Fine-mapping, candidate gene identification, and marker development for the apple scab resistance gene Rvi2.

Area of Science:

• Plant genetics and breeding
• Molecular biology
• Agricultural science

Background:

• Apple scab, caused by Venturia inaequalis, poses a significant threat to global apple production.
• Fungicide reliance is unsustainable due to rapid pathogen evolution and environmental concerns.
• Previous breeding efforts introduced novel resistance genes, like Rvi2, through backcrossing.

Purpose of the Study:

• To dissect the genetic basis of the Rvi2 scab resistance locus in apple.
• To identify the specific genetic element responsible for Rvi2-mediated resistance.
• To develop a molecular marker for efficient marker-assisted selection of scab resistance.

Main Methods:

• Generated haplotype-phased and Oxford Nanopore genome assemblies of resistant apple accessions.
• Performed fine-mapping using a segregating 'Royal Gala' × TSR34T15 population.
• Identified and characterized structural variants (SVs), including long terminal repeat (LTR) retrotransposons.

Main Results:

• Fine-mapping delimited the Rvi2 locus to a narrow genomic interval.
• A 10,041 bp LTR retrotransposon insertion, a structural variant (SV), was identified and strongly linked to Rvi2.
• The LTR harbours an FPPS gene adjacent to a candidate defence gene, suggesting a cis-regulatory role in resistance.

Conclusions:

• The identified LTR insertion is a key structural variant associated with Rvi2 scab resistance.
• This SV, potentially regulating adjacent defence genes, provides a novel target for breeding.
• A validated marker derived from this SV enables efficient marker-assisted selection, streamlining the development of scab-resistant apple cultivars.