Source: MICHIGAN STATE UNIV submitted to
ROSBREED: COMBINING DISEASE RESISTANCE WITH HORTICULTURAL QUALITY IN NEW ROSACEOUS CULTIVARS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
EXTENDED
Funding Source
OTHER GRANTS
Reporting Frequency
Annual
Accession No.
1004205
Grant No.
2014-51181-22378
Project No.
MICL05083
Proposal No.
2014-07898
Multistate No.
(N/A)
Program Code
SCRI
Project Start Date
Sep 1, 2014
Project End Date
Aug 31, 2018
Grant Year
2017
Project Director
Iezzoni, A.
Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824
Performing Department
Horticulture
Non Technical Summary
The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and tart cherry) provides vital contributions to human health and is economically significant in communities across the U.S. Industry stakeholders have given high priority to development of new cultivars that exhibit both disease resistance and superior horticultural quality to mitigate production, handling and market risks. Rosaceous crop breeders have responded to the need for genetic solutions by using resistance from wild and/or unadapted germplasm, but few have achieved commercial success because of difficulties breeding cultivars with both high fruit quality and disease resistance. This project addresses this need through a national coordinated effort that will enable breeding programs of U.S. rosaceous crops (apple, peach, cherry, strawberry, pear, blackberry, and rose) to routinely apply modern genomics and genetics tools to efficiently and effectively deliver cultivars with producer-required disease resistances and market-essential horticultural quality. The long term target outcome is improved consumption, satisfaction, profitability, and sustainability of U.S. rosaceous fruit, nut and floral crops due to a continual supply of new disease resistant cultivars with superior horticultural quality.
Animal Health Component
0%
Research Effort Categories
Basic
5%
Applied
40%
Developmental
55%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
2011110108120%
2011112108120%
2011114108120%
2011122108120%
2011115108110%
2012199108110%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1112 - Cherry; 1122 - Strawberry; 1110 - Apple; 1114 - Peach; 1115 - Pear; 2199 - Ornamentals and turf, general/other;

Field Of Science
1081 - Breeding;
Goals / Objectives
The overall project goal is to assist U.S. Rosaceae crop breeding programs to more efficiently, accurately, creatively and rapidly deliver new cultivars with market-essential horticultural quality and producer-required disease resistance. Specific objectives are to: (1) develop donor parents with multiple alleles for disease resistance; (2) enrich breeding families with alleles for disease resistance and superior horticultural quality; (3) advance selections with alleles for superior horticultural quality and disease resistance with improved confidence; (4) increase routine use of DNA information in rosaceous crop breeding; and (5) engage industry stakeholders in project outcomes, evaluation, and adjustment.
Project Methods
(Obj. 1) Participating teams of U.S. Rosaceae breeders and pathologists will identify and validate alleles for disease resistance by QTL analysis and incorporate these by marker-assisted introgression into breeding parents, termed "multiple resistance allele donors". Multiple resistance allele donors, with pyramided resistance alleles from multiple sources for one disease and/or combined resistance alleles for multiple diseases, will be made available to breeders U.S.-wide. (Obj. 2) New large-effect fruit quality alleles will be discovered by leveraging syntenic genomic locations of QTLs and using a genome-wide pedigree-based analytical approach. Alleles within regions contributing to desired phenotypes will be identified by haplotype blocking to expand selection decisions from individual loci and traits to many linked loci and traits. Marker-assisted parent and seedling selection will combine disease resistance with superior horticultural quality in the next generation of breeding families. (Obj. 3) Influences of genetic background and non-genetic factors will be identified using new statistical approaches to improve accuracy of predictions of genetic potential based on large-effect horticultural quality and disease resistance QTLs in apple, peach, sweet cherry, and strawberry breeding germplasm. Genome-wide prediction models will calculate relative effects of genetic background (cumulative effects of individually small-effect alleles) using existing high-resolution phenotypic and genotypic datasets. Genomic relationship matrices using dense SNP array will be used to merge RosBREED datasets with trials in the U.S. and other countries. Effects of non-genetic factors (e.g., management, climate, G × E) will be evaluated to improve prediction accuracy of genetic potential among and within these factors. In case studies, performance stability of elite selections under alternative growing conditions will be predicted, validated, and used to streamline selection advancement and engage stakeholders in the latter stages of their breeding programs. (Obj 4) Cutting-edge DNA diagnostic tools will be developed and crop-specific DNA testing services will be made available. Information will be integrated into enhanced decision-support software. Cost-benefit analyses will be conducted that identify tangible dollar values for DNA-informed breeding applications. Breeders and allied scientists will receive technical training in use of DNA information in breeding. (Obj. 5) Stakeholder decisions on new cultivar adoption will be systematically investigated in two breeding programs. Stakeholders will be engaged in project outcomes, evaluation, and adjustments engage industry stakeholders in project outcomes, evaluation, and adjustment.

