Small RNA Profiling Reveals a Role of miRNAs in Response to Ralstonia solanacearum Infection in Tomato

Apart from being a major vegetable crop, tomato (Solanum lycopersicum) is an efficient scientific research model. However, it is vulnerable to bacterial wilt (Bw) caused by Ralstonia solanacearum (Rs); the infection results in severe yield and quality loss. microRNA (miRNA), a class of endogenous non-coding single-stranded RNA, plays an important role in plant growth and development and stress response. To understand the function of miRNA-targets in regulating the resistance to Rs infection, we conducted small RNA (sRNA) sequencing in resistant and susceptible tomato lines following infection with Rs. In all, 2.56 Gb high-quality reads were generated in eight libraries, and 336 miRNAs, including 193 novel miRNAs, were identified. Among these, 31 differentially expressed miRNAs targeting 575 genes were identified, including 17 genotype-specific miRNA-targets. In total, 556 DE miRNA-targets were annotated that corresponded to plant-pathogen interactions, plant hormone signal transduction, defense responses, and certain other metabolic processes. In addition to typical TATA-box, CAAT-box, W-box, and TC-rich repeats, the novel_miR_87-WRKY and sly-miR396a-5p-GRF module downstream regulatory gene promoters consisted of hormone, abiotic stress, and other response elements. RT-qPCR confirmed three Bw response patterns in tomatoes, namely negative-positive, negative-negative, and positive-negative associated with six pairs of miRNA-targets. Altogether, our findings revealed the possible functions of miRNAs in protecting the tomato crop against Rs infection and enriched the tomato miRNA repository. We believe our study results will aid in understanding and deciphering the potential molecular mechanism underlying Rs infection in different tomato genotypes.