Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4.

Rui Shi,Dilip R Panthee

doi:10.3390/ijms21114070

Abstract

Bacterial spot (BS) is one of the most devastating foliar bacterial diseases of tomato and is caused by multiple species of Xanthomonas. We performed the RNA sequencing (RNA-Seq) analysis of three tomato lines 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 resistant genotype Solanum pimpinellifolium accession PI 270443 had more DEGs (834), followed by susceptible genotype tomato (S. lycopersicum L) breeding line NC 714 (373), and intermediate genotype tomato breeding line NC 1CELBR (154). Gene ontology (GO) terms revealed that more GO terms (51) were enriched for upregulated 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) for the susceptible NC 714 genotype. Resistant genotype PI 270443 has three upregulated DEGs for pathogenesis-related (PR) proteins, 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 chr11, which has multiple reported resistance quantitative trait loci (QTLs) to BS race T4, is identical between two resistant lines, PI 270443 and NC 1CELBR, suggesting that these two lines share the same resistance QTLs on this chromosome. Several loci for PR resistance proteins with sequence variation between the resistant and susceptible tomato lines were near the known Rx4 resistance gene on chr11, and additional biotic stress associated DEGs near to the known Rx4 resistance gene were also identified from the susceptible NC 714 line.

Highlights

Bacterial spot (BS) is a foliar disease of tomato caused by multiple species of Xanthomonas
The resistance level of 30 tomato breeding lines was evaluated by inoculation with BS (X. perforans) race T4 in the greenhouse at Mountain Horticultural Crops Research and Extension Center, Mills River, NC, USA
In exploring RNA sequencing (RNA-Seq) library relationships by using plotting analysis, we found that the expression variation between different tomato lines was much bigger than inoculation treatment within the same tomato genotype based on calculated variation distance

Summary

Introduction

Bacterial spot (BS) is a foliar disease of tomato caused by multiple species of Xanthomonas. Multiple resistance genes and loci for BS have been identified in tomato and have been summarized by Pei et al [3]. Hawaii 7998 is a differential genotype for identifying race T1, which includes Xanthomonas spp.—carrying the avrRxv gene [4]. The dominant allele Rx3 confers resistance in the field, explaining 41% of the phenotypic variation [7] and is considered to be the most effective locus for T1 resistance. It is not clear yet whether rx and Rx3 are alleles of the same gene or closely associated genes on the same chromosome [3]

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