Fine Mapping Of QGL1.1,a QTL For Grain Length In Rice(Oryza Sativa L.)

Grain weight and grain size are typical quantitative traits,which are closely related to the yield and quality of rice.Identification of quantitative trait loci?QTL?for grain weight and grain size is of great significance to reveal their genetic mechanism in rice.In the previous study,two minor QTL for1000-grain weight?TGW?were dissected in an 835.2-kb region on the long arm of rice chromosome 1.Of which,qTGW1.1b was mapped in the 521.8-kb interval of RM11554-RM11569.The Milyang 46allele could significantly increase grain length?GL?and TGW by 0.017 mm and 0.06 g,respectively.In this study,qTGW1.1b was validated and fine mapped using new mapping populations,followed by candidate gene analysis.The main results were as following:1.Validation of qTGW1.1bTwo plants carrying qTGW1.1?RM11437-RM11615?and qTGW1.2?RM11615-RM11800?,respectively,were selected from a BC₂F₉ population of Zhenshan 97³/Miyang 46.They were crossed and produced three sets of F_5:6 near-isogenic lines?NILs?.Highly significant differences for TGW,GL and grain width?GW?between the two homozygous genotypic groups were detected in Y1 segregating in the interval Wn28826-RM1231.The additive effects were 0.13 g,0.023 mm and 0.008 mm,respectively,and the increased allele were all from Milyang 46.In Y2 that segregated in Wn28990-RM1231 interval,Milyang 46 allele significantly enhanced GL by 0.015 mm.No significant difference for three traits was identified in Y3 with the segregating region of interval Wn29154-RM1231.The effect and the allele direction of QTL were consistent with qTGW1.1b.Therefore,qTGW1.1b was narrowed to a 210.2-kb interval between Wn28944 and Wn29154.2.Fine mapping of qGL1.1Two plants carrying heterozygous segments in the region of Wn28826-RM1231 were selected from the F₅ population where Y1 was derived.Six sequential residual heterozygotes carrying smaller heterozygous segments overlapped in the target region were identified and subsequently developed six sets of NILs.In LP4,which segregated in Wn29048-Wn29125 interval covering qTGW1.1b,significant differences for GL and TGW between two parental genotypic groups were detected in Lingshui and Hangzhou trials.Whereas marginal effect were found only for GL in LP5 in Hangzhou trial,indicating that the segregating interval of Wn29125-RM1231 might contain both qTGW1.1b and another tightly-linked QTL in repulsion phase.As a result,qTGW1.1b was delimited into a 76.8-kb region flanked by Wn29077 and Wn29154.Considering that qTGW1.1b stably showed significant effect to GL but not to GW in both previous and this study,qTGW1.1b was renamed as qGL1.1.3.Candidate gene analysis of qGL1.1A total of eight annotated genes were predicted in the target region.Among them,ORF6 and ORF7failed to obtain PCR products,while no sequence variation in coding region between parantal alleles were found in other six genes.The quantitative Real-time PCR and RNA-seq revealed that the transcript level of ORF4,encoding a dehydrin family protein?RAB25?,showed significant difference between NIL^ZS97 and NIL^MY46.Totally,1409 differentially expressed genes between NIL^ZS97 and NIL^MY46 were identified.As compared to NIL^ZS97,the numbers of differentially expressed genes up-and down-regulated in NIL^MY46 were 1196 and 213,respectively.The KEGG pathway enrichment exhibited that the largest proportion of differentially expressed genes were involved in the Mitogen-activated protein kinase?MAPK?signal pathway.It suggested ORF4 might be the candidate gene for qGL1.1,and qGL1.1 probably regulated grain size through MAPK signal transduction pathway in rice.