Associative Transcriptomics of Pathogen Associated Molecular Pattern (PAMP) Responses in Brassica napus

Pathogen resistance and immune responses are highly polymorphic between different cultivars of Brassica  napus (Lloyd, 2013). In order to identify the genetic polymorphisms underlying this variation and find potential markers for pathogen resistance, association transcriptomics of defense-related traits was used in an Illumina-sequenced panel of diverse B. napus cultivars. Associative transcriptomics uses whole trancriptome sequencing to identify single nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) between diverse ecotypes and correlates this with phenotypic variation to identify trait-linked markers (Bancroft, 2012). Variations in the oxidative burst in response to the bacterial pathogen-associated molecular patterns flg22 and elf18 and in resistance to the pathogens Pseudomonas syringae and Botrytis cinerea were scored in a diversity set of 95 cultivars. Association transcriptomics identified over 2000 significant SNP associations and 8000 significant GEM markers correlated with variation in the defense traits studied. Annotation of the genes identified as markers for the traits indicate an enrichment of genes annotated in the plant model Arabidopsis thaliana (a relative of B. napus) as being involved in response to biotic and abiotic stresses. Associative transcriptomics studies, as performed here, could help identifying markers for disease resistance crop breeding in the future.