Enabling marker-assisted breeding in Rosaceae crops

ISSUE: Almond, apple, caneberries, cherry, peach, pear, rose, and strawberry all belong to the same plant family, Rosaceae. Profitability and sustainability of U.S. rosaceous crop industries require an understanding of changing production, market, and consumer preferences, so breeders and supporting programs can develop and deploy new varieties addressing those preferences.

To efficiently and more rapidly deliver superior, commercially successful new varieties, breeding efforts can benefit greatly from new technologies and personnel trained in these appropriate technologies. Marker-Assisted Breeding (MAB) using DNA diagnostic information is one such technology that is particularly effective to select for desirable fruit quality traits such as size, color, flavor, and texture.

DNA diagnostic information helps breeders make creative parent combinations and select for desirable traits at the seedling stage, before plants even flower. This early screening reduces expenditures for planting, maintaining, and testing full-grown plants. While this approach can enhance all rosaceous crop breeding programs, it is especially helpful in perennial rosaceous crops such as fruit trees, because it can take more than 25 years to develop and commercialize a new variety. Tools, knowledge, and training in this area were needed for Rosaceae breeding to capitalize on decades of upstream scientific advances.

WHAT HAS BEEN DONE: The RosBREED project has developed and, for the first time, enabled the application of DNA diagnostic information to assist fruit breeding decisions on four rosaceous crops: apple, cherry, peach, and strawberry. United States breeding programs can now efficiently identify superior parents for making crosses and reduce expenses required to grow seedlings of unknown quality to maturity for field selection. The technologies are applicable for all Rosaceae crops.

RosBREED has created an advanced set of broadly accessible software tools and online resources so breeders can readily use MAB technologies. Socio-economists surveyed Rosaceae breeders, growers, market intermediaries, and consumers so that project resources for genetic test development were directed to better understand which traits would best be improved via MAB. A cohort of new graduate students was trained in modern breeding techniques.

IMPACT: Using RosBREED’s socio-economic and DNA diagnostic information and tools, breeders can now make exciting crosses by selecting parents that provide the highest proportion of desired offspring types for valuable fruit quality traits. DNA information then allows breeders to efficiently eliminate offspring unlikely to have desired fruit qualities preferred by industry sectors and consumers. Newly-trained professionals are now available to conduct MAB for efficient, accurate, and creative development of superior new cultivars addressing consumer and industry needs.
For example, the apple breeding program at the University of Minnesota used DNA tests to select parents most likely to produce the highest number of desirable offspring with superior crispness and juiciness, long fruit storability, disease resistance, and attractive skin color. Combining this information with flowering time, tree availability, and pollen quality, the team made many exciting crosses in 2012. Because only some of the resulting offspring will bear the desired trait combinations, MAB was further used to eliminate undesirable seedlings and reduce costs of field testing.

Bridging the Chasm – Collaborations between breeders and genomicists

ISSUE: Until the RosBREED project, genomics research had not been translated into routine practical application in breeding Rosaceae fruit crops (almond, apple, caneberries, cherry, peach, pear, strawberry, and others). There was a disconnect between crop genomicists and plant breeders. Genomicists had been generating information they believed would be valuable to plant breeders without asking them what they needed. Plant breeders were largely ignoring the efforts of genomicists, who they felt were unconcerned about ‘real world’ breeding problems.

WHAT HAS BEEN DONE: RosBREED provided a vehicle to facilitate discussion between genomicists and plant breeders working on apple, peach, strawberry, sweet cherry, and tart cherry crops. Genomicists, geneticists, and plant breeders met two to three times a year as crop-focused teams to facilitate communication and technology transfer. Geneticists used scientific advances made by genomicists to develop tests to identify individuals carrying valuable genetic factors contributing to desirable attributes prioritized by breeders of each crop. A stepwise process equipped breeders and their students to implement new genetic tests and statistical tools in their programs. Genomics advances were thereby leveraged to improve breeding efficiency, accuracy, and creativity by the technique of marker-assisted breeding (MAB).

IMPACT: Programs in targeted crops now use genomic information to enhance breeding efforts. None of them were using these tools before RosBREED. Participating programs now routinely use genetic testing to verify parentage. For example, the tart cherry breeding program at Michigan State University (MSU) discarded 30% of its seedlings in one breeding population because DNA markers indicated they derived from unintended parentage. Similarly, the MSU and USDA-Corvallis strawberry breeding programs discarded 42 individuals from 13 populations when DNA test results showed them to be of unintended parentage. Genetic tests were used to correct the pedigrees for 200 selections in the peach breeding program at UC-Davis.

Parents are now selected using genetic tests in all RosBREED breeding programs:

• Programs at Cornell University, University of Minnesota (UM), UC-Davis, and Washington State University (WSU) use genetic tests for fruit texture and storability.
• Peach breeding programs at Clemson University, University of Arkansas, Rutgers, and Texas A&M use genetic tests for flesh type, bacterial leaf spot resistance, acidity, blush, and soluble solids concentration.
• The sweet cherry breeding program at WSU uses genetic tests for self-fruitfulness, ripening season, and fruit firmness and size.
• The tart cherry breeding program at MSU uses genetic tests for fruit color and cherry leaf spot resistance.
• The strawberry breeding programs at MSU and USDA-Corvallis use genetic tests for red stele root rot resistance and the everbearing fruiting characteristic.

