COMPARATIVE AND TRANSLATIONAL GENOMICS IN TOMATO AND PEPPER FOR DEVELOPING PRE-BREEDING LINES AND TOOL KITS FOR ANTHRACNOSE RESISTANCE

The main goal of this project is to develop pre-breeding tomato and pepper lines resistant to anthracnose fungal infection. We will explore and characterize our tomato RIL population and Capsicum germplasm pools to identify cultivars with varying degrees of resistance or susceptibility. This proposal will utilize genomic colinearity from well-studied species, like the tomato and its distant relative pepper, for the identification of PCR-based high-throughput assays targeting common QTLs between the two species, promising for allele mining in anthracnose-resistant loci. To complement the comparative genomic approach, we propose the development of PCR Allele Competitive Extension (PACE) assays targeting resistant Quantitative Trait Nucleotides (QTNs) within the core germplasm repositories of both tomato and pepper to identify and characterize underlying candidate genes associated with anthracnose resistance/susceptibility in tomato and pepper. This proposal not only enables the integration of resistances to various strains of Colletotrichum spp. but also revolutionizes tomato and pepper breeding for enhanced food security and sustainability. Additionally, it will facilitate the development of resistant varieties and pre-breeding lines for on-farm trials and participatory selection strategies, ultimately leading to improved varieties. These activities will be supported by intensive education and outreach efforts to introduce existing varieties and those bred using genomic tools and other consumer-assisted approaches to tomato and pepper farming communities in the United States.The current proposal will address the need to integrate modern technologies that can create a set of common tools for marker-assisted breeding with the specific objectives mentioned below.Comparative transcriptomics of pathogen-challenged tissues between pepper and tomato to identify orthologous anthracnose resistance genes.Develop PACE markers from orthologous loci in tomato and pepper and assay them in core Capsicum chinense collection and Tomato RILs.Evaluation of tomato and pepper lines as potential pre-breeding lines for anthracnose.