title: Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus.
abstract: Brassica napus is one of the most important oil crops in the world, and stem rot caused by the fungus Sclerotinia sclerotiorum results in major losses in yield and quality. To elucidate resistance genes and pathogenesis-related genes, genome-wide association analysis of 347 accessions was performed using the Illumina 60K Brassica SNP (single nucleotide polymorphism) array. In addition, the detached stem inoculation assay was used to select five highly resistant (R) and susceptible (S) B. napus lines, 48 h postinoculation with S. sclerotiorum for transcriptome sequencing. We identified 17 significant associations for stem resistance on chromosomes A8 and C6, five of which were on A8 and 12 on C6. The SNPs identified on A8 were located in a 409-kb haplotype block, and those on C6 were consistent with previous QTL mapping efforts. Transcriptome analysis suggested that S. sclerotiorum infection activates the immune system, sulphur metabolism, especially glutathione (GSH) and glucosinolates in both R and S genotypes. Genes found to be specific to the R genotype related to the jasmonic acid pathway, lignin biosynthesis, defence response, signal transduction and encoding transcription factors. Twenty-four genes were identified in both the SNP-trait association and transcriptome sequencing analyses, including a tau class glutathione S-transferase (GSTU) gene cluster. This study provides useful insight into the molecular mechanisms underlying the plant's response to S. sclerotiorum.
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Lijuan
authors.initials: L
authors.lastname: Wei
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Hongju
authors.initials: H
authors.lastname: Jian
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Kun
authors.initials: K
authors.lastname: Lu
authors.affiliation: Queensland Department of Agriculture and Fisheries (QDAF), Ecosciences Precinct, Brisbane, Old, Australia.
authors.forename: Fiona
authors.initials: F
authors.lastname: Filardo
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Nengwen
authors.initials: N
authors.lastname: Yin
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Liezhao
authors.initials: L
authors.lastname: Liu
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Cunmin
authors.initials: C
authors.lastname: Qu
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Du
authors.affiliation: Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing, China.
authors.forename: Jiana
authors.initials: J
authors.lastname: Li
mesh_terms: D001203:Ascomycota / Q000502:physiology*; D029688:Brassica napus / Q000235:genetics* / Q000378:metabolism / Q000382:microbiology; D060467:Disease Resistance / Q000235:genetics; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D054884:Host-Pathogen Interactions / Q000235:genetics*; D005810:Multigene Family; D018547:Plant Stems / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome
keywords: Brassica napus; Sclerotinia sclerotiorum; association mapping; differential expression