Project Number: 8042-21000-274-00-D
Project Type: In-House Appropriated
Start Date: Jun 21, 2013
End Date: Mar 25, 2018
Diverse Solanaceous germplasm resources exist for enhancement of cultivated forms of tomato and pepper. Genes that may be valuable for crop improvement are often not well characterized, they may be associated with undesirable traits, or crossing barriers hinder introgression from distant crop relatives. Changes in pathogen virulence and introduction of new crop pathogens can overcome available host resistance, leaving producers vulnerable to crop loss. Available cultivars may not adequately address producer and consumer needs for new crop uses and high-value alternative crops. This project focuses on determining the underlying genetic bases of important traits of tomato and pepper – including fruit quality attributes and resistance to recurring or emerging diseases - and deploying them as finished cultivars, breeding lines, and genetic stocks. Over the five year project period, the following specific objectives will be addressed. Objective 1: Exploit homology between tomato and pepper to identify and transfer anthracnose-resistance from tomato to pepper, and release new pepper anthracnose resistant germplasm, along with molecular markers for marker-assisted selection. Sub-objective 1A. Identify anthracnose resistance-linked markers and candidate loci in tomato and pepper. Sub-objective 1B. Determine identity of species and relatedness of Colletotrichum isolates responsible for pepper anthracnose and relate these findings to knowledge of host/strain virulence specificity for isolates infecting pepper fruit. Objective 2: Identify and characterize genetic resistance to the emerging diseases Groundnut ringspot virus (GRSV) infecting pepper and Potato spindle tuber viroid (PSTVd) infecting tomato, and deliver/release appropriate materials to researchers and breeders. Sub-objective 2A. Identify and characterize pepper host resistance to GRSV. Sub-objective 2B. Identify and characterize tomato host resistance to PSTVd. Objective 3: Develop and release pepper breeding lines with improved quality attributes for the culinary, culinary/ornamental, and minimally processed fresh-cut market. Sub-objective 3A. Develop and release pepper breeding lines with improved quality attributes for the culinary and culinary/ornamental market. Sub-objective 3B. Develop and release pepper breeding lines with improved quality attributes for the minimally processed fresh-cut market.
Next generation sequencing technology will be used for map-based cloning of anthracnose resistance loci from a recombinant, inbred line tomato population that ARS has developed. To bolster identification of candidate genes for anthracnose resistance, a proteomic survey will also be conducted using resistant and susceptible tomato lines. Markers developed from tomato will henceforth be utilized to identify resistance homologues in the pepper species C. baccatum. Resistance loci will be transferred to C. annuum using bridge lines that ARS has developed. Different Colletotrichum species have been identified as the causative organism responsible for recent outbreaks of green pepper anthracnose fruit rot in Ontario and Midwestern, Southeastern and Mid-Atlantic production areas in the U.S. Isolate species identity and relatedness from these regions will be characterized to ascertain if these isolates share a common lineage. Initial screening surveys for GRSV resistance will focus on C. chinense, the species where resistance to the Tospoviruses TSWV and CaCV has been previously identified. Reported Tospovirus resistance and accession passport data will be assessed and a subset of the available C. chinense accessions will be selected to maximize coverage of the species’ native distribution range. C. annuum land races and accessions representative of the distribution range of C. frutescens, C. chacoense and C. baccatum will be evaluated in a similar manner. Accessions that exhibit high levels of resistance will be crossed to susceptible genotypes to characterize the inheritance of resistance. Initial screening for PSTVd will focus on core collections established for wild relatives of the cultivated tomato. Core collections to be screened will include S. chilense, S. habrochaites, S. pennellii, S peruvianum, and S. pimpinellifolium. Initial screening will focus on a PSTVd variant isolated from an outbreak in tomato and a second variant isolated from potato with confirmed infectivity on tomato. Infectivity will be quantified using real-time PCR. Ongoing development of ornamental and dual-purpose ornamental/culinary pepper germplasm is carried out via breeding strategies that include backcross breeding for simple traits and pedigree and inbred backcross breeding for complex traits. Improved germplasm is evaluated in cooperation with collaborators and released by ARS. Initial germplasm screening for fresh-cut pepper will focus on accessions that bear fruit with thick pericarp. Using knowledge of market types and available passport data, C. annuum accessions will be selected from commercial sources and the USDA, ARS, Plant Genetic Resources Conservation Unit. Accessions with varied fresh-cut quality attributes will be selected to assess applicability of hyperspectral imaging for high throughput phenotyping of fresh-cut quality. Accessions with divergent fresh-cut quality will be intercrossed in a diallel mating scheme to evaluate combining ability for fresh-cut attributes. Superior accessions will be hybridized with sweet and hot pepper breeding lines and BC2 generation hybrids advanced for phenotyping and public release.