High-throughput genotyping platform for apple scab resistance marker-assisted selection

Overview

Apple scab, caused by Venturia inaequalis, is the most significant disease affecting apple production in Chile and other temperate regions worldwide. INIA-Chile's apple breeding program (ABP) develops approximately 4,000 segregants annually, aiming to produce new cultivars with genetic resistance to scab. Currently, seedling-stage inoculation eliminates only 25% of segregants, while at least 50% of sensitive genotypes are expected in F1 progenies. After seven years and substantial investment in nursery, grafting, and planting phases, only 0 to 3 genetic lines from 2,500 advanced segregants are typically selected as potential cultivars. This proposal addresses the urgent need to improve early-stage selection efficiency and reduce the costs associated with phenotyping sensitive genotypes.

The proposed solution is a high-throughput, low-cost genotyping platform based on molecular markers linked to apple scab resistance genes. By implementing a marker-assisted selection (MAS) strategy, the platform will enable earlier and more accurate identification of resistant genotypes, significantly reducing the time, labor, and cost required to develop new scab-resistant apple cultivars.

Technical specifications

• Molecular marker types: Simple sequence repeats (SSR) and single nucleotide polymorphisms (SNP) markers linked to 18 apple scab resistance genes
• Marker compilation: Molecular markers compiled from multiple studies, including Khajuria et al. (2018, Tree Genetics & Genomes)
• Genotyping approach: High-throughput and low-cost platform designed for routine use in breeding workflows
• Target population: Founding population and 10 scab resistance lines of the INIA-Chile apple breeding program
• Selection strategy: Marker-assisted selection (MAS) designed based on cost-benefit analysis to maximize efficiency gains
• Expected impact: Increased selection efficiency at early breeding stages and reduced costs associated with phenotyping scab-sensitive genotypes
• Application scope: Apple breeding programs focused on developing disease-resistant cultivars for temperate production regions

Technology readiness level

The platform is currently at the development and validation stage. The molecular markers linked to 18 scab resistance genes have been identified and compiled from existing scientific literature. The next phase involves genotyping the founding population and 10 scab resistance lines to characterize the scab resistance genes present, followed by designing a MAS strategy based on a cost-benefit analysis. Validation will focus on demonstrating that MAS increases selection efficiency and reduces costs compared to the current phenotyping-based approach. The platform is intended for integration into the operational workflow of INIA-Chile's apple breeding program, with potential scalability to other breeding programs targeting apple scab resistance.