis,genes were obtained within a 200-kb genomic region(± 100 kb from the peak SNPS identified under long-day environment),and the result showed that three closely linked candidate genes(PL1,PL2 and PL3),which were related to gibberellin synthesis.Expression profiles analysis showed that PL1 and PL2 were mainly expressed in panicle and PL3 was mainly expressed in root,followed by panicle.3.We obtained CSSL_N by introducing the japonica(NPB)fragment,containing the candidate genes,into 93-11(indica).Meanwhile,CSSL_K was obtained by introducing the indica(Kasalath)fragment into NPB.CSSL_N exhibited significant increase in panicle length while CSSL_K exhibited significant decrease in panicle length.4.The phenotypic analysis was performed on the corresponding CSSL.CSSL_N showed increased rice yield per plant with risen plant height,lessen tillering,increased leaf length,slender grains and higher grain number per spike.CSSL_K showed decreased rice yield per plant with reduced plant height,increased tillering,decreased leaf length,shorten grain length and lower grain number per spike.5.The gibberellin(GA)content in CSSL_N was analyzed.Increased bioactive GA content accumulation was detected in CSSL_N.The result indicated that increased GA content may contribute to panicle length increase.6.The result of GA treatment anlysis reveal that CSSL_N showed weaker response to different concentration of GA(0?mol/L,50?mol/L,100?mol/L and 150?mol/L)when compare with 93-11 during seedling stage.Exogenous GA3 spray treatment on the mature CSSL_N showed similar result.These results suggested that the japonica genotype showed weaker response to GA.