Progress 09/01/16 to 08/31/17

Outputs
Target Audience:Target audiences include breeders of tree fruits, berries, and flowers in the Rosaceae family, pathologists, germplasm collection curators, molecular geneticists, and other allied scientists, producers of crops in the Rosaceae family, processors, marketers, and marketing organizations, the tree fruit, berry, and rose nursery industries, and consumers. Changes/Problems:Due to the retirement of the pear breeder, the fire blight screening phenotyping was delayed one year. Additionally the objective to validate candidate genes for sweetness in pear was discontinued as a strategic response to the continued budget cut. What opportunities for training and professional development has the project provided?Project participants include four fully-funded post-doctoral associates and numerous partially-funded technicians, graduate students, and undergraduate students. These trainees and technicians are participating in performance evaluations, DNA profiling, and implementation of DNA-informed breeding strategies, thereby gaining knowledge, experience, and skills in rigorous, standardized measurement of fruit and disease characteristics, determining trait inheritance, designing and implementing genetic tests, and managing breeding programs. The major project-wide face-to-face training opportunity was the Annual Project Participant Meeting held on 8-10 March 2017. Immediately prior to this meeting, a one-day training workshop in software and concepts was conducted and attended by 20 project participants including six faculty, five post-doctoral associates, and six graduate students. Project participants will attend the 2017 American Society for Horticultural Science Conference to deliver oral and poster presentations, and participants will share RosBREED advances at several other international and national conferences. How have the results been disseminated to communities of interest?Communities received project results via presentations at industry and scientific meetings, grower field days, industry trade publications, scientific publications, project newsletters, the project website (www.rosbreed.org), and the Genome Database for Rosaceae (www.rosaceae.org). Results were disseminated to, and input received, from 26 Advisory Panel members in San Diego, CA on 12 January 2017. What do you plan to do during the next reporting period to accomplish the goals?Activities for each objective will focus on: (1) identification and validation of disease resistance alleles and generation of breeding parents with combined resistance alleles from multiple sources for each disease; (2) discovery of new large-effect genomic regions influencing fruit quality, expansion of genetic knowledge about effects of selection of such genomic regions on performance, and increased breeding efficiency by routine implementation of DNA information in parent and seedling selection; (3) generation and use of predictive models to capture effects of genetic background and non-genetic factors; (4) development of cutting-edge DNA-based diagnostic tools, provision of accessible crop-specific DNA testing services with a transition to commercial facilities, preliminary cost:benefit analysis of DNA-informed breeding applications in two case studies, and technical training in DNA information application in Rosaceae breeding; and (5) systematic investigation of industry stakeholder decisions on new cultivar adoption in two case studies, engagement of industry stakeholders and allied scientists through development and delivery of project content, presence at industry and scientific meetings and conferences, and Advisory Panel interaction.

Impacts
What was accomplished under these goals? This project is bridging the gulf between scientific advances in genomics and genetics and the application of that information in specialty crop breeding. RosBREED supports U.S. breeding programs of apple, peach, strawberry, cherry, and related crops in the Rosaceae family with DNA-based diagnostic tools to develop superior new varieties. New cultivated varieties (cultivars) must meet or exceed consumer expectations for appearance, aroma, flavor, shelf life, and texture and also industry needs for durable disease resistances and productivity. This goal has remained elusive using traditional breeding practices that rely on tedious performance evaluations. RosBREED has created a coordinated, sustained effort in research, training, and extension to accelerate the use of DNA-based information in U.S. rosaceous crop breeding programs. Eight crops are included: apple, blackberry, peach, pear, rose, strawberry, sweet cherry, and tart cherry. Sixteen diseases of these crops, prioritized by stakeholders, are targeted. U.S. Rosaceae crop breeders are working with scientists to identify genetic factors underlying superior fruit quality and disease resistance, then using the resulting DNA tests to more efficiently and creatively incorporate these natural genetic factors into breeding parents and the next generation of desirable, profitable cultivars. Socio-economic analyses of DNA information use are suggesting approaches to more effectively use resources, including the huge diversity within rosaceous crops and their wild relatives. The long-term goal is improved consumption, profitability, and sustainability of U.S. Rosaceae family crops due to a continual supply of new disease-resistant cultivars with superior quality. Obj. 1 - Incorporate durable disease resistance into breeding parents: Standardized protocols were used to evaluate disease susceptibility of 5,539 individuals for 16 targeted diseases: apple scab, blue mold, and fire blight; peach bacterial spot and brown rot; pear fire blight; Armillaria root rot in Prunus; rose black spot; sweet cherry powdery mildew; tart cherry leaf spot; and strawberry bacterial angular leaf spot and five root and crown rot diseases. Evaluation of plant materials and their performance associated with genome-wide DNA profiles have led to discovery of twenty regions in the crop genomes that are associated with disease resistance. These discoveries enabled development and utilization of trait-predictive DNA tests that are increasing breeding effectiveness. New breeding families were made via DNA-informed crossing to combine genetic factors for resistance to multiple pathogens. Breeders will now use such individuals as breeding parents to more rapidly develop new cultivars with more durable disease resistance than current cultivars carrying only single resistance factors. Obj. 2 - Combine disease resistance and horticultural quality: Discoveries of twenty-six genomic regions associated with fruit quality, phenology, and pollen compatibility are providing knowledge to increase breeding efficiency and accuracy. A standardized evaluation protocol for peach postharvest fruit quality consisting of 24 traits was implemented for individuals in four collaborating breeding programs for the second year in 2016. DNA testing was conducted for up to five traits at a time for ~55,000 seedlings in U.S. breeding programs of apple, sweet cherry, peach, and