ISSUE: New strawberry varieties with improved fruit quality will lead to increased consumer enjoyment and consumption, and will contribute to the profitability and sustainability of the U.S. strawberry industry. To meet this challenge, new strawberry varieties are needed that are high yielding due to continuous flowering and that are resistant to soil pathogens that cause serious diseases like root rot. However, breeding new strawberry varieties is slow and inefficient. Predicting which selections will be the best parents is difficult. Thousands of seedlings must be grown and tested in the field to identify the few with commercial potential.
WHAT HAS BEEN DONE: Strawberry breeders in California, Florida, Michigan, New Hampshire, and Oregon evaluated more than 900 individuals including old and new varieties, wild plants from North and South America, elite breeding parents, and experimental crosses from the Netherlands, United Kingdom, Spain, France, and the United States. This data was used to enable the development of genetic tests that strawberry breeders can use to verify plant identity and determine the best parents to combine, giving them the best seedlings to advance. A genetic test was developed to predict resistance to one of the sources of root rot resistance. This genetic test enables breeders to identify seedlings that have this source of resistance without the need to carry out expensive, time-consuming disease inoculation tests.
IMPACT: As a result of genetic testing of strawberry selections in the USDA-ARS Corvallis, Oregon and Michigan State University breeding programs and extensive performance evaluations of these strawberries:
- Forty-two individuals from 13 crosses were discarded because DNA tests identified them as derived from unintended parentage.
- For several important varieties used as parents, plants from multiple sources were found to be different genetically and therefore somehow mislabeled during cultivation and breeding use.
- Fourteen strawberry selections were identified as having new sources of root rot resistance.
- Two interspecific hybrids of wild strawberries were found which are strongly continuously flowering in multiple environments (California, Michigan, and Oregon). These individuals will provide breeders with a unique genetic source of repeat flowering.
ISSUE: The development of new crop varieties of the Rosaceae plant family with improved horticultural performance and market potential can be accelerated with use of DNA information in breeding, benefiting all supply chain members through more efficient, accurate, and creative breeding for desirable crop traits. However, DNA-informed breeding requires extensive genetic knowledge, trained personnel, and sufficient financial resources. Therefore, it is crucial for breeders to focus their efforts and resources on valuable crop attributes throughout the whole supply chain and of value to consumers.
However, systematically identifying these valuable attributes is challenging. Very few studies of crop plants have evaluated the importance of attributes across the supply chain members and consumers. Breeders have therefore had to focus their breeding programs on specific targets with little systematic knowledge of the relative value of incremental improvements in those traits for producers, market intermediaries, and consumers.
PROGRESS: The relative importance to different stakeholders (breeders, growers, market intermediaries, and consumers) of trait levels for apple, peach, strawberry, sweet cherry, and tart cherry were investigated. In addition, economic values of achieving particular fruit quality trait thresholds (added dollar value per pound) for growers and marketing intermediaries were estimated in these crops. Marginal values for consumers of achieving fruit quality trait thresholds in fresh market apples were also estimated.
IMPACT: Project resources for genetic test development were directed to those genomics discoveries having the highest relative value of importance across stakeholders. Information about the economic values of specific crop trait levels is now available to inform the ongoing work of geneticists and breeders as they develop new genetic tests and direct those to efficiently, accurately, and creatively developing superior new crop varieties of value ot stakeholders.
Examples of high value trait levels for which genetic tests have been developed include: apple exceptional crispness, juiciness, tartness, and freedom from bitter pit blemishes, various peach fruit types (normal/low acid, yellow/white flesh, peach/nectarine, melting/non-melting, and freestone/clingstone) that can be targeted across the fruiting season, strawberry sufficient acidity, sweet cherry large size and firmness, and tart cherry red fruit color.
ISSUE: Learning how crop traits are related to specific DNA markers requires a measuring many individual plants for many valuable characteristics – known as “phenotyping”. These traits must be evaluated and recorded in a consistent, standardized manner regardless of the location, personnel, or time. With this high quality phenotypic data, links between specific DNA sequences and important fruit and plant traits can be accurately determined because confounding “noise” is greatly reduced. Furthermore, when several breeders use standardized phenotyping protocols they can pool the data. The resulting large data sets give incredible power to identifying and characterizing genomic regions influencing important traits. Prior to RosBREED, phenotypic data was collected in small, isolated studies, limiting the size of data sets and limiting the extent to which results could be extended.
WHAT HAS BEEN DONE: Each RosBREED crop team (apple, peach, strawberry, sweet cherry, and tart cherry) chose a reference set of several hundred individual plants (including ancestral and modern varieties, breeding selections, and seedlings) that represent the pedigrees of current important parents in U.S. breeding programs. Participating breeders agreed on the traits to be evaluated and then developed and documented standardized protocols to collect measurements of these plant and fruit characteristics. They compiled extensive databases for fruit quality and other critical traits, with measurements were made over multiple years and locations.
