Speed cloning of fungal resistance genes in tomato for network analysis using transcriptomic approaches

Abstract

Early Blight and Late Blight caused by Alternaria solani and oomycete Phytophthora infestans are major factors of destruction of tomato plants resulting 49 to 91 % yield loss. Transcriptome analysis of Early Blight and Late Blight on tomato would help to identify the NLR genes that conferred resistance mechanism. In this study some R genes are unveiled that contain NB: LRR domains and involved in regulation of genes to confer resistance mechanism in tomato plants. NLR genes were identified from the downloaded raw RNA-seq data analysis. NRC4, R1B16, RPP13, RPM1 gave High FPKM values. These genes expression was checked on three cultivated tomato accessions of Solanum Lycopersicum (38046, 19890, Roma) and one wild specie accession of Solanum Chilense (19906). NRC4, R1B16 showed upregulation and R1B12 showed down regulation in infected plants of LB and RPP13, RPM1 showed upregulation in infected plants of EB. Protein -Protein interaction represented no significant interaction between these NLR genes as many genes were not annotated. Genes Co-occurrence analysis predicted conservation of these NLR genes is higher in Solanaceae family. RPP13 showed broad spectrum resistance against diseases. In this study RPP13 gene was cloned from Solanum lycopersicum accession 19890. The cloned RPP13 gene showed 70% homology with existing genes sequences. Further research is required to unveil more NLR genes that are involved in resistance mechanism against fungus diseases.