Incorporation of Marker–Assisted Breeding (MAB) in the University of Arkansas and Three Other RosBREED Demonstration Peach Breeding Programs

The RosBREED project (http://www.rosbreed.org/) has successfully identified functional alleles associated with nine important peach traits: Fruit resistance to bacterial spot (Xap1 and Xap6), maturity date (G4mat), fruit type (G), blush, flesh color (Y), texture type (F-M), acidity (D), acidity and soluble solid content (G7Flav), and mealiness. Forty-eight single nucleotide polymorphism (SNP) markers significantly associated with these phenotypic traits and capable of distinguishing all functional alleles were selected and divided into two 24-SNP mini arrays v1. Two DNA service providers [University of Arizona Genetics Core (UA) and BioDiagnostics (BDI)] were charged with the design and testing of the mini SNP arrays. Leaf samples from 240 breeding selections or seedlings as well as control samples from the four RosBREED peach demonstration breeding programs [University of Arkansas (UofA), Clemson University, Texas A&M University and University of California, Davis] were genotyped with the arrays. Genotyping data were successfully translated into trait predictions and results were provided to each breeding program. Depending on the material genotyped, genotypic data accurately predicted phenotypic performance in 80-90% of cases across material from all breeding  programs. The additional 20-10% of material required specific attention to assigning the correct haplotypes to the correct phenotypes. By associating phenotypic data with genotypic data, this molecular information was validated and for the first time put into use in the UofA breeding program. The first step to advance towards marker-assisted breeding (MAB) involves marker-assisted parent selection (MAPS), thus a MAPS breeders template was created for the 72 individuals included on the mini-SNP array v1, and the 21 cultivars and selections on the 9K Peach SNP array v1. Crosses were designed using this molecular information in February 2014 to extend and diversify the later part of the Arkansas peach season: both melting, non-melting, and non-softening flesh types, peach and nectarine, white and yellow flesh, high and low acid, high blush and resistance to bacterial fruit spot. This template will be modified as more material becomes genotyped and additional traits become incorporated, to enhance continual future use of MAPS in the program. Additionally, primers for simple sequence repeat (SSR) markers located within the validated SNP marker haplotypes are being generated and validated for use in marker-assisted seedling selection (MASS). Overall, the collective impact of MAB in the UofA breeding program is increased efficiency in developing superior peach cultivars that meet the needs and desires of both producers, shippers and consumers.