RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops

Iezzoni et al. Horticulture Research (2020)7:177 https://doi.org/10.1038/s41438-020-00398-7 REVIEW ARTICLE Horticulture Research www.nature.com/hortres Open Access RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Amy F. Iezzoni1, Jim McFerson2, James Luby3, Ksenija Gasic 4, Vance Whitaker5, Nahla Bassil 6, Chengyan Yue3, Karina Gallardo7, Vicki McCracken8, Michael Coe9, Craig Hardner10, Jason D. Zurn 6, Stan Hokanson11, Eric van de Weg 12, Sook Jung13, Dorrie Main8, Cassia da Silva Linge4, Stijn Vanderzande8, Thomas M. Davis 14, Lise L. Mahoney14, Chad Finn6 and Cameron Peace8 Abstract The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a “chasm” existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project (“Ros” signifying a Rosaceae genomics, genetics, and breeding community initiative, and “BREED”, indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement. This review Rosaceous fruit, nut, and floral crops provide high-value nutritious foods, contribute to our esthetic enjoyment, and are economically important globally. Related through their ancestral genome1, rosaceous crops have been Correspondence: Amy F. Iezzoni () 1 Michigan State University, East Lansing, MI 48824, USA 2 Washington State University, Wenatchee, WA 98801, USA Full list of author information is available at the end of the article Deceased: Chad Finn. selected and bred to provide an assortment of superior cultivars on which modern production is based. However, the next generation of cultivars is needed to improve consumer satisfaction, profitability for industry stakeholders, and environmental sustainability. In the “genomics era”, many crop scientists routinely access database resources, leverage increasingly detailed knowledge of plant genomes, and apply genetic tools to significantly enhance the efficiency and effectiveness of new-cultivar development. However, adoption of such DNA-informed © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Iezzoni et al. Horticulture Research (2020)7:177 breeding had lagged in rosaceous crops, with a daunting chasm between ongoing scientific discoveries and practical breeding applications. The RosBREED projects were a 10-year collaborative effort that bridged this chasm. This review presents a synopsis of the history, approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. RosBREED in a historical context An extraordinary coming-together of the global rosaceous research community2 coincided with the U.S. crop industry’s prioritization of new-cultivar development as a research goal3. Equally important, the USDA-NIFA Specialty Crop Research Initiative (SCRI) provided significant funding opportunities and stimulated investment in breeding. RosBREED was an outcome of this unprecedented situation. The RosBREED approach was based on the premise that diverse rosaceous crops all shared a need for genomics information and diagnostic tools and envisioned addressing this need by a multi-crop, multi-state, transdisciplinary research and extension effort. Rosaceous crop breeders, industries, and allied scientists, united in this common goal, were the foundation upon which the RosBREED projects were developed. Page 2 of 23 Table 1 Rosaceous crops grown in the U.S. in 2018: bearing hectares, total production, and value of utilized production in 2018193,194. Crop Bearing Total production Value of utilized hectares (metric tonnes equivalent) production (US $1000) Almond 441,100 1,698,700 5,468,040 Apple 117,800 4,652,500 3,013,713 Apricot 4,300 35,900 48,465 Blackberry 2,600 18,300 20,100 Cherry, sweet 34,400 312,400 637,700 Cherry, sour 14,200 135,300 56,635 Nectarine 5,700 109,300 119,650 Peach 30,100 591,000 511,226 Pear 18,700 730,700 428,940 Plum 5,700 90,700 92,570 Prune 17,800 253,700 194,832 Raspberry 6,800 99,200 367,001 Strawberry 19,900 1,296,300 2,670,523 Rose – – 28,069 The Rosaceae family Total 719,100 10,025,000 13,654,464 Crops in the Rosaceae family are produced worldwide, primarily in temperate climates. While most are grown for their fruit, in both fresh and processed forms, the family also includes important nut (e.g., almond) and ornamental (e.g., rose) crops. The fruit crops, comprising apple, apricot, blackberry, nectarine, peach, pear, plum, red and black raspberry, strawberry, sweet cherry, and sour cherry, exhibit wide morphological diver (...truncated)