Use of PediMap in RosBREED for Visualizing Genetic and Phenotypic Data Across Pedigrees in Rosaceous Crops

RosBREED is a multistate, multi-institution project dedicated to genetic improvement of U.S. rosaceous crops and will be using applications of genomics knowledge and tools to accelerate and increase the efficiency of breeding programs. This project focuses on fruit quality traits in apple, peach, sweet cherry, tart cherry, and strawberry to demonstrate marker-assisted breeding. DNA markers that are genetically linked to fruit quality traits can play a critical role in identifying desirable parents for crossing. Breeders can efficiently make informed crossing decisions with DNA marker information when relevant data is displayed in a format that is easily visualized. PediMap is software designed to graphically present genetic information in pedigrees and can be used to present information such as phenotypic data, observed marker alleles, identity by descent probabilities, and QTL functional allele probabilities, thus allowing breeders to visualize the distribution of desirable alleles for important breeding traits across their germplasm. The freely available PediMap software is currently being used by 12 RosBREED demonstration breeders. These breeders have collaborated to develop Crop Reference sets representing U.S.-wide breeding germplasm and Breeding Pedigree sets to further represent their own individual programs, and are already using PediMap to visualize pedigree relationships. Demonstration breeders have found PediMap to be a valuable tool even before the integration of DNA information. RosBREED outreach will extend the training and use of PediMap to the U.S. community of Rosaceae breeders, building on experiences and successes of the project’s demonstration breeders.