strawberry. DNA testing of seedlings for target traits in 2017 resulted in only those seedlings predicted as superior to be advanced for field planting, dramatically increasing efficiency with discard rates of 40% to 60%. Obj. 3 - Advance selections with improved confidence: This objective is to develop two new DNA-based approaches for selective breeding. The approaches focus on identifying individuals with sufficient levels of desirable fruit traits to justify their inclusion in multi-location performance trials. The first approach is "genome-wide selection". For this, performance predictions for apple based on DNA information alone were observed to be useful only when the original experimental population and the actual breeding population were highly related. These findings help ensure the approach is appropriately used in the future. A study in strawberry indicated that the next generation could be genetically improved by 30-80% over traditional methods of resource-intensive direct evaluation of fruit. In addition, strawberry progeny were selected, advanced, and used as parents one year earlier (in two years rather than three) with improved confidence using predictions based on whole-genome DNA profiles. The second approach to increase selection accuracy dissects performance predictions into genetic and external components. RosBREED's genome-scanning tools now allow the genetic component to be considered as multiple small pieces of DNA replicated in various combinations within multiple individuals spread over locations. This approach ties together trials across the world that previously could not be compared because they used different sets of reference cultivars. A network of collaborators (>25) was built, particularly across North America, Europe, and Australia, who have provided historical trial data and scientific expertise. Analyses of the DNA profiles are already predicting performance of any sweet cherry plants' genetic potential for maturity time in commercial environments. Obj. 4 - Increase routine use of DNA information: Rosaceae family breeders used crop-specific DNA testing facilities supported by RosBREED. These facilities offered DNA tests for apple, cherry, peach, strawberry, and pear disease resistance and fruit quality, bringing the total number of trait-predictive DNA tests available to 35. U.S. Rosaceae crop breeding programs thereby had unprecedented access to DNA-based diagnostic services. Collaborations with international partners resulted in the design of DNA-based diagnostic tools to reduce costs and increase power of DNA profiling at various levels of resolution. Economics of DNA information use, based on the break-even selection rate, is being calculated in two case studies. On-site visits to U.S. strawberry, raspberry, blackberry, and stone fruit breeders were conducted, delivering RosBREED project advances, tools, and DNA-based knowledge to help tailor DNA-based diagnostic solutions to each breeding program. Adoption of DNA-informed breeding is being monitored yearly in 20 Rosaceae family breeding programs. Obj. 5 - Utilize stakeholder input: Case studies of strawberry and peach cultivar releases were continued to determine the trade-offs associated with grower decisions to adopt cultivars with varying levels of disease resistance and fruit quality. A survey of southeastern U.S. peach growers assessed decision-making within stakeholder-breeder evaluations of the commercial potential of elite selections trialed in grower fields. Eighteen one-page summaries, called "RosBRIEFs", were circulated among industry commodity group leaders. RosBRIEFs included descriptions of reviews of major diseases targeted in RosBREED, protocols for determining disease resistance, DNA tests available, and new cultivar releases by U.S. breeders. The RosBREED Executive Committee met with 26 (of 31) Advisory Panel members in San Diego on 12 January 2017. Panel recommendations were discussed at the annual project meeting in March 2017 and appropriate adjustments made to project activities. Advisory Panel members were also engaged all year, contributing to RosBREED quarterly newsletters, industry briefs, brochures, and DNA test cards

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Bassil NV, Finn CE, Clark JR, Peace C, Iezzoni A. 2016. Development of a multiplexed fingerprinting set in blackberry. Acta Horticulturae 1133:89-96.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Dong Q, Wang X, Byrne D, Ong K. 2017. Characterization of partial resistance to black spot disease of Rosa sp. HortScience 52(1):4953.
  • Type: Book Chapters Status: Published Year Published: 2017 Citation: Evans K, Peace C. 2017. Advances in marker-assisted breeding for apple. Ch 7 in Achieving Sustainable Cultivation of Apples (Ed. K. Evans), Burleigh Dodds, Cambridge, UK.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Gezan S, Osorio L, Verma S, Whitaker V. 2017. An experimental validation of genomic selection in octoploid strawberry. Horticulture Research 4, 16070.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hardner C, Kumar S, Peace C, Luby J, Evans K. 2016. Reconstructing relationship matrices from dense SNP arrays for the prediction of genetic potential in unreplicated multiplication plantings of apple progeny. Acta Horticulturae 1127:275-281.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Howard, N., E. van de Weg, D. Bedford, C. Peace, S. Vanderzande, M. Clark, SL Teh, L. Cai, J.J. Luby. 2017. Elucidation of the Honeycrisp pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus � domestica) pedigree-connected SNP dataset. Horticulture Research 4:17003 doi:10.1038/hortres.2017.3.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Iezzoni A, Peace C, Bassil N, Fazio G, Gallardo K, Gasic K, Luby J, Main D, van de Weg E, Weebadde C, Yue C. 2016. Where are we now as we merge genomics into plant breeding and what are our limitations? Experiences from RosBREED. Acta Horticulturae 1117:1-6.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Peace C. 2017. DNA-informed breeding of rosaceous crops: promises, progress and prospects. Horticulture Research 4, 17006; doi:10.1038/hortres.2017.6
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Mathey MM, Mookerjee S, Mahoney LL, G�nd�z K, Rosyara U, Hancock J, Stewart P, Whitaker V, Bassil N, Davis T, Finn C. 2017. Genotype by environment interactions and combining ability for strawberry families grown in diverse environments. Euphytica 213: 112. doi:10.1007/s10681-017-1892-6
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Noh Y-H, Lee S, Whitaker V, Cearley K, Cha J-S. 2017. A high-throughput marker-assisted selection system combining rapid DNA extraction and high-resolution melting and simple sequence repeat analysis: strawberry as a model for crops. Journal of Berry Research 7(1):23-31
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Norelli J, Wisniewski M, Fazio G, Burchard E, Gutierrez B, Levin E, Droby S. 2017. Genotyping-by-sequencing markers facilitate the identification of quantitative trait loci controlling resistance to Penicillium expansum in Malus sieversii. PLoS One 12(3): e0172949.
