S01 - Session O3 - RNA-seq analysis of tomato genotypes resistant to bacterial spot (Xanthomonas perforans) race T4

Authors: Dilip Panthee *, Rui Shi

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato caused by multiple species of Xanthomonas . We performed an RNA-Seq analysis of three tomato genotypes with different levels of resistance to Xanthomonas perforans race T4 to study the differentially expressed genes (DEGs) and transcript-based sequence variations. Analysis between inoculated and control samples revealed that the resistant Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible tomato ( S. lycopersicum L) breeding line NC 714 (373), and intermediate tomato breeding line NC 1CELBR (154). Gene functional analysis based on Gene Ontology (GO) terms revealed that more GO terms (51) were enriched for upegulated DEGs in the resistant genotype PI 270443, and more downregulated DEGs (67) were enriched in the susceptible genotype NC 714. DEGs in the biotic stress pathway showed more upregulated biotic stress pathway DEGs (67) for PI 270443 compared to more downregulated DEGs (125) in the susceptible NC 714 genotype. Resistant genotype PI 270443 had three upregulated DEGs for PR-protein, and susceptible genotype NC 714 has one downregulated R gene. Sequence variations called from RNA-Seq reads against the reference genome of susceptible Heinz 1706 showed that chromosome 11, which has multiple reported resistance QTLs to BS race T4, was identical between the two resistant genotypes, PI 270443 and NC 1CELBR, suggesting that these two genotypes share the same resistance QTLs on this chromosome. Several loci for PR-resistance proteins with sequence variation between the resistant and susceptible tomato genotypes were identified near the known Rx4 resistance gene on chromosome 11.