Expression profiling in Pinus radiata infected with Fusarium circinatum

Fusarium circinatum is the causal agent of pitch canker, a serious disease that affects numerous Pinus species worldwide. Pinus species have varying degrees of susceptibility to this pathogen, being Pinus radiata one of the most susceptible species. Quantitative phenotypic variation and intermediate heritability in response to F. circinatum have been observed by studies of controlled inoculations in several families of P. radiata, suggesting the existence of a genetic component to resistance. Recent experiments in conifer genomics have identified several genes with functions that confer resistance to various biotic and abiotic stresses. In this investigation, high-throughput mRNA sequencing (RNA-seq) is used to identify differentially expressed genes during the interaction of P. radiata with F. circinatum at several time points including uninfected plants at 2, 6, and 12 days post inoculation (dpi) in two contrasting genotypes. The 470,612 Roche 454-HQ reads were de novo assembled into a transcriptome containing 26,215 unigenes with an average length of 1523 bp. Functional annotation indicated that 86% had significant protein alignments and 23,897 (91%) could be assigned to one or more Gene Ontology (GO) terms. Pairwise comparisons of the differentially expressed genes, up and downregulated between the inoculated genotypes, wounded and unwounded control for the resistant genotype at time 2, 6 and 12 dpi were performed. A total of 39,242 and 51 commonly upregulated genes in response to pitch canker infection at 2, 6, and 12 dpi, respectively, during three pairwise comparisons were identified. This RNA-seq analysis identified a total of 293 putative candidate genes and validated a set of genes involved in cellular processes and defense mechanisms, among them, 32 upregulated genes have been associated with defense response in plants against pathogens, thereby providing the first comprehensive evaluation of the putative mechanisms of F. circinatum resistance in pine.