Marker development and applications in the University of Minnesota apple and grape breeding programs

The University of Minnesota (UMN) fruit breeding programs have participated in several multistate USDA-NIFA-SCRI projects in a nationally coordinated effort to expedite breeding for quality and stress resistance in fruit crops through routine applications of modern genomics and genetics tools. In the UMN apple breeding program, the use of a genotyping array developed through RosBREED enabled map construction for quantitative trait locus (QTL) discovery and haplotype analysis. Here, we present progress toward dissecting pedigree relationships through a high-resolution map that is precursory to identification of key loci for several traits targeted at the apple breeding program, such as texture, apple scab resistance, soft scald, and acidity. Markers are now used routinely in the program to facilitate selection of parents and culling of seedlings for loci controlling fruit color, texture and flavor traits, storage disorders, harvest date, and apple scab resistance. In the UMN grape breeding program, the use of next-generation sequencing technology and centralized phenotyping centers through VitisGen enabled gene mapping for targeted traits, such as powdery mildew, foliar phylloxera, and flower sex. Construction of high-density SNP maps facilitated QTL identification and marker discovery for use in marker-assisted breeding (MAB). Here, we report the identification of loci for powdery mildew resistance and foliar phylloxera resistance. We also report the utility and challenges of MAB, as well as an opportunity to apply AmpSeq, a product of VitisGen, for MAB in grape.