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Salinas NR, Zurn JD, Mathey M, Denoyes B, Finn CE, Hancock JF, Stewart P, Bassil NV. 2017. Validation of molecular markers associated with perpetual flowering in octoploid Fragaria germplasm. Mol Breeding (Accepted)
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Sandefur P, Frett T, Clark J, Gasic K, Peace C. 2017. A DNA test for routine prediction in breeding of peach blush, Ppe-Rf-SSR. Molecular Breeding. Molecular Breeding 37:11
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Wang J, Yue C, Gallardo K, McCracken V, Luby J, McFerson J. 2017. What consumers are looking for in strawberries: implications from market segmentation analysis. Agribusiness, 33: 5669
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Zhao S, Yue C, Luby J, Gallardo K, McCracken V, McFerson J, Layne D. 2017. U.S. peach producer preference and willingness to pay for fruit attributes. HortScience 52(1):116121
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Yin MH, Clark M, Peterson M, Finn CE, and Clark JR. 2017. Development of a standardized phenotyping protocol for blackberry and evaluation of its effectiveness in characterizing seedling populations. 81st Annual Meeting of the Southern Region American Society for Horticultural Science. Mobile, AL, February 3-5. Oral Presentation
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Norelli J. 2017. Rapid cycle breeding in apple for resistance to blue mold. Potomac Division 73rd Annual Meeting of the American Phytopathological Society. March 22-24, 2017, Morgantown WV.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Worthington M, and Clark JR. 2017. Peach Breeding at the University of Arkansas. IX International Peach Symposium. Bucharest, Romania. July 2-6, 2017. Accepted Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Hardner C, Peace C, Quero-Garcia J, Vanderzande S, Giovannini D, Barreneche T, Campoy JA, Charlot G, Liverani A, Oraguzie N, Villamil-Castro M, Cai L, Ordidge M, W�nsch A, Sotiropoulos T, Kazantzis K, Patocchi A, Perren S, Graetz D, Iezzoni A. 2017. Building international partnerships for the collation of historical data to study the environmental stability of genomic predictions in sweet cherry. ISHS International Cherry Symposium, Yamagata, Japan June 5-9, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Hokanson S, Byrne D, Klein P, Yan M, Zlesak D, Kummeth S, Bradeen J, Iezzoni A, Peace C. 2017. RosBREED2: Combining Disease Resistance with Horticultural Quality in New Rosaceous Cultivars, Including Rose! 7th International Rose Symposium, Angers, France, July 2-7, 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Anciro A, Mangandi J, Verma S, Lee S, Whitaker V. 2017. QTL discovery and vailidation for resistance to Colletotrichum crown rot in strawberry (Fragaria � ananassa). Plant and Animal Genome Conference XXV, San Diego, CA, January 14-18. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Blissett E., McKay S., Luby J., Bernardo R. 2017. Using Genomewide Selection to Increase the Efficiency of Apple Breeding. 25th Annual International Plant and Animal Genome Conference. San Diego, CA, January 14-18. Poster Presentation
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Davis T, Yang Y, Mahoney L, Sargent D, Ward J, Wood D. 2017. De novo assembly of the diploid strawberry Fragaria iinumae Genome, Plant and Animal Genome Conference XXV, San Diego, California, January 14-18, 2017, P0624 Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Mangandi J, Verma S, Peres Natalia, Bink M, van de Weg E, Bassil N, Whitaker V. 2016. Pc1: a large-effect QTL conferring resistance to Phytophthora cactorum in strawberry. Plant and Animal Genome Conference XXIV, San Diego, CA, poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Miller P, Srivastava SD, Ramos-Onsins S, Lawton-Rauh A. 2016. Comparative Population Genomics Resource for Rosaceous Crop Improvement from Wild Relatives. Presented at the Clemson University Summer Undergraduate Research Symposium. Clemson, SC. September 2016. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Noh Y-H, Mangandi J, Verma S, Isobe S, Cha J-S, Whitaker V, and Lee S. 2016. Development of high-throughput markers for Phytophthora crown rot resistance in strawberry. Plant and Animal Genome Conference XXIV, San Diego, CA, poster presentation.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Noh Y-H, Mangandi J, Verma S, Whitaker V, Isobe S, Kim J-H, Cha J-S, and Lee S. 2016. Fine mapping a Phytophthora crown and root rot resistance locus, FaRPc1, in octoploid strawberry (Fragaria � ananassa Duch.). Ameri. Path. Soc. Wimauma, FL, December 2016. Poser presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Shields M, Davis T. 2017. Implementation of the IStraw90 Axiom� SNP Array Genotyping Platform for Genetic Linkage Map Construction in the Diploid Strawberry Model Species, Fragaria vesca. Plant and Animal Genome Conference XXV, San Diego, California, January 14-18, 2017, P0623 Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Srivastava SK, Norelli J, Iezzoni A, Cai L, and A Lawton-Rauh. 2016. A diversity-based haploblocking approach across diverged genotypes using re-sequenced genomes in Malus � domestica (apple). Clemson University Research Excellence Symposium (May 2016). Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Yang Y, Davis T. 2017. Toward a pentaploid-based assembly of an octoploid strawberry reference genome. Plant and Animal Genome Conference XXV, San Diego, California, January 14-18, 2017, P0625 Poster presentation.
  • Type: Other Status: Published Year Published: 2016 Citation: Evans K. 2016. Tree fruit breeding and selection at WSU. Washington State Horticultural Association, Wenatchee, WA. Oral presentation
  • Type: Other Status: Published Year Published: 2017 Citation: Norelli J., Evans K., Peace, C. 2017. Fire blight resistance and fruit quality in new Washington cultivars. Washington Tree Fruit Research Commission, Apple Crop Protection Research Review. January 26, 2017, Yakima, WA. Oral presentation.
