Introduction

Fresh and processed products derived from the Rosaceae plant family (almonds, apples, apricots, blackberries, peaches, pears, plums, sweet cherries, tart cherries, strawberries, raspberries, roses and other ornamentals) provide vital contributions to human nutrition, health, and well-being, and collectively their production constitutes the economic backbone of many rural communities in the U.S. Although current domestic production value of these crops is over $7 billion, and global per-capita production and consumption is expanding in both domestic and export markets, the U.S. rosaceous crop industries face numerous limitations to profitability and sustainability. Overcoming these limitations requires rapid development and deployment of new cultivars with improved characteristics that meet dynamic industry, market, and consumer preferences. The improvement of rosaceous cultivars by targeted application of genomics research in breeding programs will exploit the extraordinary diversity of Rosaceae species. Hence, moving “genomics to the marketplace” by accelerating and increasing efficiency of cultivar development to match consumer demand within constraints of the production and marketing system is the primary goal of the project.

Rosaceae genetics and genomics information, and associated enabling technologies, are developing rapidly, leading to numerous discoveries with potential application. In 2009, not only are genetic linkage maps available for all major crop species, but also the apple, peach and strawberry genomes are being sequenced, and hundreds of QTLs and major genes have been identified. The vast majority of these QTL projects are being undertaken by RosBREED co-PDs and collaborators. In addition, 2009 will be a watershed year for Rosaceae genomics with the upcoming publication of draft genome sequences of apple, peach and diploid strawberry, all involving RosBREED collaborators.

Despite these advances in Rosaceae genetics and genomics, MAB implementation has been minimal in U.S. Rosaceae breeding programs. Most rosaceous crops are clonally propagated for commercial production (often as a scion-rootstock composite plant) and have long generation times before the commercial product (fruit, nut, flower) can be phenotyped. For all, evaluation of individual plants requires intensive greenhouse and/or extensive field space; thus, phenotyping individual plants is expensive. Application of genetic markers is an obvious opportunity, but has not been implemented, due to several significant barriers: (1) lack of validated QTLs, (2) QTL discovery performed in genetic backgrounds not relevant to breeder’s germplasm, (3) lack of robust markers polymorphic in relevant germplasm, (4) undefined linkage drag with favorable QTL/gene alleles, (5) lack of knowledge on the mode of action of these QTLs (additivity, epistasis), (6) lack of knowledge on robustness of QTLs over environments, (7) lack of statistical tools and software for genetic studies in polyploid genomes, (8) lack of genotyping capacity, and (9) lack of breeding personnel trained in the application of MAB. Bridging the gap between gene discovery and sustainable implementation of MAB in rosaceous crop breeding through establishment and implementation of a MAB pipeline is a focus of RosBREED.

RosBREED is rooted in our vision that the common ancestral origin of the diverse rosaceous genera can be harnessed to leverage knowledge and resources across commodity boundaries. This project exploits homology among the genomes of three fruit-bearing genera of Rosaceae: Malus (apple), Prunus (peach and cherry), and Fragaria (strawberry) to develop practical outcomes. These three lineages collectively represent the majority of the rosaceous fruits produced and consumed in the U.S. RosBREED focuses on improvements in fruit quality because of its direct impact on producer profitability and consumer demand.