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Objectives: To understand the genetic mechanism of S.sclerotiorum resistance in B.napus and identify the candidate genes related with resistance to S.sclerotiorum through GWAS and transcriptome analysis.Methods: Totally 347 B.napus were collected in the study and cultivated in southwest university of Beibei,Chongqing,China in 2012 and 2013,the Sclerotinia resistance of detached stem inoculation was evaluated according to Mei et al.(2012).SNP genotyping was performed using the Brassica 60K Illumina SNP array,and significant associated SNP loci were identified.In addition,transcriptome sequencing of stem in resistant and susceptible B.napus after 48 h inoculation withS.sclerotiorum was conducted.Results: A total of 17 significant associations were identified for stem resistance on A8 and C6.SNPs on A8 were located in a 409 kb haplotype block and those on C6 were consistent with previous QTL mapping.After B.napus infected by S.sclerotium,photosynthesis,glyoxalic acid and carbon metabolism were suppressed,while secondary metabolites,sulfur metabolism,especially GSH and glucosinolates were synthesized and immune system was activated,and these systems played an important role in defense response.Numerous ERF and WRKY genes were also found and mostly were up-regulated.Besides,specific genes related with jasmonic acid pathway,lignin biosynthesis,defense response,signal transduction and transcription factors responsible for stem resistance were found.Conclusions: Combining the SNP-trait association and transcriptome sequencing results,24 common genes were found,including a tau class glutathione S-transferase(GSTU)gene cluster.This study provides useful insight into the molecular mechanisms underlying the plants response to S.sclerotiorum.