The production of tree fruits in most countries is predominantly a small farm/orchard endeavor. However, tree fruits are significant economic drivers worldwide in particular in many low to mid-income countries. Tree fruits not only provide income but also represent a substantial portion of the normal dietary intake; they are high in nutritional value and important components of a healthy diet. Fruit tree plantations are ideally suited to small farm settings as well as urban plantings and marginalized lands. They provide protection from drought and localized desertification. Additionally, fruit trees are important parts of many forest ecosystems worldwide and as a tree species they are important for land preservation and carbon assimilation. As with other tree species, Prunus fruit tree breeding programs however are continually challenged to find genetic solutions for producing nutritionally improved varieties while facing dynamic problems of disease and pests and ever-changing environmental landscapes. The most critical challenge in stone fruit agriculture are the current uncontrolled spread of Plum Pox Virus (PPV, a devastating disease of all stone fruits), the potential loss of production associated with insufficient winter chilling due to global warming, and the necessity to rapidly couple genetic solutions to these problems with the goal of increased nutritional quality of the fruit product. Unfortunately, these important characters are quantitative in genetic nature and thus present significant challenges to rapid genetic manipulation for varietal improvement. Genomics resources (genes, markers etc.) offer the tools to substantially augment the traditional breeders toolbox to improve the speed and efficiency of the character selection process. However, in order to capitalize on the use of the Prunus genomics resources and translate them into breeding programs, the genetic resolution of trait containing intervals in the genome needs to be substantially improved. This is no simple task as the physical limitations (time, space) required for tree species genetics complicates studies to refine QTL intervals into marker selectable units. Thus, new approaches to QTL resolution (e.g. association studies and candidate gene approaches) are rapidly supplementing more traditional approaches (F1 or F2 mapping populations) with the promise of higher resolution of QTLs for marker assisted breeding purposes. In this proposal, we address these major challenges by capitalizing on the robust genomics/genetics data in key Prunus species, the rich germplasm resources in European and other partner countries, innovative genotyping by whole genome sequencing and marker assisted breeding strategies to explore the translation of markers to accelerate improvement of varieties: A) in the short term (during the proposal research period) for genes controlling resistance to PPV, and chilling requirement (CR) and bloom date (BD); B) in the long term (part of the continuing research, post proposed period) for genes significantly impacting nutritional value of Prunus fruits. To tackle these specific aims we have developed a partnership of laboratories with particular expertise and resources ideally suited to this project. We propose to establish a Chaire of Excellence in the French host institution, INRA UMR BFP, hosting as scientific coordinator the reference senior scientist in the field of Prunus genomics, Pr A.G. Abbott (a world renowned expert in fruit tree genomics and genetics). We will be assisted locally by a bio-informatic-specialized research unit, CBiB, allowing us to optimize the analysis of large data sets. We will be supported by both the French Apricot breeding institution (INRA UGAFL) and the laboratory of Forestry genomics (Biogeco, Cestas-Pierroton) in order to ensure optimal translation of our results to fruit and forest trees.