Genetic Analysis And Fine Mapping Of QTL Qpl6-3 And Qpl6-5 For Panicle Shape In Rice

Rice panicle shape is a complex quantitative trait and is also the important component of yield.Panicle traits mainly include panicle length,grain number per panicle,primary branch number and secondary branch number.These traits coordinate with each other,affecting the spike shape and regulating rice yield.Until now,the molecular mechanism of panicle shape such as panicle length and grain number is still not clear.Mapping and cloning more main QTL for panicle shape,which is of great significance to deepen the understanding of spike development and provide favorable genes for molecular improvement of rice panicle shape.A high-density genetic linkage map of F₂ population of Nipponbare/R1128 was constructed by high-throughput sequencing technology.QTL mapping was carried out on four panicle related traits such as panicle length,grain number,primary branch number and secondary branch number.Multiple sets of backcross overlapped populations were used to decompose the panicle QTL clusters on the chromosome 6,and two main QTL qpl6-3 and qpl6-5 were fine mapped.The specific location and genetic effects of qpl6-3 were analyzed in detail,and the candidate genes of qpl6-5were predicted.The effect of qpl6-5 under the near isogenic line background was evaluated.The concrete results are as follows:1.Total of 6819 bin markers from F₂ population Nipponbare/R1128 were developed,and then a high density genetic linkage map with 1346.59cM length was constructed.The average distance between each bin was 0.197cM.2.Panicle length,primary branch number,secondary branch number and grain number of 781 separate plants were investigated in the F₂ population.Total of 31QTLs were mapped by using the composite interval mapping method,and some important QTL clusters for panicle length and kernel number per spike within the range of 4.81-28Mb of the chromosome 6 were detected too.Three new QTL qpl12-1,qgn11-1 and qpbn10-1 were also found in the F₂ population.3.Five sets of backcross isolate populations from R1128 and Nipponbare were used for the decomposition of the key QTL clusters on chromosome 6.A total of 10QTLs related to grain number,panicle length,primary branch number and secondary branch number were mapped.The location of most QTLs were overlapped with the QTL detected in F₂ population,and two main effect QTLs qpl6-3 and qpl6-5 for panicle shape were excavated.4.The main effect QTL qpl6-3 was mapped in many environments and different genetic groups,which explained 12.69%of the phenotypic variation rate,and the synergistic allele came from the large spike parent R1128.A set of secondary populations containing 384 individuals was used to define qpl6-3 in the 1.3Mb physical interval of chromosome 6,located between RM20118 and RM003,and only600Kb from the centromere region.Data analysis showed that the genetic distance between marker RM20118 and RM003 was only 1.4cM,but the area was equivalent to 928.6 Kb/cM after conversion.It could be concluded that severe suppression of recombination occurred in this area.Bioinformatics analysis showed that there were no reports of panicle length QTL in the 1.3Mb physical interval on chromosome 6.5.The main QTL qpl6-5 of panicle shape was located in the 570Kb interval of long arm of chromosome 6,which could explain 28.37%of panicle length phenotypic variation,and the allele of R1128 showed dominance effect for the large spike.The qpl6-5 was fine mapped to the 22Kb interval by using a set of secondary population containing 1006 single plants.The database alignment shows that there are 4predictive genes in this range,of which LOC_Os06g45460 encodes a protein containing the F-box domain.Sequence comparison and expression analysis showed LOC_Os06g45460 is probably the candidate gene of qpl6-5,while LOC_Os06g45460is identificated to the APO1 gene for the inflorescence structure.6.The near isogenic lines of qpl6-5 were developed,and multiple agronomic traits related to panicle shape were investigated for 2 years.Phenotypic evaluation showed the allele qPL6-5 from the R1128 is impactful to the panicle length,grain number,primary branch number,secondary branch number and plant height.However,the panicles per plant,seed setting rate,heading date,panicle exsertion length,grain shape,chalkiness degree and grain weight are not significantly changed between the NIL-qpl6-5 and NIL-qPL6-5.The comprehensive analysis of gene structure and phenotypic evaluation show that the main effect QTL qPL6-5 may be a new allele of APO1.