RosBREED: A Jewel Of A Program
February 6, 2014 
Every January for the past four years, I have made a trip to San Diego, partly because of the fishing, but mostly to go prospecting.
While the fishing has been marginally productive, I have been amazingly successful prospecting, encountering gemstones of all sorts. These jewels, however, are not mineral, but biological. More precisely, these are “jewels in the genome,” a term coined by Dr. Amy Iezzoni, a tart cherry breeder at Michigan State University.
The term “genome” refers to all the DNA an individual inherits from its parents. That DNA is composed of only four molecules called nucleotides. These nucleotides are strung together one after the other on the double helices constituting an organism’s chromosomes. Their pattern forms the basis of all the characteristics that an organism possesses, including specific stretches called genes, which govern specific characteristics like flowering time, fruit size, or disease resistance.
Of course, the surrounding environment plays a huge role in determining how those genes are expressed in an individual genotype. For many fruit and nut crops, complicating factors like a rootstock make things even more complex!
Ultimately, whether it is a single bacterium or a wild rose or a grafted almond, an organism’s genes and environment interact to produce a phenotype, a technical term to describe all its observable characteristics.
Like other crop producers, the tart cherry growers Iezzoni works with care about phenotype, because that is what they grow in order to produce the product they hope someone will buy. They want trees that establish well, are reliably productive, resist diseases, and harvest easily. They want fruit that exceeds expectations of consumers and market intermediaries for size, color, and quality attributes. And all that starts with genetics — superior phenotypes come from superior genotypes.
A tart cherry scion’s genetic information sets a biological limit for the productivity of its trees and the quality of its fruit. Growers do everything they can to get the most out of each genotype, striving for high yields of superior quality fruit, but both those aspects are fundamentally dependent on having the best genetics in place.
Remarkable Track Record
As a practical tart cherry breeder, Iezzoni is most interested in phenotypes that can contribute the most to her industry’s profitability. And here is where the jewels come in. If she is able to identify favorable genes, ones the confer attributes like large fruit size and excellent external color and disease resistance, she can polish and set these jewels in the right genotype, thereby upping the genetic potential her growers can use to excel at what they do.
Of course, this is what plant breeders have been doing for centuries, prospecting for jewels based on assessing an individual phenotype, but often with little knowledge of the underlying genotype.
Modern genomics and genetics technologies have changed all that, yet breeding programs in rosaceous crops have lagged far behind other crops. We have jewels in our genomes, but we have not been able to find them effectively or efficiently.
Fortunately, we are catching up. That is exactly why I have been going to San Diego, prospecting for jewels and meeting with the dozens of scientists and industry stakeholders involved in the RosBREED project, of which Dr. Iezzoni is Project Director.
Funded from 2009-2013 through the USDA Specialty Crop Research Initiative (SCRI), RosBREED is over, but its deliverables have transformed the effectiveness and efficiency of plant breeding programs in rosaceous crops, trained the next generation of plant breeders, and revealed an amazing set of jewels in the rosaceous genome.
Now that we know complete or partial DNA sequences in many rosaceous crops (almond, apple, apricot, blackberry, cherry, peach, pear, raspberry, rose, and strawberry), we can analyze the underlying nucleotide patterns with high-powered statistical tools and associate specific DNA variation with desirable tree and fruit phenotypes.
Sometimes, if we are lucky, we can tell exactly where that jewel is located and track the gene in the breeding process. Variation in the pattern of nucleotides can also be used to identify chromosomal regions physically close to the real jewels. RosBREED has discovered many such DNA markers and enabled their use in breeding programs.
Rosaceous crop breeders can now choose the best parents for their crosses, based on their industry’s priority traits, as well as select progeny for priority traits while screening young seedlings, thus avoiding the expense of multiyear field evaluations.
While I have mentioned RosBREED in this column during its four-year run, it was not always clear that we would find or polish any jewels in the rosaceous genome. Now, we can say that the prospecting has paid off.
We can also point to the remarkable track record of the SCRI program in motivating and supporting such large-scale, results-oriented research as well as obtaining buy-in from industry stakeholders, including Brian Sparks, editor of American/Western Fruit Grower. RosBREED has compiled an easy-to-read portfolio of one-pagers summarizing its deliverables, located at www.rosbreed.org/node/370. We have invited policymakers and legislators to take a look and invite readers here to do the same.
It has been terrific to be part of RosBREED’s successful prospecting for rosaceous jewels, but the project’s most significant impact might be encapsulated in a question at the recent meeting of the Michigan Tart Cherry Advisory Committee: “So, Amy, when will you get the NEXT marker?”
I will miss visiting San Diego, but a national team of researchers is working on RosBREED2. With any luck (including a new Farm Bill), we will return to San Diego for more prospecting, and perhaps, a little fishing.
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