In Silico Integrated Analysis of Genomic, Transcriptomic, and Proteomic Data Reveals QTL-Specific Genes for Bacterial Canker Resistance in Tomato (<i>Solanum lycopersicum</i> L.)
Ibrahim Celik
Bacterial canker of tomato, caused by <i>Clavibacter michiganensis</i> subsp. <i>michiganensis</i> (<i>Cmm</i>), is a devasting disease that leads to significant yield losses. Although QTLs originating from three wild species (<i>Solanum arcanum</i>, <i>S. habrochaites</i>, and <i>S. pimpinellifolium</i>) were identified, none of the QTLs was annotated for candidate gene identification. In the present study, a QTL-based physical map was constructed to reveal the meta-QTLs for <i>Cmm</i> resistance. As a result, seven major QTLs were mapped. Functional annotation of QTLs revealed 48 candidate genes. Additionally, experimentally validated <i>Cmm</i> resistance-related genes based on transcriptomic and proteomic studies were mapped in the genome and 25 genes were found to be located in the QTL regions. The present study is the first report to construct a physical map for <i>Cmm</i> resistance QTLs and identify QTL-specific candidate genes. The candidate genes identified in the present study are valuable targets for fine mapping and developing markers for marker-assisted selection in tomatoes for <i>Cmm</i> resistance breeding.
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