Active Projects

Rosbreed II

The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and tart cherry) provides vital contributions to human health and is economically significant in communities across the U.S. Industry stakeholders have given high priority to development of new cultivars that exhibit both disease resistance and superior horticultural quality to mitigate production, handling and market risks. Rosaceous crop breeders have responded to the need for genetic solutions by using resistance from wild and/or unadapted germplasm, but few have achieved commercial success because of difficulties breeding cultivars with both excellent fruit quality and disease resistance. The Rosbreed project addresses this need through a national coordinated effort that will enable breeding programs of U.S. rosaceous crops to routinely apply modern genomics tools for efficient and effective delivery of cultivars with producer-required disease resistances and market-essential horticultural quality. Objectives are to: (1) develop donor parents with multiple alleles for disease resistance; (2) enrich breeding families with alleles for disease resistance and superior horticultural quality; (3) advance selections with alleles for superior horticultural quality and disease resistance with improved confidence; (4) increase routine use of DNA information in rosaceous crop breeding; and (5) engage industry stakeholders in project outcomes, evaluation, and adjustment. This Coordinated Agricultural Project(CAP) addresses SCRI Focus Area 1: Research in plant breeding, genetics, genomics and other methods to improve crop characteristics such as (a) product taste quality and appearance, and (d) disease resistance. Website can be found at: https://www.rosbreed.org/home

Short and long-term solutions for Armillaria Root Rot in Prunus

Armillaria root rot (ARR) disease is affecting forest and fruit tree crops throughout the U.S. and is the greatest threat to peach and cherry orchard sustainability in the southeastern U.S. and the Great Lakes Region, respectively. ARR has become a serious and widespread problem in the major tart and sweet cherry production regions of Michigan and is responsible for tens of millions of dollars in losses in historic peach production regions of Georgia and South Carolina. Continued tree losses from ARR on formerly highly productive orchard sites have reached uneconomical levels in the Southeast. Industry stakeholders, local economies and communities are in critical need of a long-term durable solution mitigating this threat. This project brings together multi-state teams to develop short term and long term solutions to practical ARR problems that cross State boundaries and addresses the needs of specialty crop growers in the areas of plant pests and disease, and research in Prunus rootstock breeding, genetics and genomics. The proposed project evaluates and promotes novel horticultural approaches such as above ground root collar excavation for immediate implementation and addresses long-term industry needs by enabling and accelerating the discovery and translation of natural (local and exotic) sources of ARR resistance directly into DNA and biochemical diagnostic tools that will lead to developing new rootstocks for long-term sustainability of the peach and cherry industries. Website can be found at: https://www.clemson.edu/cafls/arr-solutions/index.html

Genome Database for Rosaceae: Empowering Specialty Crop Research through Big-Data Driven Discovery and Application in Breeding

Accounting for more than 50% of U.S. fruit, nut, and berry crop production, the economically important Rosaceae family provides valuable contributions to consumers’ dietary choices and overall health. Increasing risk from pests, diseases, and climate change pose challenges to the competitiveness and sustainability of the U.S. Rosaceae industry. Meeting these challenges requires high-resolution dissection of traits and relating molecular diversity to functional variation for efficient development of new cultivars through marker-assisted breeding. Concomitant advances in high-throughput sequencing, phenotyping, and computational technologies, coupled with significant investment by government, universities, and industry, are generating petabytes of genomic, genetic, and breeding data for Rosaceae crops. Efficient utilization of such “big data” requires analysis, integration, and visualization. Enhancing the resource-efficient Genome Database for Rosaceae will enable basic, translational, and applied Rosaceae research and be extendable to other specialty crops. Specific objectives are to: (1) collect, analyze, curate, and integrate large-scale Rosaceae genomics, genetics, and breeding data to facilitate cross-species data utilization and fundamental discovery; (2) provide data-mining resources for basic scientists and breeders to facilitate knowledge discovery and expedite development of cultivars; and (3) extend community outreach in genomics, genomics-assisted breeding, and crop management. This SREP addresses SCRI Focus Area 1: Research in plant breeding, genetics, and genomics to improve crop characteristics (70%), Focus Area 2: Efforts to identify and address threats from pests and diseases (20%), and Focus Area 3: Efforts to improve production efficiency, productivity, and profitability over the long term (10%). This project is submitted for consideration as a long-term project. Website can be found at: https://www.rosaceae.org/

Understanding the molecular basis of carotenoid synthesis and accumulation in stone fruits: A platform to enhance fruit value

Carotenoids provide fruit with attractive colors and aromas which play an important role in determining fruit marketability. Many carotenoids are also essential or beneficial nutrients in the human diet. Stone fruit species of the genus Prunus (e.g. peach, apricot, and plum) exhibit wide variation in carotenoid-based coloration and aromas, but our knowledge about the biochemical and molecular regulation of carotenoid accumulation in these species is extremely poor. Development of new stone fruit varieties that meet consumers' expectations and satisfy producers and retailers requirements is a long process. Marker-assisted selection (MAS) could significantly reduce the lengthy and expensive process of breeding new high quality stone fruit varieties with improved carotenoid composition. However, to employ MAS we must first identify the markers associated with our traits of interest.

Enabling Marker-Assisted Breeding for fruit size in peach

Large fruit size is highly attractive to consumers and commands a premium in the fresh peach market. Peach producers desire that new varieties have increased size alongside other evolving consumer preference traits such as appearance and aroma and cultural traits like disease resistance. Unfortunately, assessing fruit size in conventional breeding programs is inefficient in time and resources which reduces the speed at which new germplasm can be developed, assessed, and placed into the hands of growers. New tools are needed for the breeder that will allow selection of trees early in the breeding pipeline which possess size characteristics that are sought by South Carolina growers. Therefore, we will discover and develop cost effective, easy to use genetic markers for peach fruit size potential. Implementing marker-assisted selection for fruit size into our breeding program will increase the speed and cost-efficiency with which multiple desirable traits can be accumulated into new varieties for the growers of South Carolina. Rapid and efficient production of new varieties with increased fruit size will enhance profitability, competitiveness and economic sustainability of peach producers in South Carolina.