Three RosBREED programs now use genetic tests to cull seedlings and the rest are poised to follow. Nearly 15,000 seedlings in the apple breeding programs at WSU and UM were discarded prior to planting over the last three years, based on the prediction they would have inferior fruit quality traits or disease susceptibility. Nearly 4000 sweet cherry seedlings at WSU were discarded prior to planting, based on the prediction their flowers would be self-sterile and the fruit small and soft. These applications of MAB saved resources totaling $250,000 that would have otherwise been spent on seedlings likely to have inferior characteristics.

Adoption of Marker-Assisted Breeding

ISSUE: To safeguard sustainability of the rosaceous fruit industry in a highly competitive business environment, Rosaceae crop breeding programs need to develop and commercialize new varieties that are productive and appealing to stakeholders, including producers, processors, shippers and packers, retailers, and consumers. However, many rosaceous crops are long-generation tree crops. Development and commercialization of new varieties can take more than 25 years. To serve the needs of a wide range of stakeholders, breeders face challenges in allocating appropriate attention and resources to the many possible traits. Breeders also have limited tools for efficiently and accurately improving “complex” traits that are influenced by many genetic factors acting in concert.

WHAT HAS BEEN DONE: Demonstration breeders are now routinely using and benefiting from the DNA diagnostic tools developed by RosBREED to assist breeding decisions on five rosaceous crops: apple, peach, sweet cherry, tart cherry, and strawberry. During several workshops, the wider community of U.S. Rosaceae breeders was trained in the core concepts of marker-assisted breeding (MAB) and provided with resources to enable their adoption of efficient MAB approaches.

IMPACT: RosBREED genomics and genetics researchers eliminated the need for individual breeders to develop DNA diagnostic tests. Because the new DNA diagnostic information was developed using germplasm from U.S. breeding programs, the new tools are directly applicable in these programs. The workshops helped breeders overcome various concerns. Breeders are now better prepared to use MAB to make their programs more effective.

A baseline survey conducted in 2009 established the level of MAB adoption among U.S. Rosaceae breeders and allied scientists at that time. Both groups reported moderately positive attitudes toward the future importance of MAB but low levels of actual use of genetic tests in their work. A follow-up survey in December 2013 will allow us to quantify change in adoption over these years.

During the project period, RosBREED provided three in-depth workshops for the dozen RosBREED “demonstration” breeders and five workshops for the wider community of U.S Rosaceae breeders. On average, more than 80 percent of workshop participants “strongly” or “moderately” agreed that they gained new knowledge which they intended to apply in their work. In interviews with a random sample of breeders in winter 2011-12, almost three quarters reported using markers for plant identification and about one quarter were using markers for more advanced applications.

RosBREED’s Demonstration Breeding Programs

RosBREED crop teams include demonstration breeding programs and breeder advisory panelists in five rosaceous fruit crops. They evaluated germplasm for fruit quality traits and other critical traits in multiple US production regions: 

Strawberry - California, Florida, Michigan, New Hampshire, Oregon
Peach – Arkansas, California, South Carolina, Texas
Apple – Minnesota, New York, Washington
Sweet Cherry – Washington
Tart Cherry - Michigan

Apple Breeding

ISSUE: New apple varieties with improved fruit quality will lead to increased consumer consumption, enjoyment, and health, and will contribute to the profitability and sustainability of the U.S. apple industry. However, breeding a new apple variety is a slow and inefficient process that can take 15 to 25 years. Predicting which individuals will serve as the best parents is difficult. From the seedlings produced after crossing, thousands must be grown and tested in evaluation orchards to identify the few with commercial potential.

WHAT HAS BEEN DONE: Apple breeders in Washington, New York, and Minnesota evaluated many important breeding parents, their ancestors, and their offspring for fruit quality traits and other critical attributes like disease resistance. Evaluating these individuals across different sites added to our understanding of key traits and their interrelationships, making it possible to more efficiently improve them genetically.

DNA tests were developed to predict apple skin color, fruit firmness, crispness, juiciness, acidity, storability, and storage disorders. These new genetic tests enable apple breeders to select parents with the greatest likelihood of transmitting favorable traits. The tests also identify the best seedlings for advanced testing, reducing the need to grow out and sort through thousands of seedlings with unacceptable fruit quality.

Using this strategy, called Marker-Assisted Breeding, apple breeders can now more efficiently, accurately, and creatively develop superior new apple varieties that meet the needs and desires of consumers and producers.

IMPACT: As a result of genetic testing in the apple breeding programs:

• New crosses designed since 2011 and earlier have incorporated expanded genetic knowledge of each parent’s potential to transmit desirable traits to their offspring, resulting in greater genetic gain in the next generation.
• More than 14,000 seedlings were discarded in 2011 to 2013, prior to field planting, after DNA screening predicted that they would have inferior fruit quality or disease susceptibility, thus avoiding resource expenses totaling nearly $200,000.