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

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.

Fig. 1. U.S.-wide demonstration breeding programs.

apple Univ. of Minn., Wash. State Univ., Cornell Univ., USDA-ARS Kearneysville, WV; peach Clemson Univ., Univ. of Ark., Texas A&M Univ., Univ. Calif. – Davis; sweet cherry Wash. State Univ.; sour cherry Mich. State Univ.; strawberry USDA-ARS Corvallis, OR, Mich. State Univ., Univ. Florida, Univ. New Hampshire; blackberry Univ. of Ark., USDA-ARS Corvallis, OR; pear USDA-ARS Kearneysville, WV; rose Univ. of Minn., Texas A&M Univ.; Prunus rootstock Clemson Univ., Mich. State Univ. The two “newly adopting” breeding programs that participated in cost analyses were strawberry at Wash. State Univ. and peach at Mich. State Univ.

Fig. 2. RosBREED’s reference germplasm sets were designed to represent alleles of important breeding parents (IBPs) to support simultaneous QTL discovery and validation in breeding program germplasm.

A subset of the apple Crop Reference Set is shown here, which involved collaboration among breeding programs from three institutions. IBPs in this subset are in bold. “Honeycrisp” was represented directly by immediate descendant F₁ families (here shown with 19 + 28 + 9 offspring) as well as indirectly by closely related families (such as the “Sweet Sixteen” × BC-8S-27-43 family). “Cripps Pink” and “Granny Smith” were each represented by the other’s direct F₁ families. The dashed lines and family indicate further representation of “Cripps Pink” with the possible inclusion of 20 offspring in a Breeding Pedigree Set family. IBPs were also often represented by other families via ancestral relationships (e.g., “Sansa” was represented by all families also descended from “Golden Delicious” or “Delicious”). The germplasm sets were chosen based on pedigree knowledge at the time. Much additional allelic representation was provided by many other pedigree connections later discovered, such as “Golden Delicious” being a grandparent of “Honeycrisp” and “Splendour” being the offspring of “Golden Delicious” and “Delicious”. Some pedigree records were also corrected (e.g., “Regent” was discovered to not be “Duchess of Oldenburg” × “Delicious” but rather the child of “Haralson” and “McIntosh”)