Development of SNP-based assays for disease resistance and fruit quality traits in apple (Malus × domestica Borkh.) and validation in breeding pilot studies

The development of molecular markers linked to specific traits is now routine practice, but the gap between genomics and breeding often delays their application. In the frame of the FP7 European project FruitBreedomics, apple pilot studies were designed to exploit the project’s outcomes towards the practical application of marker-assisted breeding (MAB) programs. The aim of this pilot study was to develop an outsourcing genotyping pipeline, which will provide access to the single nucleotide polymorphism (SNP) markers analysis for breeding companies without an internal DNA lab. The process from seed sowing to genotypic and phenotypic seedling selection was optimized. KASP™ (competitive allele-specific PCR) genotyping assays were developed for a number of major resistance genes for apple scab (Rvi2, Rvi4, Rvi6, and Rvi15); powdery mildew (Pl2); and rosy apple aphid (Dp-fl). In addition, KASP™ assays for the genes Md-ACS1, Md-ACO1, and Md-PG1 involved in fruit quality (firmness, texture, and storability) were also developed. The pilot study demonstrated the efficacy of the SNP-based selection strategy, especially for those programs dealing with traits not easily assessable in vivo, such as pyramided resistances and fruit quality traits.