EDIT, FEB. 27: Kate Evans and Bruce Barritt (Washington State University breeders of the Cosmic Crisp apple) would like to clarify that no funding from the USDA-ARS NIFA RosBREED projects was used for the development of the apple variety. The WSU apple breeding program was funded with university and Washington grower funding.

RosBREED is a multi-institutional project funded in part by the USDA’s National Institute of Food and Agriculture (USDA-NIFA), with the objective of fast-tracking genetic improvement of crops in the Rosaceae family via DNA diagnostic tools so breeders can use genetic markers to better select for cultivars which combine disease resistance and fruit quality.

Pome fruit, stone fruit and some berries are being improved due to widespread research. The project’s tagline – “Disease resistance X Horticultural Quality = Superior Cultivars” – summed up the project’s overall purpose. RosBREED relied on the sharing of data between stakeholders, united by the goal of utilizing genetic markers to inform breeding programs, to more quickly develop the traits growers need (and consumers desire) to rapidly bring new cultivars to market.

According to data in the project’s last newsletter, 49% of the breeders across all 100 Rosaceae breeding programs in the U.S. have used or routinely use DNA information for marker-assisted parent selection, compared to less than 5% who did so when the project began in 2009. And 38% rely on that genetic data when selecting seedlings, up from 1% in 2009.

The December 2019 commercial release of the first Cosmic Crisp apple made headlines. The Cosmic Crisp, selected in part for the attractive color of one of its parent cultivars, Enterprise, along with the crisp texture and juicy taste of its Honeycrisp lineage – minus the problematic cultivation concerns which plague that cultivar – has been in the spotlight. It was developed by breeders Kate Evans and Bruce Barritt of Washington State University. Select growers in Washington will have exclusive rights to plant the apple until 2027.

Cornell’s 2013 release, RubyFrost®, developed by Susan Brown, exclusively grown and distributed by Crunch Time Apple Growers of New York, is Braeburn x Autumn Crisp cross, combining the desired traits of slow flesh browning and high vitamin C content. It has been phenotyped and genotyped and is being utilized in the RosBREED program to help pinpoint the location of genes that control these and other desirable traits.

While the cultivars which resulted from RosBREED research may be licensed, the program combines knowledge from participating universities, harnessing an incredible amount of genomic information to help researchers more efficiently and accurately select for targeted traits in their breeding programs. This marker-assisted breeding is needed to transmit targeted traits from the parent cultivars and combine them into an improved offspring with more accuracy and more rapid results than in traditional crossbreeding. One benefit of decoding the genome is that breeders can select plants they know have the specific genes for the traits they want to combine.

Apple growers are watching closely for new developments in fire blight and scab resistance, which have been made possible via rapid breeding techniques and other processes made available through the RosBREED program. Dr. Jay Norelli, USDA-ARS Appalachian Fruit Research Station in West Virginia, is breeding apple cultivars with genetic resistance to scab and fire blight. Wild apples have many of the genes needed. Using DNA technology to select accurately for parents with the multiple genes needed for disease resistance, as well as for the fruit quality traits desired, can significantly reduce the plant generations, and therefore time, needed to bring cultivars to market.

Speaking at the American Society for Horticultural Science 2019 conference, Jim Luby, University of Minnesota and RosBREED’s pome fruit breeding team leader, said that RosBREED DNA mapping plays an important role in their apple breeding program. It is utilized in cultivar parent selection as crosses are designed, and in seedling selection. A genomic scan of seedlings confirms pedigree, and with 99% of seedlings generated during breeding trials discarded, utilizing genetic mapping to better narrow the field has financial incentives too.

In designing crosses, phenotype information – taste, texture, storage and appearance – is selected, and then genotypic information is used to further refine parent selection, Luby explained. Once suitable phenotypic traits are identified, the germplasm loci are found, and breeders are able to better predict the effect of each parent used in the breeding program to further refine how selections are made.

Honeycrisp, a favored parent with some good phenotypic traits, also has storage concerns. Honeycrisp is homozygous for alleles which result in soggy breakdown and soft scald, and the trait is coded for at allele two. When making crosses, the probability of these traits occurring decreases if Honeycrisp is crossed with a cultivar that does not contain this trait on either of its respective alleles.

Peach breeders are using RosBREED to help combine disease resistance, maturity and eating quality to develop new cultivars. Finding the genetic loci coding for foliar bacterial spot and brown rot resistance has been a focus of the peach breeding program.

Cherry researchers are getting closer to determining the combination of genes which promote firmness in sweet cherries. The trait is recessive – at least on some of the genes responsible. The ability to select parents who carry the gene for the trait, even if their own fruit is soft, will help breeders when developing crosses combining disease resistance and fruit quality. Fruit size and self-fertility are also being targeted. Foliar powdery mildew resistance is another priority, with breeders working to develop DNA testing predictive for infection. Sour cherry breeders are using DNA to test for red color and cherry leaf spot resistance, and are seeking genomic markers for late bloom times.

Strawberry breeders, led by the University of Florida, are seeking that elusive genetic loci which protects against Phytophthora crown rot. Two alleles which offer protection in a semi-dominant manner have been located, and the development of DNA testing to identify plants which carry these markers is underway.

Bramble genomes are being studied for sweet flavor markers, and are already tested for trueness-to-type which confirms paternity and removes the guesswork, by using a DNA test which was developed and made available via RosBREED.

Although RosBREED has concluded, the diagnostic tools and genomic database for Rosaceous crops generated by the project remain. Growers can look forward to the continued exploration and mapping of genomes, enabling breeders to further use marker-assisted breeding techniques to more quickly and accurately select for phenotypic traits on the genotypic level. By seeing into the genes and locating areas on chromosomes which code for certain attributes, and testing for plants with these markers, new cultivars that taste good and provide disease resistance can get to market sooner, not later. The project’s website is www.rosbreed.org.