  • Type: Other Status: Accepted Year Published: 2017 Citation: Zurn J, Finn C, Seonghee L, Whitaker V, Bassil N. 2017. DNA-informed breeding in strawberry. In Strawberry Open House at Oregon State Universitys North Willamette Research and Extension Center, June 7.
  • Type: Other Status: Accepted Year Published: 2017 Citation: Worthington M. 2017. University of Arkansas fruit breeding program update. University of Arkansas Division of Agriculture Southwest Research and Extension Center Horticulture Field Day. Hope, AR. June 15.
  • Type: Other Status: Accepted Year Published: 2017 Citation: Bushakra J, Finn C, Dossett M, Bassil N. 2017. What existing DNA tests in blackberry and black raspberry can tell us? In Caneberry Open House at Oregon State Universitys North Willamette Research and Extension Center, June 28.
  • Type: Other Status: Published Year Published: 2017 Citation: McFerson J, DeVetter L, Iezzoni A, Peace C, Bell R, Vanderzande S, Edge-Garza D. 2017. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 7 Issue 2.
  • Type: Other Status: Published Year Published: 2016 Citation: Iezzoni A, McFerson J, Probst C, Peace C. 2016. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 7 Issue 1.
  • Type: Other Status: Published Year Published: 2016 Citation: Peace C, Main D, Layne D, Olmstead M, Iezzoni A, DeVetter L, Piaskowski J, McFerson J, Coe M, Wilson D. 2016. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 6 Issue 3.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Andersen K. 2016. Comparison of resistant, tolerant, and susceptible host responses to cherry leaf spot and assessment of trait inheritance. M.S. Thesis in Plant Breeding and Genetics, Michigan State University. Awarded Dec 2016.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Liang S, Wu X, Byrne D. 2017. Flower-size heritability and floral heat-shock tolerance in diploid roses. HortScience. 52(1):49-53.
  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Yue C, Zhao S, Gallardo RK, McCracken V, Luby JL, McFerson J. 2017. U.S. Growers Willingness to Pay for Improvement in Rosaceous Fruit Traits. Agricultural and Resource Economics Review 6(1), 103-122
  • Type: Journal Articles Status: Accepted Year Published: 2017 Citation: Yue C, Choi JW, Luby J, Zhao S, Gallardo RK, McCracken V, McFerson J. 2017. Estimating Strawberry Attributes Market Equilibrium Values. HortScience (Accepted)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Yan M, Byrne DH, Zurn J, Dong Q, Klein P. 2017. The development of a dense SNP-based consensus map and QTL detection for black spot resistance in five diploid rose populations. Ornamental Genomics. Plant and Animal Genome XXV conference. San Diego, CA. Jan. 2017.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2017 Citation: Fu W, Burrell R, Gasic K. 2017. Enabling Breeding for Brown Rot (Monilinia spp.) Resistance in Peach. 81st Annual Meeting of the Southern Region American Society for Horticultural Science. Mobile, AL, February 3-5. Oral Presentation
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Yan M, Dong Q, Byrne DH, Klein P. 2017. The development of a dense SNP-based consensus map and QTL detection for black spot resistance in three diploid rose populations. Oral presentation at the International Rose Symposium. Angers, France. August 3-7, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Lau J, Roundey E, Anderson N, Byrne DH. 2017. Fieldbook app: Use in data collection in rose breeding. Oral presentation at the International Rose Symposium. Angers, France. August 3-7, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Xu W, Shi Y, Byrne DH. 2017. Digital image analysis to assess flower productivity and foliage retention in garden roses throughout the season. Oral presentation at the International Rose Symposium. Angers, France. August 3-7, 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Fu W, Burrell R, Schnabel G, Gasic K. 2017. Enabling breeding for brown rot resistance (Monilinia spp.) in Clemson University peach breeding program IX International Peach Symposium, Bucharest, Romania, 4-7 July 2017.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2017 Citation: Hardner C, Gasic K, Da Silva Linge C, Iezzoni A, Peace C. 2017, Using SNP arrays to leverage historical data sets for improved prediction accuracy and study of G�E�M in peach. IX International Peach Symposium, Bucharest, Romania, 4-7 July 2017.
  • Type: Theses/Dissertations Status: Published Year Published: 2017 Citation: Yin M. 2017. Studies in Blackberry: Development and Implementation of a Standardized Phenotyping Protocol and Evaluation of Storage Potential. M.S. Thesis, University of Arkansas. Awarded May 2017.


