Gene profiling in partially resistant and susceptible near‐isogenic tomatoes in response to late blight in the field

Abstract

In order to better understand resistance to Phytophthora infestans in tomato, we compared the global gene expression of the susceptible tomato, M82, with its more resistant near-isogenic line, 6-2 (IL6-2), under field conditions using a microarray with more than 12 800 tomato expressed sequence tags (ESTs). Because variance in the field was a major concern, we investigated the likelihood of false positives or false negatives and demonstrated that either probability was very low. The two isolines had indistinguishable constitutive gene expressions prior to inoculation. However, a few genes were particularly prone to variation in both isolines in the absence of P. infestans. Included among these genes were catalase, genes coding for pathogenesis-related proteins, endochitinase and cytochrome P450. In response to inoculation with P. infestans, a time course of gene expression identified 1248 transcripts that were similarly induced or repressed in each line, and 991 that were differentially expressed between the two lines. These differences provide hypotheses to explain the difference in resistance between the two isolines. For example, one hypothesis is that genes up-regulated in IL6-2 in response to inoculation with P. infestans, but not up-regulated in M82, contribute to the resistance in IL6-2. Using virus-induced gene silencing (VIGS), we were able to partially silence two such genes-one encoded a protein with homology to an R gene with the Toll/interleukin-1 receptor-nucleotide-binding site-leucine-rich repeat (TIR-NBS-LRR) motif (37O19) and the other encoded a peroxisomal membrane protein (35P7). Partial silencing of 37O19 reduced the resistance in IL6-2 (P = 0.001), but had no effect on the response of M82. Partial silencing of 35P7 reduced the resistance in IL6-2 moderately significantly (P = 0.067), but had no effect in M82. We expect that hypotheses developed from this gene expression study performed under field conditions will provide an important avenue to an accurate understanding of the genes involved in resistance.

Analysis of the tomato leaf transcriptome during successive hemibiotrophic stages of a compatible interaction with the oomycete pathogen Phytophthora infestans

“…After pathogen infection, we noted a decrease in transcript abundance of genes associated with the production of ROS, which continued through the transition stage. A similar decline in ROS during the biotrophic stage was detected in a study investigating gene expression conducted in the field in the highly compatible P. infestans –tomato interaction ( US17 ‐M82; Cai et al ., ). This contrasts with the P. infestans ( US17 )–tomato interaction involving the partially resistant IL6‐2, where ROS were highly expressed as early as 36 hai (Cai et al ., ).…”

“…A similar decline in ROS during the biotrophic stage was detected in a study investigating gene expression conducted in the field in the highly compatible P. infestans –tomato interaction ( US17 ‐M82; Cai et al ., ). This contrasts with the P. infestans ( US17 )–tomato interaction involving the partially resistant IL6‐2, where ROS were highly expressed as early as 36 hai (Cai et al ., ). Recently, it has been shown that the cysteine protease effector HopN1 of the hemibiotrophic pathogen Pseudomonas syringae pv.…”

Transcriptome analysis highlights preformed defences and signalling pathways controlled by the prAe1 quantitative trait locus (QTL), conferring partial resistance to Aphanomyces euteiches in Medicago truncatula

“…The identification of a large set of genes more highly expressed in one NIL versus another is not common. A comparison of resistant and susceptible NILs of tomato indicated that their transcriptomes were indistinguishable in non-inoculated lines, whereas several hundreds of DEGs were revealed after inoculation with Phytophthora infestans (Cai et al, 2013). Similarly, DEGs between NILs were identified only after inoculation of Fusarium graminearum in wheat (Schweiger et al, 2013) or in maize (Ye et al, 2013).…”

Transcriptional dynamics of Phytophthora infestans during sequential stages of hemibiotrophic infection of tomato

“…The P. infestans –tomato interaction can be highly compatible, partially compatible or incompatible, and these differences can be a consequence of both the plant genotype and whether or not the P. infestans strain is tomato specialized (Smart et al ., ). Importantly, it has been demonstrated previously that the P. infestans –tomato interaction is characterized by a prolonged biotrophic phase and a distinct necrotrophic phase at later stages of infection with tomato‐specialized isolates (Berg, ; Cai et al ., ; Smart et al ., ; Vega‐Sanchez et al ., ). We analysed the transcriptomes of the tomato‐specialized P. infestans isolate ( US‐11 ) and its host tomato (M82) in a highly compatible interaction using RNA sequencing (RNA‐Seq), in order to identify suites of co‐expressed genes that could be associated with each stage of the interaction and to infer regulated pathways from both the pathogen and host plant.…”

“…The subsequent necrotrophic phase is characterized by hyphal ramification and water soaking, followed by necrosis of the tissue (Grenville-Briggs et al, 2005). However, marked differences in the duration of both biotrophic and necrotrophic growth, depending on the host-P. infestans isolate interaction, have been reported previously (Berg, 1926;Cai et al, 2013;Smart et al, 2003;Vega-Sanchez et al, 2000). There is an extended period of biotrophy between tomato and certain tomato-specialized isolates of P. infestans, (Berg, 1926;Cai et al, 2013;Smart et al, 2003;Vega-Sanchez et al, 2000).…”