Cameron Peace, DNA-Informed Breeding Team Leader

Welcome to the future! Whether you’re charging in with open arms, simply enjoying the ride, or being dragged along kicking and screaming, the art of Rosaceae crop breeding is changing. It’s becoming more scientific. More objective, planned, efficient, accurate, creative, exciting, transformative!

Large genetic gains are still possible in a single generation, and opportunities abound for unusual and valuable crossing outcomes. Because relatively few generations separate our crops from their wild ancestors, alleles providing large, commercially relevant phenotypic contrasts for most target traits still segregate in breeding germplasm. So a chance cross can still result in an industry-changer.

Recent advances in the technology known as DNA-informed breeding are providing breeders with an unprecedented window on and access to the genetic factors and combinations underlying commercial success and environmental sustainability. Desired outcomes can be more efficiently, accurately, and creatively targeted than ever before.

How can each Rosaceae breeder take advantage of scientific advances in the genetics of their crop? By keeping up to date with the latest knowledge, tools, and concepts. This regular RosBREED Newsletter column, and its associated webpage (http://www.rosbreed.org/breeding/community-breeders), is intended as a reference resource to keep the community of rosaceous crop breeders in touch with upstream research approaches, technology interfacing, new DNA information, and events.

Upstream Research Approaches

RosBREED is investigating many interesting research approaches to gain insights into the genetics of rosaceous crops. These investigations are “upstream” of breeding because they are not directly for breeding application. Instead, the insights gained will be used to develop tools and knowledge for subsequent breeding application.

For example, the SNP array-based genome scanning developed in the first project is an upstream research approach. Use of the SNP arrays in well-planned experiments provided us with unprecedented genomic resolution on relatedness and functional allelic diversity for U.S. breeding germplasm of peach, apple, strawberry, and cherry. The SNP arrays were not meant for direct breeding use, as the raw results obtained from genome-wide SNP genotyping – just a huge file of As and Bs – do not immediately reveal anything of breeding utility. Even now, as geneticists have interpreted what many of those binary bits mean, we do not yet recommend breeders scanning the genomes of their important breeding parents and elite selections. Only a few demonstration breeders of the first project with postdocs or advanced graduate students ready to spend months to years analyzing the SNP datasets are daring to use the arrays. We’re not yet at the interpretive stage of human genome-scanning companies like 23andMe! But we’re aiming for it during the next five years of this project.

While geneticists supporting breeding programs will be the most likely to find utility in these topics, breeders should find it useful remaining abreast of the latest scientific approaches being trialed and refined for their crops.

Technology Interfacing

The outputs of successful upstream research become new technologies that Rosaceae breeders can use to enhance their endeavors. But how do they work conceptually? Where can they be accessed? How can they be best integrated with ongoing breeding operations?
In this category of Community Breeders’ Page article, answers to these questions will be provided for available technological innovations in DNA-based diagnostics. An example research outcome is a valuable trait-predictive DNA test. Articles will extend to advice on what features about a DNA test that a breeder should ask for, strategies for using a little to a lot of DNA information in various breeding operations, what to expect and how to find service providers for DNA-based diagnostics, available decision-support software, and so on. And to ensure we’re all on the same planes of communication and understanding, now and then there will be updates on terminology in the DNA-informed breeding arena.

Terminology:
DNA-informed breeding: The use of DNA-based information, obtained via direct assays of an organism’s DNA, to directly support breeding decisions.

In this definition, the word “information” implies data interpreted for its breeding utility, not raw data from the assays of DNA marker genotyping or DNA sequencing. DNA-informed breeding is often successfully used synonymously with “marker-assisted breeding” (MAB). Both include use of DNA marker information for phenotype predictions as well as relatedness/identity. However, MAB is not a term to be thrown around in polite (non-geneticist) company, as you’ll find yourself back-tracking to painfully explain what a “marker” is. DNA-informed breeding provides a much less jargoned term that anyone can appreciate.

For what it’s worth, the term is also free of GMO connotations. In two ways, “DNA-informed breeding” is not quite the same as MAB: (1) it does not encompass the MAB strategy of using morphological markers in breeding selection, such as apple seedling leaf color to predict flesh color (red leaves = red flesh); but (2) it does include genome-wide selection, also known as genomic selection, which uses performance predictions based on genome-wide markers designed to capture both large-effect and small-effect loci segregating in breeding families. Thus, DNA-informed breeding is not restricted to using information only about significant QTLs.

New DNA Information

The successful application of new technologies on publicly available germplasm by publicly funded researchers leads to new DNA information that can be shared in this category of article. Information that breeders should find valuable are new insights into trait genetics, relatedness, and functional genotypes at trait-predictive loci for specific breeding germplasm individuals.

Did you hear about the discovery by Rosyara and co-workers (2014) that the sweet cherry industry standard ‘Bing’ was fathered by the old French ‘Napoleon’? This pedigree connection significantly increases the known inbreeding coefficients among numerous North American cultivars. Which publicly available important breeding parents are heterozygous for dominance-effect Mendelian trait loci, such as peach flesh color (Y locus), acidity (D locus), and peach vs. nectarine (G locus)? Find out in upcoming Community Breeders’ Page articles.

Events

Over the coming years, RosBREED will host numerous in-person information delivery and DNA-informed breeding training events for U.S. Rosaceae breeders. Other momentous and interesting events are on the international stage. The plans and outcomes of these events will be described here.

If you have a request for a Community Breeders’ Page topic in one of the above categories, please email me at cpeace@wsu.edu.
Community Breeders’ Web-Page: http://www.rosbreed.org/breeding/community-breeders.

Reference cited

Rosyara U, Sebolt A, Peace C, Iezzoni A. 2014. Identification of the paternal parent of ‘Bing’ sweet cherry and confirmation of descendants using Single Nucleotide Polymorphism markers. J. Amer. Soc. Hort. Sci. 139:148–156.