Progress 09/01/15 to 08/31/16

Outputs
Target Audience:Target audiences include breeders of tree fruits, berries, and flowers in the Rosaceae family, pathologists, germplasm collection curators, molecular geneticists, and other allied scientists, producers of crops in the Rosaceae family, processors, marketers, and marketing organizations, the tree fruit, berry, and rose nursery industries, and consumers. Changes/Problems:The peach postharvest phenotyping protocol applied in 2015 was simplified to exclude collection of data for traits relevant only to processing peach. Integration of a data curation pipeline in the Genome Database for Rosaceae is delayed until resources required can be evaluated by further clarity of the process. Breeders engaged directly with their industry advisory committees or other informal industry groups to obtain feedback on RosBREED activities, rather than having RosBREED extension members perform this function. This adjustment was made due to excellent breeder-industry communication channels already present for most programs. What opportunities for training and professional development has the project provided?Project participants include four fully-funded post-doctoral associates and numerous partially-funded technicians, graduate students, and undergraduate students. These trainees and technicians are participating in performance evaluations, DNA profiling, and implementation of DNA-informed breeding strategies, thereby gaining knowledge, experience, and skills in rigorous, standardized measurement of fruit and disease characteristics, determining trait inheritance, designing and implementing genetic tests, and managing breeding programs. The major project-wide face-to-face training opportunity was the Annual Project Participant Meeting held on 8-10 March 2016. Immediately prior to this meeting, a two-day software training workshop was conducted; the first day was advanced-user software (FlexQTLTM) training for two faculty and six post-doctoral associates, and the second day was a software training session for 35 project participants including seven faculty, nine post-doctoral associates, and seven graduate students. Project participants will attend the 2016 American Society for Horticultural Science Conference to deliver oral and poster presentations, and participants will share RosBREED advances at several other international and national conferences, respectively. How have the results been disseminated to communities of interest?Communities received project results via presentations at industry and scientific meetings, industry trade publications, scientific publications, project newsletters, the project website (www.rosbreed.org), the Genome Database for Rosaceae, and social media. Results were disseminated to and input received from 26 Advisory Panel members in San Diego, CA on 7 January 2016. What do you plan to do during the next reporting period to accomplish the goals?Activities for each objective will focus on: (1) identification and validation of disease resistance alleles and generation of breeding parents with combined resistance alleles from multiple sources for each disease; (2) discovery of new large-effect genomic regions influencing fruit quality, expansion of genetic knowledge about effects of selection of such genomic regions on performance effects, and increased breeding efficiency by routine implementation of DNA information in parent and seedling selection; (3) generation and use of predictive models to capture effects of genetic background and non-genetic factors; (4) development of cutting-edge DNA-based diagnostic tools, provision of accessible crop-specific DNA testing services, preliminary cost:benefit analysis of DNA-informed breeding applications in two case studies, and technical training in DNA information application in Rosaceae breeding; and (5) systematic investigation of industry stakeholder decisions on new cultivar adoption in two case studies, engagement of industry stakeholders and allied scientists through development and delivery of project content, presence at industry and scientific meetings and conferences, and Advisory Panel interaction.

Impacts
What was accomplished under these goals? This project is bridging the gulf between scientific advances that have been made in genomics and genetics and the application of that information in specialty crop breeding. RosBREED supports U.S. breeding programs of apple, peach, strawberry, cherry and related crops in the Rosaceae family with DNA diagnostic tools to develop superior new varieties. New cultivated varieties (cultivars) must meet or exceed consumer expectations for appearance, aroma, flavor, shelf life, and texture and also industry needs for durable disease resistances and productivity. This goal has remained elusive using traditional breeding practices that rely on tedious performance evaluations. RosBREED has created a coordinated, sustained effort in research, training, and extension to accelerate the use of DNA-based information in U.S. rosaceous crop breeding programs. Eight crops are included: apple, blackberry, peach, pear, rose, strawberry, sweet cherry, and tart cherry. Sixteen diseases of these crops, prioritized by stakeholders, are targeted. U.S. Rosaceae family breeders are working with scientists to identify genetic factors underlying superior fruit quality and disease resistance, then using the resulting DNA tests to more efficiently and creatively incorporate these natural genetic factors into breeding parents and the next generation of desirable, profitable cultivars. Socio-economic analyses of DNA information use will suggest approaches to more effectively use resources, including the huge diversity within rosaceous crops and their wild relatives. The long-term goal is improved consumption, profitability, and sustainability of U.S. Rosaceae family crops due to a continual supply of new disease-resistant cultivars with superior quality. Obj. 1 - Incorporate durable disease resistance into breeding parents: Standardized protocols were used to evaluate disease susceptibility of 7238 individuals for 16 targeted diseases. Plant materials and their performance associated with genome-wide DNA profiles have led to the discovery of twenty regions in the crop genomes that are associated with disease resistance. These discoveries enabled development and utilization of trait-predictive DNA tests that are increasing breeding effectiveness. New breeding families (120) were made via DNA-informed crossing to combine genetic factors for resistance to multiple pathogens. Breeders will now use such individuals as breeding parents to more rapidly develop new cultivars with more durable disease resistance than current cultivars carrying only single resistance factors. Obj. 2 - Combine disease resistance and horticultural quality: New discoveries of genomic regions associated with fruit and flower quality are providing knowledge to increase breeding efficiency and accuracy. An online tool to visualize regions of shared ancestry across rosaceous crops was used to identify common locations in the genome for apple, peach, and strawberry for sweetness genetic factors. This new tool provides new genomic regions to target for sweetness for the previously little-studied crops of blackberry and pear. A standardized evaluation protocol for peach postharvest fruit quality consisting of 24 traits was implemented for 588 individuals in four