IMPACT: A database of trait measurements on approximately 500 hundred individuals in each apple, peach, strawberry, sweet cherry, and tart cherry is now documented and publicly accessible. Breeders and allied scientists now use the database to discover specific genomic regions that are associated with important crop traits. The resulting genetic tests enable efficient marker-assisted breeding for more than 150 critical fruit quality and production traits in rosaceous fruit crops.
- Apple: 43 fruit traits evaluated at harvest and after cold storage of fruit, and five production traits
- Peach: 29 fruit traits and seven production traits
- Strawberry: 30 fruit traits, six disease resistance traits, and 13 plant architecture and production traits
- Sweet Cherry: 19 fruit traits
- Tart Cherry: 23 fruit traits, 12 production traits, and nine disease resistance traits The standardized phenotyping protocols are available at www.rosbreed.org. By using these protocols in future work to measure more individual plants, the public database can be expanded, and private datasets can be developed that are compatible and lead to even more powerful analyses and thereby more accurate genetic tests.
Enabling Genetic Technologies
ISSUE: Prior to this project, genetic tests for traits of interest in Rosaceae crops either had not yet been developed or they were expensive and cumbersome to use. Genome-scanning DNA markers were small in number which did not allow the efficient identification of chromosome regions influencing important traits. Moreover, most of these markers were laborious to use and relatively expensive, therefore limiting their applications in genetic discovery and breeding.
PROGRESS: Cost-effective, high throughput marker technologies were developed, commercialized, and made available to the U.S. and worldwide scientific community. Thousands of single nucleotide polymorphism (SNP) markers were developed for apple, peach, cherry, and cultivated strawberry in international RosBREED-led efforts. The genome scan platforms developed were the 9K (9000 genetic points testable across the crop’s chromosomes) peach, 8K apple, and 6K peach SNP marker Infinium® II arrays partnering with the commercial genomics technology company, Illumina Inc., and the 90K SNP marker (IStraw90™) Axiom® genotyping array, partnering with Affymetrix Inc.
IMPACT: Rosaceous breeders and geneticists can now efficiently generate and analyze thousands of well-performing genetic markers at low cost. These genetic marker tools are being used by numerous U.S. breeding programs to better understand the genetic control of highvalue
traits and make more informed crosses.
IStraw90™ is the first genome-wide scan ever developed for an octoploid crop (which is an organism like strawberry that has eight rather than two sets of chromosomes). This enabling genetic technology paves the way for further advances in genomics and breeding for other important polyploid crops (organisms with more than two sets of chromosomes).
As a result of developing and using these genome-wide scans:
- Arrays to process 20,000 samples at a value exceeding 1.3 million dollars were purchased from Illumina Inc., by ten groups in ten countries.
- Fourteen scientific articles were published to date describing the use of these tools to identify genomic regions influencing important traits, to characterize the genetic architecture of complex traits in apple, peach, and cherry, and other genetics and breeding applications like confirming or deducing pedigrees.
- IStraw90™, the first high-resolution genome-wide scan ever developed for an octoploid crop, is now available for use by breeders and researchers.
Enabling Statistical Tools
ISSUE: The first step in the development of genetic tests for use in Marker-Assisted Breeding is the discovery of genomic regions influencing traits of interest. The second step is to determine whether these discoveries are relevant for breeding germplasm. In the past, discoveries for rosaceous crops were conducted in dedicated experimental families for which the underlying genetic models were simple and the statistical tools well developed. The discoveries were rarely and inconsistently validated in breeding families, because such families are genetically complicated due to great diversity and unbalanced pedigree structures.
WHAT HAS BEEN DONE: Advanced statistical methods and software tools were developed to help genetic researchers manage and analyze data directly using breeding genepools. The statistical software developed were also adapted to efficiently process the large and unprecedented amount of genetic data available from genome scans. The first applications of these new software tools were performed on RosBREED data.
IMPACT: An efficient pipeline from genetic discovery to breeding application is now available. U.S. rosaceous crop breeders and geneticists can now efficiently analyze thousands of well performing DNA markers across each crop’s entire genome. Finding genomic regions influencing important traits for breeding is now commonplace. Genetic discoveries leading to new genetic tests include:
- Peach: Fruit texture, flesh type, flavor, size, skin color, maturity date, and bacterial spot tolerance
- Apple: Fruit firmness, crispness, juiciness, sweetness, acidity, skin color, bitter pit incidence, and storability
- Sweet cherry: Fruit size, firmness, skin and flesh color, sweetness, acidity, and maturity date
- Tart cherry: Fruit and pit size, cherry skin and flesh color, ability to self-pollinate, and resistance to cherry leaf spot fungus
- Strawberry: Red stele resistance, continuous flowering