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

Abstract Background Tomato (Solanum lycopersicum) is a globally significant crop that faces challenges from various pathogens, including Phytoplasma solani. Phytoplasmas are obligate parasitic bacteria that disrupt plant metabolism and manipulate host defenses. Our current understanding of tomato-Phytoplasma solani interaction is very limited and currently nothing is known at the whole genome or transcriptome level. Bulk segregant analysis (BSA) is a powerful method for identifying markers linked to target genes for desired traits. BSR-seq combines BSA with RNA-seq, allows the identification of SNP markers based on transcriptome data. Results In this study, we have analyzed and compared the transcriptome of a resistant and a susceptible wild tomato accession and their healthy and diseased F2 bulks in response to P. solani infection using the RNA-seq technology. Variant analysis through PyBSASeq pipeline detected 145142 SNPs among bulks and an average of 101 SNPs per sliding window were found. Five, three and one; three regions on chromosome 1, 7, 8 and 9 respectively, exhibited statistical significance for the G-test statistic in the healthy F2 bulk. We have identified 1305 and 173 differentially expressed genes (DEGs) in resistant vs susceptible comparison of parent and bulk samples respectively. Functional annotation of DEGs revealed substantial transcriptional reprogramming of diverse physiological and cellular processes, particularly the response to stimulus and response to bacterium upon P. solani treatment. By comparison of differential expression and variant analysis, two genes were found linked to resistance development in tomato against P. solani. Conclusion The BSR-seq analysis provided valuable insights into the molecular mechanisms of tomato-P. solani interactions. Two candidate genes, Solyc01g079140 and Solyc07g017980 were found linked to the P. solani infection in tomatoes. Our results lay out a strong foundation for future studies aimed at improving genetic resistance of tomato cultivars against Phytoplasma solani.