Candidate resistance genes selection and transcriptome analysis for the early responses to Plasmopara viticola infection in grape cultivars

Abstract

Grape downy mildew (Plasmopara viticola) is one of the most destructive diseases of grapevine worldwide. In order to better understand the cellular processes involved in resistance to downy mildew, leaves of Vitis vinifera cv. ‘Centennial Seedless’ (susceptible) and Vitis labrusca×Vitis riparia cv. ‘Beta’ (resistant) were inoculated with Plasmopara viticola, and were used in the Illumina HiSeq™2000 platform for deep transcriptome sequencing. We performed transcriptome analysis and identified a total of 1091 differentially expressed genes (DEGs) in the disease-resistant cultivar and 849 in the susceptible cultivar. To increase understanding of the DEGs, the datasets were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genome (KEGG) database. Most of them were found to be associated with plant–pathogen interaction, flavonoid synthesis, phenylpropanoid synthesis metabolism and phytohormone signal transduction. Moreover, transcription factors ERF, MYB, WRKY, and bHLH associated with disease resistance were screened. A total of 196 genes were identified as the candidate resistant genes. The expression of 18 differentially expressed genes was detected by RT-qPCR. Finally, the pattern of differentially expressed genes was consistent with the result of transcriptome sequencing. The present study identified several candidate resistance genes and signal transduction pathways that may contribute to downy mildew resistance in grapes.