Marker-assisted breeding for chilli leaf curl virus resistance using rga-based markers in hot pepper

Overview

Chilli Leaf Curl Virus (ChLCV) is one of the most destructive diseases affecting hot pepper production, causing significant yield losses for growers worldwide. Conventional breeding for ChLCV resistance is slow and imprecise due to the lack of molecular markers linked to resistance genes. This solution addresses that gap by using Resistance Gene Analog (RGA) based markers to establish marker-trait associations, enabling breeders to efficiently identify, select, and introgress ChLCV resistance into elite pepper lines. The approach leverages four diverse, stable resistance sources previously identified by the research team, crossed with a common susceptible genotype to generate segregating populations for analysis.

Technical specifications

• Resistance sources: Four diverse and stable Capsicum genotypes with confirmed ChLCV resistance, crossed with a common highly susceptible genotype.
• Population development: F2 and F3 generations derived from four diverse crosses to capture a broad range of resistance alleles.
• Marker system: RGA-based markers designed from conserved domains and motifs of well-characterized R-genes, as reported in chilli by Naresh et al., 2017. RGAs are highly conserved across plant species, making them effective candidate markers for resistance gene identification.
• Selective genotyping approach: Used to establish associations between RGA markers and ChLCV resistance, reducing genotyping cost while maximizing informative data.
• Phenotyping: Challenge inoculation of F2:F3 progenies to confirm ChLCV resistance responses under controlled conditions.
• Validation: Marker-trait associations confirmed through single marker analysis to ensure reliability before deployment in breeding programs.
• Expected outcomes: Identification of different resistance genes originating from diverse sources and development of markers suitable for marker-assisted selection (MAS) in introgression breeding.

Technology readiness level

This research is at an early-to-mid stage of development (TRL 3–5). The resistance sources and crossing populations have already been established, and the marker system is based on published, validated RGA primers. The proposed one-year project focuses on genotyping and phenotyping to confirm marker-trait associations. Upon successful validation, the markers and associated breeding lines will be ready for pilot deployment in commercial hot pepper breeding programs. The research team is seeking partnership for genotyping facility access to complete the validation phase.