| Rice is one of the important ration crops in China.After two green Revolutions,the rice yield has been steadily improved,and the goal of genetic improvement of rice has changed from high yield to both high yield and good quality.Chalkiness is one of the most important quality traits of rice,which directly affects the quality of rice processing,appearance and cooking and eating.Therefore,mapping QTL for chalkiness in rice is of great significance for cloning chalkiness control genes and clarifying the genetic mechanism of chalkiness.In our previous study,F2 and BC1F2 populations were constructed from low chalkiness japonica rice material Shuijing 3 and high chalkiness japonica rice material Lamujia,and two QTL loci controlling chalkiness in japonica rice were mapped using QTL-seq combined with molecular markers.According to the transcriptome and resequencing data,the genes in the target region were analyzed to predict the candidate genes of this QTL,which laid a foundation for fine mapping and cloning of chalkiness regulation genes in japonica rice.Specific research results are as follows:1.According to QTL-seq study results of F2 population in previous laboratory,chalkiness related QTL existed on chromosome 8.In this study,we identified the chalky QTL(q CR8)on chromosome 8 of 200 F2 strains by molecular marker mapping and narrowed the candidate range to 0.8 Mb(17.7 Mb-18.5 Mb).The peak LOD of this QTL was 7.08.The phenotypic variance explained(PVE)was 15.9%.2.Combined with the transcriptome sequencing gene expression analysis results of Lamujia and Shuijing 3 and 36 germplasm resources with different chalky grain rate and the functional analysis of resequencing gene variation loci of parents,60 genes in the q CR8 range were screened,and finally 15 candidate genes for q CR8 were obtained.3.BC1F2 population was constructed by backcrossing the extremely low chalkiness single plant,which was similar to the low chalkiness parent Shuijing 3,with the high chalkiness parent Lamujia.The chalkiness single plant had a continuous distribution, the lowest was 7.52%,the highest was 100%,and the chalkiness rate was skewed to the high chalkiness parent.QTL-seq sequencing was used to analyze the mixed DNA of 25 plants at both ends of the chalkiness grain rate distribution in BC1F2 population.Five chalkiness related QTLs were detected on chromosome 1,2,5,6 and 10,respectively.The QTL on chromosome 1(q CR1)was repeatedly detected in F2 and BC1F2 populations in the same environment.4.Designed and screened polymorphic primers within the q CR1 mapping interval detected by QTL-seq based on parental resequencing results.The chalkiness QTL on chromosome 1 of 213 BC1F2 strains was verified by molecular markers and the candidate interval was reduced to 0.2 Mb(6.9 Mb-7.1 Mb).The peak LOD of this QTL was 9.80 and the phenotypic variance explained(PVE)was 19.8%.5.Combined with transcriptome sequencing gene expression analysis and resequencing gene mutation site function analysis,27 genes contained in the q CR1 range were screened,and finally 13 candidate genes for q CR1 were obtained. |
