Identification and characterization of nucleotide binding site leucine rich repeats NBS LRR genes and simple sequence repeats SSR markers associated with fungal resistance in grapes vitis vinifera

Abstract

Due to the development of fungal diseases such as powdery mildew (PM) and downy mildew (DM), the productivity of viticulture is on immense loss. Therefore, it is imperative to find genes or resistance loci that impart resistance against such diseases. In the present study, grapevine genome was explored to identify various defense-responsive genes and SSR markers associated with PM and DM resistance in grapes. In total, 386 NBS-LRR genes were identified in grapevine genome; broadly classified into two classes: 30 TIR-NBS-LRRs and 148 CC-NBS-LRRs. Some other domains identified were 18 RPW8, 13 P-loop and 125 RX-CC like and 52 NBS-LRRs. Their functional annotations revealed that majority of genes were having role in defense response. Digital expression analysis was conducted to identify PM and DM-responsive NBS-LRR and other classes of defensive genes (EDS, NDR1, NPR, RAR1, PAD4, TFs and PR) in grapevine genome. In total, 110 PM-responsive and 98 DM-responsive differentially expressed genes were identified in 10 different Vitis vinifera accessions represented as heat maps. Gene interaction studies for these genes were conducted based on co-expression analysis. Consequently, 24 PM-responsive and 22 DM-responsive highly interacting genes were identified. Based on this co-interaction, a pathway of ETI was configured that might be occurring in grapes during PM and DM infection. Further, the characterization of these genes was performed using various bioinformatics tools and softwares such as BLAST2GO for functional annotation, Splign and GSDS2.0 for gene structure analysis, MEME Suite and Pfam for motif analysis, ProtParam for depicting physicochemical characteristics, TargetP 1.1 for subcellular localizations depiction, PlantCare for prediction cis-regulatory elements, Ensembl Plants portal and Grape Genome Browser for chromosomal locations predictions. The quantitative expression levels of PM and DM-responsive defensive genes were assessed during 3 different conditions i.e. SA treatment, PM infection and DM infection.