Pepper germplasm screening for SNP markers linked to ChLCV and anthracnose resistance
Genome-wide association mapping of Capsicum germplasm to identify SNP markers linked to resistance genes against chili leaf curl virus and anthracnose. The project seeks SNP genotyping support to enable marker-assisted selection in pepper breeding programs.
Overview
This research initiative aims to unlock the genetic basis of disease resistance in pepper (Capsicum species) by screening a diverse germplasm collection for resistance to two economically damaging pathogens: chili leaf curl virus (ChLCV) and anthracnose (Colletotrichum capsici). The goal is to identify SNP markers and SNP haplotypes that are statistically linked to resistance-conferring genomic regions using genome-wide association studies (GWAS). These markers can then be deployed in marker-assisted selection (MAS) to make pepper breeding faster, more accurate, and less costly than conventional field-based phenotypic selection.
The work addresses a critical gap in pepper improvement programs by moving beyond traditional biparental mapping, which captures limited allelic diversity, toward a broader association-mapping approach that taps into historical recombination events across a genetically diverse panel.
Technical specifications
Approach and methodology:
- An association panel of approximately 180 Capsicum accessions, including indigenous collections and exotic germplasm from the World Vegetable Center (WVC) in Taiwan, spanning seven Capsicum species
- Two-year phenotypic evaluation under challenge inoculation for both anthracnose lesion diameter and ChLCV infection response
- Genotyping-by-sequencing (GBS) to generate genome-wide SNP data across the panel
- GWAS analysis to identify SNP markers and haplotypes in linkage disequilibrium with resistance loci for both diseases
- Validation of identified markers in separate and/or connected cross-derived mapping populations
Scientific basis:
- Preliminary work in the lab has already tagged genomic regions controlling lower lesion diameter of C. capsici to SSR loci in intra-C. baccatum and intra-C. annuum mapping populations
- ChLCV resistance has been characterized as governed by two interacting loci acting in duplicate dominant manner, confirmed across F2 and F3 generations
- Prior SSR-based mapping in biparental populations identified markers spanning 15.7 cM associated with ChLCV resistance regions
Technology readiness level
The project is at an active validation stage with ongoing field and genotyping work. The association panel has been assembled and two-year phenotyping is planned. The research team is actively seeking a partnership that can provide SNP genotyping facility capacity to complete the genotyping-by-sequencing work needed to fulfill the research hypothesis. The expected timeline to completion is approximately one additional year from partnership initiation. Outputs will include validated SNP markers ready for deployment in marker-assisted breeding pipelines for pepper improvement targeting ChLCV and anthracnose resistance.
About University of Agriculture Faisalabad
The Institute of Horticultural Sciences is a specialized academic and research unit within the public University of Agriculture Faisalabad in Pakistan, embedded in a large agricultural campus with a strong applied orientation. Corporate partners access field research farms, controlled‑environment greenhouses, and postharvest laboratories to prototype, validate, and scale solutions under near‑commercial conditions. Strong outreach and extension ties connect faculty and students with growers, packers, and input suppliers, enabling rapid field trials, training, and technology adoption. Research is supported by national funding programs and competitive international development grants. A dedicated technology transfer office facilitates IP protection, licensing, sponsored research, and access to pilot‑ready facilities.
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