collaborating breeding programs in 2015. DNA testing was conducted for up to six traits at a time for ~25,000 seedlings in U.S. breeding programs of apple, sweet cherry, peach, and strawberry. Those seedlings predicted to be inferior were culled. Such early evaluation and culling of seedlings in 2015 is expected to save approximately $200,000 that can be reallocated to more effectively achieving breeding targets rather than spending years managing inferior seedlings. Obj. 3 - Advance selections with improved confidence: This objective is developing two new DNA-based approaches for selective breeding. The approaches focus on identifying individuals with sufficient levels of desirable fruit traits to justify their inclusion in multi-location performance trials. The first approach is "genome-wide selection". For this, genomic performance predictions for apple based on DNA information alone were observed to be useful only when the original experimental population and the actual breeding population were highly related. These findings help ensure the approach is appropriately used in the future. A study in strawberry indicated that the next generation could be genetically improved by 30-80% over traditional methods of resource-intensive direct evaluation of fruit. The second approach to increase selection accuracy dissects performance predictions into genetic and external factors. RosBREED's genome-scanning tools now allow the genetic component to be considered as multiple small pieces of DNA replicated in various combinations within multiple individuals. This approach ties together trials across the world that previously could not be compared because they used different sets of reference cultivars. A network of collaborators (>25) was built, particularly across North America, Europe, and Australia, who have provided historical trial data and scientific expertise. Analyses of the DNA profiles are already predicting performance of cultivars under new growing conditions, such as performance under French conditions for a new cultivar bred in Washington. Obj. 4 - Increase routine use of DNA information: Rosaceae family breeders used crop-specific DNA testing facilities supported by RosBREED that offered 19 newly-developed DNA tests for apple, cherry, peach, strawberry, and pear disease resistance (five tests) and fruit quality (14 tests), bringing the total number of trait-predicted DNA tests available to 32. DNA testing "Portals" provided unprecedented access to U.S. Rosaceae crop breeding programs to DNA-based diagnostic services. Collaborations with international partners resulted in design of DNA-based diagnostic tools that reduce costs and increase power of DNA testing at various levels of resolution. Economics of DNA information use based on the break-even selection rate is being calculated in two case studies. On-site visits to U.S. strawberry, raspberry, blackberry, and stone fruit breeders were conducted, delivering RosBREED project advances, tools, and DNA-based knowledge to help tailor DNA test solutions to each breeding program. Adoption of DNA-informed breeding is being monitored yearly in 20 Rosaceae family breeding programs. Obj. 5 - Utilize stakeholders input: Case studies of strawberry and peach cultivar releases were continued to determine the trade-offs associated with grower decisions to adopt cultivars with varying levels of disease resistance and fruit quality. A survey of southeastern U.S. peach growers assessed decision-making within stakeholder-breeder evaluations of commercial potential of elite selections trialed in grower fields. Eighteen one-page summaries, called "RosBRIEFs", were circulated among industry commodity group leaders. RosBRIEFs included descriptions of DNA tests available, reviews of major diseases targeted in RosBREED, protocols for determining disease resistance, and new cultivar releases by U.S. breeders. The RosBREED Executive Committee met with 26 (of 31) Advisory Panel members in San Diego on 7 January 2016. Panel recommendations were discussed at the annual project meeting in March 2016 and appropriate adjustments made to project activities. Advisory Panel members were also engaged all year, contributing to RosBREED quarterly newsletter, industry briefs, brochures, and DNA test cards.

Publications

  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner: Sweet Sensation
  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner Columbia Star Blackberry
  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner: Cosmic Crisp
  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner: Prime-Ark �Traveler Blackberry
  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner: Ruby Frost"
  • Type: Other Status: Published Year Published: 2016 Citation: New Cultivar Corner: SnapDragon"
  • Type: Other Status: Published Year Published: 2016 Citation: Jewels in the Genome: Cherry Maturity Date
  • Type: Other Status: Published Year Published: 2016 Citation: Rosaceae Nemesis: Apple Fire Blight
  • Type: Other Status: Published Year Published: 2016 Citation: Rosaceae Nemesis: Peach Bacterial Spot
  • Type: Other Status: Published Year Published: 2016 Citation: Rosaceae Nemesis: Rose Black Spot
  • Type: Other Status: Published Year Published: 2016 Citation: Rosaceae Nemesis: Strawberry Root and Crown Rot Diseases
  • Type: Other Status: Published Year Published: 2016 Citation: Phenotyping Protocol: Peach Chilling Injury
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Frett T. 2016. Genetic determinism of Xanthomonas arboricola pv. pruni (Xap) resistance, fruit quality, and phenological traits in peach and incorporation of marker-assisted selection (MAS) in the University of Arkansas peach and Nectarine Breeding Program. PhD Diss., University of Arkansas.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Ru S. 2016. Theoretical and empirical evaluation of efficiency of marker-assisted seedling selection in Rosaceae tree fruit breeding. PhD Diss., Washington State University, Pullman, Wash.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Sandefur P. 2016. Enhancing efficiency in tree-fruit breeding by developing trait-predictive DNA tests. PhD Diss., Washington State University, Pullman, Wash.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Salgado A. 2015. Applying molecular and phenotypic tools to characterize flesh texture and acidity traits in the Arkansas peach breeding program and understanding the crispy texture in the Arkansas blackberry breeding program. PhD Diss., Univ. of Ar., Fayetteville.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Shields ME. 2015. Genomic resource development and candidate gene evaluation in Fragaria vesca (L.). Ph.D. Thesis in Genetics, University of New Hampshire. Accepted Dec. 2015. Ph.D. awarded May 2016.
  • Type: Theses/Dissertations Status: Published Year Published: 2016 Citation: Yang Y. 2016. Investigation of subgenome composition in octoploid strawberries. Ph.D. Thesis in Plant Biology, University of New Hampshire. In submission. Ph.D. awarded May 2016.
  • Type: Other Status: Published Year Published: 2016 Citation: Olmstead M, Coe M, Iezzoni A, Piaskowski J, Peace C, Wilson A, Main D, Lanye D, DeVetter L, Whitaker V. 2016. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 6 Issue 3.
  • Type: Other Status: Published Year Published: 2016 Citation: Brown SK and Maloney KE. 2016. Overview of apple resources at Cornell. NY Fruit Quarterly 24(1):24-30.
