Grey mold, caused by the fungus Botrytis cinerea Pers ex Fr., is one of the most destructive spoilage diseases, severely affecting tomato production in Henan Province, China. Spraying fungicides from the flowering to the harvest stage is a necessary measure to reduce losses associated with B. cinerea infection. However, B. cinerea has developed resistance to fungicides in many countries. Boscalid is a succinate dehydrogenase inhibitor (SDHI) fungicide, and was registered for the control of grey mold. In this study, a total of 269 B. cinerea isolates were collected from tomato in commercial greenhouses in different locations of Henan Province, in 2014 and 2015. The sensitivity and resistance of B. cinerea field isolates were determined based on mycelial growth. The effective concentration 50 (EC50) ranged from 0.11 to 15.92 μg ml−1 and 0.16 to 8.54 μg ml−1, in 2014 and 2015, respectively. The frequency of low resistance to boscalid was 12.6% and 7.6%, and moderate resistance were 2.7% and 1.3%, in 2014 and 2015, respectively. No high-resistant isolates were found in Henan Province, China. Mycelial growth, mycelial dry weight, spore production, and pathogenicity were not significantly different between resistant and sensitive phenotypes of the B. cinerea isolates. The results of cross-resistance test showed no correlation between boscalid and carbendazim, procymidone, pyrimethanil, fluazinam or fluopyram. In this study, the succinate dehydrogenase gene B (sdhB), C (sdhC), and D (sdhD) were analyzed and compared in sensitive, low and moderately resistant B. cinerea isolates to boscalid. Results showed point mutations occurred simultaneously at sdhC amino acid positions 85 (G85A), 93 (I93V), 158 (M158V), and 168 (V168I) in 4 out of 10 sensitive isolates, 23 out of 26 low and 5 out of 5 moderately resistant B. cinerea isolates to boscalid. No point mutations were found in the sdhB and sdhD genes of all isolates. Furthermore, no point mutations were found in sdhB, sdhC and sdhD genes in 3 out of 26 low resistant B. cinerea isolates to boscalid. Therefore, we speculate the simultaneous point mutations in the sdhC gene may not be related to the resistance of B. cinerea to boscalid. These results suggested that there might be a substitution mechanism for the resistance of B. cinerea to the SDHI fungicide boscalid.

Background Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reductions every year. The application of fungicides is the most common and effective method of controlling Alternaria-caused diseases. The differentially expressed transcripts of A. solani infecting potato were identified, revealing a group of valuable candidate genes for a systematic analysis to increase the understanding of the molecular pathogenesis of A. solani, and providing scientific data for formulating additional measures to prevent and control potato early blight. In this study, a deep RNA-sequencing approach was applied to gain insights into A. solani pathogenesis. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected with A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis, and compared to the transcriptome obtained 0 dpi. Results A total of 4430 (2167 upregulated, 2263 downregulated), 4736 (2312 upregulated, 2424 downregulated), and 5043 (2411 upregulated, 2632 downregulated) genes were differentially expressed 3, 4 and 5 dpi, respectively, compared with genes analysed at 0 dpi. KEGG enrichment analysis showed that genes involved in the pathways of amino acid metabolism, glucose metabolism, and enzyme activity were significantly differentially expressed at the late infection stage. Correspondingly, symptoms developed rapidly during the late stage of A. solani infection. In addition, a short time-series expression miner (STEM) assay was performed to analyse the gene expression patterns of A. solani and Profile 17 and 19 showed significant change trends 3, 4 and 5 dpi. Both profiles, but especially Profile 17, included enzymes, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in late fungal infection. Furthermore, possible candidate effectors were identified through the adopted pipelines, with 137 differentially expressed small secreted proteins identified, including some enzymes and proteins with unknown functions. Conclusions Collectively, the data presented in this study show that amino acid metabolism, and glucose metabolism pathways, and specific pathway-related enzymes may be key putative pathogenic factors, and play important roles in late stage A. solani infection. These results contribute to a broader base of knowledge of A. solani pathogenesis in potato, as indicated by the transcriptional level analysis, and provide clues for determining the effectors of A. solani infection.

Background Alternaria solani (A. solani), the main pathogen of potato early blight, causes serious yield reduction every year. However, the molecular interaction between A. solani and its host, potato, is largely unknown. In this study, a deep RNA-sequencing approach was applied to gain insights into the pathogenesis of A. solani. At 3, 4, and 5 days post inoculation (dpi), RNA samples from the susceptible potato cultivar Favorita infected by A. solani strain HWC-168, were sequenced and utilized for transcriptome analysis. Results A total of 4430 (2167 up-regulated, 2263 down-regulated), 4736 (2312 up-regulated, 2424 down-regulated), and 5043 (2411 up-regulated, 2632 down-regulated) genes were differentially expressed at 3, 4 and 5 dpi, respectively. KEGG enrichment analysis showed that the genes of amino acid metabolism, glucose metabolism, and enzyme activity were significantly expressed at the late infection stage. Correspondingly, the symptoms developed rapidly during the late stage infection of A. solani. In addition, the short time-series expression miner (STEM) assay was conducted to analyze the gene expression patterns of A. solani and it was found that profile 17 and 19 showed significant changing trends at 3, 4 and 5 dpi. Both profiles especially profile 17 contained a large number of enzymatic proteins, including transferases, oxidoreductases, hydrolases and carbohydrate-active enzymes (CAZYmes), which may play important roles in the late process of fungal infection. Furthermore, we screened possible candidate effectors by an adopted pipeline and found 137 differentially expressed small secreted proteins, which included some enzymes and unknown function proteins. Conclusions Collectively, the data presented in this study showed that amino acid metabolism, and glucose metabolism pathways may be the key metabolic pathways and these specific enzymes were important at the late stage of A. solani infection. These results contributed to the establishment of a broader knowledge of the pathogenesis of A. solani to potato at the transcriptional level and provided clues for determining the effectors of A. solani.