POSTER PRESENTATION: Identifying Candidate Genes for Tomato Anthracnose Resistance through QTL and PACE Analyses: Implications for Sustainable Food Systems

Anthracnose, caused by the fungal pathogen Colletotrichum spp., is one of the most significant tomato diseases worldwide. No commercial cultivars with anthracnose resistance are available, leading to substantial crop losses and increased reliance on fungicides. Developing cultivars with genetic resistance is crucial for enhancing sustainability in food systems by reducing chemical inputs and preserving crop yields. To address this challenge, a recombinant inbred line (RIL) mapping population (N = 243) has been made from a cross between the susceptible US28 cultivar and the resistant but semiwild and small-fruited 95L368 to identify quantitative trait loci (QTLs) associated with anthracnose resistance. The RIL population was phenotyped for resistance by inoculating ripe field-harvested tomato fruits with Colletotrichum coccodes for two seasons. We identified twenty QTLs underlying resistance, with a range of phenotypic variance of 4.5 to 17.2%, using a skeletal linkage map and GWAS. In addition, a QTLseq analysis was performed using deep sequencing of extreme bulks that validated QTL positions identified using traditional mapping and resolved candidate genes underlying various QTLs. We further validated AP2-like ethylene-responsive transcription factor (AP2/ERF), N-alpha-acetyltransferase, cytochrome P450, bHLH transcription factor, and disease resistance protein RGA2-like using PCR allelic competitive extension (PACE) genotyping. Currently, functional research utilizing CRISPR/Cas9 gene knockout for AP2/ERF TF has been conducted, and the role of this QTN will be presented. Additionally, the PACE assays developed in this study will enable high-throughput screening for anthracnose resistance breeding and promote more resilient and sustainable tomato cultivation practices within food systems.