Bulk segregant analysis of tomato to identify polymorphism associated with tomato-Phytoplasma solani interaction using RNA-sequencing data

Tomato (Solanum lycopersicum) is a globally significant crop that faces challenges from various pathogens, including Phytoplasma solani. Phytoplasmas are parasitic microorganisms that disrupt plant metabolism and manipulate host defenses. The tomato-pathogen pathosystem serves as an excellent model for studying plant-pathogen interactions. Bulk segregant analysis (BSA) is a powerful method for identifying markers linked to target genes for desired traits. BSR-seq com-bines BSA with RNA-seq, allows the identification of SNP markers based on transcriptome data. The RNA-seq analysis involves extracting total RNA from bulks with extreme traits, constructing cDNA libraries, sequencing using Illumina Hiseq 2500 platforms followed by comprehensive sequence analysis like variant calling and differential expression analysis. The analysis relies on a reference genome and enables the screening of candidate genes based on differential expression patterns within candidate intervals. To identify the putative genetic and SNP factors involved in tomato plant resistance against P. solani infection, RNA-seq data from resistant and susceptible parents and healthy and diseased F2 bulks were analyzed. Trimming and cleaning of reads, mapping to reference genome of tomato, differential expression analysis and variant calling and sliding window analysis were performed. Two genes putatively linked to P. solani resistance in tomato were identified. Moreover the BSR-seq analysis provided valuable insights into the mo-lecular mechanisms of tomato- P. solani interactions and the findings contribute to the overall understanding of plant defense responses and the development of resilient tomato cultivars against obligate pathogens.