Mapping Of QTLs For Panicle Size And Grain Width In Rice

Panicle size is a crucial trait that determines rice yield.It is of great theoretical significance and practical value to study panicle size of rice.In previous study,we used Baodali,a large panicle cultivar,and Aigela,a small panicle cultivar,to cross and develop F2 population.QTL analysis revealed that some QTLs related to panicle size,including spikelet number per panicle(SNP),number of primary branches(NPB),number of secondary branches(NSB)and panicle length(PL),were detected in the adjacent intervals on chromosome 7.On this basis,we mapped panicle-size QTL in F2 population again.Then,we screened heterozygotes by linked markers,and developed secondary populations to verify the interval.Finally,fine-mapping,ORF function analysis,sequence alignment were performed for screening candidate genes.The following results were obtained:1.Validation of panicle-related QTLs:Four pancle-size QTL qSNP7,qNPB7,qNSB7 and qPL7 were mapped between RM542 and A28 on chromosome 7 in F2 population.Several residual heterozygotes were screened from a F3 line by linked markers of RM542 and A28 to be developed into F4 segregating lines.Further QTL analysis in a F4 line revealed that these four QTL were detected at the same interval between markers RM542 and A83.Among them,qNSB7 explained 30.74%phenotypic variation with a LOD value of 9.84.qSNP7 explained 24.61%phenotypic variation with a LOD value of 9.65.qNPB7 explained 17.15%phenotypic variation with a LOD value 6.31.And qPL7 explained 18.02%phenotypic variation with a LOD value 6.68.This result was consistent with the conclusion of the correlation analysis that some linked or a pleiotropic QTL affects these traits.2.Fine mapping of qNSB7:We construct a F4 segregating population by screening recombinants that come from the target interval in the same F3 family.Recombinants were screened by the flank markers of RM542 and A28 in F4 lines.A total of 117 recombinants were found.In this interv7al,the markers were further densified by newly developed InDel.By analysis of their recombination sites and phenotypes,qNSB7 and other 3 panicle size QTLs were narrowed to a 74.45 kb region between InDel markers X91 and X54.The results still need to confirm the phenotype of the progeny of the exchange strain.3.ORF Analysis:According to Nipponbare sequence,there are nine ORFs in the target interval.Except ORF5 is a transposon,the rest are expressed proteins.ORF1(LOC_Os07g23880)encodes Glycosyl hydrolase.ORP2(LOC_Os07g23890)encodes a protein containing the F-box protein domain and the unknown functional domain(DUF).ORF3(LOC_Os07g23900)also encodes a protein containing the F-box domain.The tissue expression prediction showed that the expression levels of ORF1 and ORF3 were higher in florescence and young panicle.While ORF2 is highly expressed in mature stage and endosperm.4.ORF sequence alignment:Sequence alignment between parents showed six ORFs have some SNPs leading to missense mutations.ORF1 has four SNPs of nucleotide substitutions in exon leading to amino acid changes.ORF2 has six sites of nucleotide substitutions in exon leading to missense mutations.ORF3 has three sites of missense mutations.ORF4,ORF7 and ORF8 respectively have one SNPs site of missense mutations.Considering gene function annotation,expression prediction and sequence alignment,ORF1 and ORP3 could be the first choice as candidate genes for further study.Grain width is an important factor in determining the grain weight in rice,and effects rice yield and quality.Grain width study has guiding significance for rice breeding.In this study,a short-grain variety Longliheinuo(LLHN),as a donor,was back-cross by a long-grain Indica variety 93-11 to develop a BC3F2 segregating population.QTL mapping revealed that two major QTLs for grain width were detected on chromosome 2 and chromosome 5,respectively.qGW2 was detected between InDel markers K118 and X12 on chromosome 2,with a LOD value of 4.96,explaining 25.84%of the phenotypic variation,which located in the same range of cloned gene GW2.qGW5 was detected between the Indel markers A56 and X25 on chromosome 5,explaining 21.84%of the phenotypic variation with a LOD value of 4.60.This site was located in the region upstream～1M of the known gene GW5/qSW5.It may be a new GW QTL that deserves further study.