QTL and PACE analysis identify candidate genes for anthracnose resistance in tomato

Authors: LOPEZ-ORTIZ, CARLOS - West Virginia State University; REDDY, UMESH - West Virginia State University; ZHANG, CHONG - Oak Ridge Institute For Science And Education (ORISE); NATARAJAN, PURUSHOTHAMAN - West Virginia State University; NIMMAKAYALA, PADMA - West Virginia State University; BENEDITO, VAGNER - West Virginia State University; FABIAN, MATHEW - Oak Ridge Institute For Science And Education (ORISE); Stommel, John

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/17/2023
Publication Date: 8/4/2023
Citation: Lopez-Ortiz, C., Reddy, U., Zhang, C., Natarajan, P., Nimmakayala, P., Benedito, V., Fabian, M., Stommel, J.R. 2023. QTL and PACE analysis identify candidate genes for anthracnose resistance in tomato. Theoretical and Applied Genetics. https://doi.org/10.3389/fpls.2023.1200999.
DOI: https://doi.org/10.3389/fpls.2023.1200999

Interpretive Summary: Colletotrichum, the causative fungal pathogen of anthracnose, causes tomato fruit rot and requires regular application of chemical control products to limit yield loss. Primitive, small-fruited tomatoes have been identified with anthracnose resistance, but commercial cultivars resistant to this pathogen are not available. Multiple genes that influence resistance have made it difficult for plant breeders to effectively transfer useful levels of resistance to modern cultivars. Using tomato populations developed from crosses of the resistant and susceptible tomatoes, we identified multiple genes that control anthracnose resistance and determined the function of these genes. These results will allow breeders to track these genes in a breeding program and efficiently transfer them to elite tomato cultivars.

Technical Abstract: Anthracnose, caused by the fungal pathogen Colletotrichum spp., is one of the most important diseases of tomato in the United States and worldwide. No commercial cultivars with genetic resistance to anthracnose in the field have been reported. Utilizing anthracnose-resistant cultivars would reduce yield losses, decrease the high cost of disease control, and diminish hazards resulting from frequent fungicide application. Utilizing a recombinant inbred line (RIL) mapping population (N=243), derived from a cross of the anthracnose susceptible US28 cultivar and unadapted small-fruited tomato line, “95L368” that exhibits a high level of resistance to a broad range of Colletotrichum species, the current investigation was designed to identify quantitative trait loci (QTLs) linked with the anthracnose resistance. The RIL population was phenotyped by inoculating ripe field harvested tomato fruits with C. coccodes during two seasons. We identified twenty QTLs associated with anthracnose resistance, individually explaining between 4.5 and 17.2% of the phenotypic variation. In this study, a QTL analysis using a high-density linkage map and QTLseq analysis of phenotypically extreme bulks identified loci underlying candidate genes. We validated underlying genes using PCR allelic competitive extension (PACE) assays. These genes included AP2-like ethylene-responsive transcription factor, N-alpha-acetyltransferase (NatA), cytochrome P450, amidase family protein, tetratricopeptide repeat, bHLH transcription factor, and disease resistance protein RGA2-like. Our findings will facilitate the use of molecular markers for efficient introgression of the resistance loci and the development of anthracnose-resistant tomato cultivars.