Skip to main content
ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Research Project #437474

Research Project: Management of Endemic and Emerging Bacterial Diseases of Capsicum by Plant Resistance, Novel Compounds, and Understanding Pathogen Diversity

Location: Vegetable Research

Project Number: 6080-22000-032-003-R
Project Type: Reimbursable Cooperative Agreement

Start Date: Oct 1, 2019
End Date: Aug 31, 2025

There exist varying levels of resistance in different pepper cultivars against different species of pathogenic bacteria collected from recent outbreaks. Recently identified resistant U.S. Plant Introductions contain novel quantitative resistance loci and durable genetic mechanisms of disease resistance to multiple pathogen races. We will generate gentic populatioins, identify the genetic loci responsible for the resistance, and develop genetic markers suitable for use in marker-assisted selection (MAS).

Single nucleotide polymorphism (SNP)-based linkage analyses will be used to identify quantitative trait loci (QTL) associated with disease resistance. Genetic populations will be developed from an initial cross of a resistant selection PI200725 x the susceptible cultivar Charleston Bell. Populations of 180 F3 families from self-pollinated F2 plants will be phenotyped for disease. Young leaf samples will be collected from the F2 individuals and parental plants for DNA extraction. Pooled, DNA samples will be prepared from the 10-20% most resistant (R) and most susceptible (S) F2s for QTL-seq analysis. Sequencing of DNA from all F2 plants will be performed. High quality SNPs will be chosen for Quantitative trait loci (QTL) analysis. QTL analysis and map construction will be performed. QTLs associated with Xanthomonas gardneri resistance will be identified using the software Rqtl. Genotypes will be imputed, followed by multiple QTL mapping with stepwiseqtl. Linkage map analysis of identified markers will be performed using JoinMap version 3.0. QTL identified in this objective will be used to develop molecular markers for marker-assisted selection (MAS), including marker validation, and translation into breeder friendly (i.e., high throughput, low cost) markers. In this project, we will focus marker development efforts on QTL regions that explain a significant portion of variation (major QTL) and are robust across environments and/or genetic background as determined by phenotyping of segregating populations in multiple environments or seasons (environmental stability), testing of segregating populations from more than one cross (stability across genetic backgrounds), and/or identification by independent approaches (e.g., segregating populations and genome-wide association studies). We will develop SNPs that can be used in the KASP (Kompetitive Allele Specific PCR) high-throughput assay system. KASP markers will be further tested against elite lines targeted for introgressing the resistance trait. Validated markers will be used to assist breeding to introgress resistance into elite lines and facilitate pyramiding of resistance genes.