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

Amy F. Iezzoni, Jim McFerson, James Luby, Ksenija Gasic, Vance Whitaker, Nahla Bassil, Chengyan Yue, Karina Gallardo, Vicki McCracken, Michael Coe, Craig Hardner, Jason D. Zurn, Stan Hokanson, Eric van de Weg, Sook Jung, Dorrie Main, Cassia da Silva Linge, Stijn Vanderzande, Thomas M. Davis, Lise L. MahoneyChad Finn, Cameron Peace

Research output: Contribution to journalReview articlepeer-review

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.

Original languageEnglish (US)
Article number177
JournalHorticulture Research
Volume7
Issue number1
DOIs
StatePublished - Dec 1 2020

Bibliographical note

Funding Information:
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.

Funding Information:
RosBREED 1 and RosBREED 2 were supported by the USDA-NIFA Specialty Crop Research Initiative (SCRI) program, an unprecedented federal grant program initiated in 2008 to support transdisciplinary research and extension activities addressing industry needs in specialty crops. In fact, the SCRI arose in response to stakeholder efforts such as the National Tree Fruit Technology Roadmap. Another key partner was the U.S. Rosaceae Genomics, Genetics, and Breeding Executive Committee (RosEXEC). Formed in 2005 and broadly representing industry, research, and extension interests among U.S. rosaceous crops, RosEXEC helps identify and communicate both stakeholder priorities and research community needs (https://www.rosaceae.org/community/us_rosexec). In 2011, the European Union funded a 4.5-year project designed to address the same chasm targeted in Ros-BREED, entitled “FruitBreedomics – Integrated approach for increasing breeding efficiency in fruit tree crops”. This project included only two crops, apple and peach, but the synergy among scientists in RosBREED and Fruit-Breedomics accelerated and enhanced the contributions from both projects18.

Funding Information:
This work was funded by USDA National Institute of Food and Agriculture-Specialty Crop Research Initiative Projects, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05858) and “RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars” (2014-51181-22378), rosaceous crop industry groups, and USDA Hatch funds provided to project participants. Three other awards to Co-PI D. Main have also acknowledged: USDA National Institute of Food and Agriculture Specialty Crop Research Initiative projects 2014-51181-22376 and 2014-51181-22378, USDA National Institute of Food and Agriculture National Research Support Project 10, and the NSF Plant Genome Research Program award #444573. The commitment and energy reflected by the entire RosBREED community, including non-U.S. research participants, Advisory Panel members, allied scientists, and industry stakeholders, is gratefully acknowledged. The RosBREED projects also benefited from the exemplary dedication and expertise of the two Project Assistants, Audrey Sebolt and Joan Schneider. Neither of the projects would have run so smoothly without their extraordinary commitment and attention to detail. We also thank Fred Bliss for his reading and helpful suggestions on the manuscript.

Publisher Copyright:
© 2020, The Author(s).

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