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Objectives: To understand the genetic mechanism of thickness of pod canopy in B.napus and identify the candidate genes regulating thickness of podcanopy(TPC)through GWAS.Methods: Totally 358 B.napus were collected in the study and cultivated in southwest university of Beibei,Chongqing,China in 2015 and 2016.SNP genotyping was performed using the Brassica 60K Illumina SNP array,and significant associated SNP loci were identified.Results: The rapeseed thickness of pod canopy is an important morphological trait providing important contribution to yield.A total of 6 significant SNPs were identified,each of them explained 5.94%-29.05%of phenotypic variation,respectively.Functional annotation of genes within the LD intervals containing significant markers showed that several genes involved in regulation of cell organization and biogenesis,floral meristem development,number of silique,and multicellular organismal development existed,such as NSN1,TPST,and SAC1,which might result in the variation of TPC through affecting the growth and development of flower or silique in B.napus.These loci and genes could be regarded as important candidate regions and genes for TPC of B.napus.These results provide insight into the genetic basis of the TPC trait in rapeseed and might facilitate marker-based breeding for improvements in plant architecture.Conclusions: According to genome-wide association study,some candidate genes regulating TPC,including NSN1,TPST,and SAC1,were found.This study was useful for further gene identification and function analysis.