Mapping Gene Markers for Apple Fruit Ring Rot Disease Resistance Using a Multi-omics Approach

Area of Science:

• Plant Pathology
• Genetics
• Horticulture

Background:

• Apple fruit ring rot (FRR), caused by *Botryosphaeria dothidea*, is a significant global disease affecting apple production, particularly in Asia.
• Limited progress has been made in mapping candidate genes and developing genetic markers for FRR resistance.

Purpose of the Study:

• To identify quantitative trait loci (QTL) and candidate genes associated with resistance to *Botryosphaeria dothidea* in apples.
• To develop effective genetic markers for apple fruit ring rot resistance.

Main Methods:

• Phenotyping 1,733 F1 apple hybrids for resistance to four *B. dothidea* isolates.
• Utilizing bulk segregant analysis by re-sequencing (BSA-Seq) to identify QTL.
• Employing integrated multi-omics strategies, including RNA-sequencing and parental re-sequencing, to predict candidate genes.
• Validating functional mutations and developing Kompetitive Allele-Specific PCR (KASP) markers.

Main Results:

• Identified 46 QTL for resistance/susceptibility to *B. dothidea*, including a 'hotspot' on chromosome 14.
• Predicted 57 candidate genes with functional mutations within the identified QTL.
• Developed ten effective genetic markers for apple fruit ring rot resistance.
• Validated functional mutations in hybrids and *Malus* germplasm accessions.

Conclusions:

• This study provides a rapid method for candidate gene mapping of complex traits in outbreeding species like apple.
• The developed markers offer a valuable tool for breeding programs aimed at enhancing apple resistance to fruit ring rot.