  • Type: Other Status: Published Year Published: 2016 Citation: Brown SK and Maloney KE. 2016. Apple breeding, genetics and genomics. NY Fruit Quarterly 23(3):5-7.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Edge-Garza D, Luby J, and Peace C. 2015. Decision support for cost-efficient and logistically feasible marker-assisted seedling selection in fruit breeding. Molecular Breeding 35:223.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Fresnedo-Ramirez J, Bink MCAM, van de Weg E, Famula T, Crisosto C, Frett T, Gasic K, Peace C, and Gradziel T. 2015. QTL mapping of pomological traits in peach and related species breeding germplasm. Molecular Breeding 35:166.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Fresnedo-Ramirez J, Frett TJ, Sandefur PJ, Salgado-Rojas A, Clark JR, Gasic K, Peace CP, Anderson N, Hartmann TP, Byrne DH, Bink MCAM, van de Weg E, Crisosto CH, Gradziel TM. 2016. QTL mapping and breeding value estimation through pedigree-based analysis of fruit size and weight in four diverse peach breeding programs. Tree Genetics & Genomes 12:25 (DOI 10.1007/s11295-016-0985-z).
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gasic K, Reighard GLR, Okie WR, Clark J, Gradziel T, Byrne D, Peace C, Stegmeir T, Rosyara U, and Iezzoni A. 2015. Bacterial spot resistance in peach: functional allele distribution in breeding germplasm. Acta Hort 1084:69-74.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Guan Y, Peace C, Rudell D, Verma S, Evans KM. 2015. QTLs detected for individual sugars and soluble solids content in apple. Molecular Breeding 35:135.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Gallardo K, Huixin L, McCracken V, Yue C, McFerson J. 2015. Market intermediaries ratings of importance for Rosaceous fruits quality traits. International Food and Agribusiness Management Review 18(4):121-153.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hancock JF, Sooriyapathirana S, Bassil N, Stegmeir T, Cai L, Finn C, van de Weg E, Weebadde C. 2016. Public availability of a genotyped, segregating population may foster marker assisted breeding (MAB) and quantitative trait loci (QTL) discovery: An example using strawberry. Frontiers Plant Sci. 7:619-623.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Mahoney LL, Sargent DJ, Abebe-Akele F, Wood DJ, Ward JA, Bassil NV, Hancock JF, Folta KM, Davis TM. 2016. A High-Density Linkage Map of the Ancestral Diploid Strawberry, Fragaria iinumae, Constructed with Single Nucleotide Polymorphism Markers from the IStraw90 Array and Genotyping by Sequencing. The Plant Genome doi:103835/plantgenome 2015.08.0071.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Roach J, Verma S, Peres N, Jamieson A, van de Weg E, Bink M, Bassil N, Lee S, Whitaker V. 2016. FaRXf1: a locus conferring resistance to angular leaf spot caused by Xanthomonas fragariae in octoploid strawberry, Theor Appl Genet DOI 10.1007/s00122-016-2695-1.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Ru S, Hardner C, Carter P, Evans K, Main D, Peace C. 2016. Modeling of genetic gain from marker-assisted seedling selection in clonally propagated crops. Horticulture Research 3, 16015; doi:10.1038/hortres.2016.15.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Sandefur P, Oraguzie N, Peace C. 2016. A DNA test for routine prediction in breeding of sweet cherry fruit color, Pav-Rf-SSR. Molecular Breeding 36:33 (DOI 10.1007/s11032-016-0458-y).
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sargent DJ, Yang Y, Surbanovski N, Bianco L, Buti M, Velasco R, Giongo L, Davis TM. 2015. HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry (Fragaria � ananassa). Plant Science 242:140-150.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Sooriyapathirana SS, Mookerjee S, Weebadde CK, Finn CE, Lewers K, Bushakra JM, Luby JJ, Stewart P, Neils S, Hancock JF. 2015. Identification of QTL associated with flower and runner production in octoploid strawberry (Fragaria � ananassa). J. Berry Res. 5: 107-116.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Volk G M, Chao C T, Norelli J, Brown SK, Fazio G, Peace C, McFerson J, Zhong G-Y, Bretting P. 2015. The vulnerability of US apple (Malus) genetic resources. Genetic Resources and Crop Evolution 62:765-797.
  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Zheng X, Yue C, Gallardo K, McCracken V, Luby J, McFerson J. 2016. What attributes are consumers looking for in sweet cherries? Evidence from choice experiments. Agricultural and Resource Economics Review 45:124-142.
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Bassil N, Amaya I, Davis T, Denoyes B, Bernardo R, Edgers P, Finn C, Hardner C, Hancock J, Ivors K, Knapp S, Lee S, Mangandi J, Mahoney L, Roach J, Salinas N, Verma S, van de Weg E, Whitaker V, Peace C, and Iezzoni A. 2016. RosBREED: From genomics to DNA-informed breeding in strawberry. Acta Hort (accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Lee S, Noh Y, Roach JA, Mangandi J, Verma S, Whitaker VM, Cearley KR. 2016. A high-throughput genotyping system combining rapid DNA extraction and high-resolution melting analysis in allo-octoploid strawberry. Acta Hort (accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Noh Y, Lee S, Whitaker VM, Cearley KR, Cha J. 2016. A high-throughput marker-assisted selection system combining rapid DNA extraction and high-resolution melting analysis: strawberry as a model for fruit crops. Journal of Berry Research (accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Oraguzie N, Watkins S, Chavoshi M. 2016. Emergence of the Pacific Northwest sweet cherry breeding program. Acta Hort (accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Wang J, Yue C, Gallardo K, McCracken V, Luby J, McFerson J. 2016. What consumers are looking for in strawberries: implications from market segmentation analysis. Agribusiness: An International Journal (accepted).
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Whitaker VM, Lee S, Osorio LF, Verma S, Roach J, Mangandi J, Noh Y, Gezan S, Peres N. 2016. Advances in strawberry breeding at the University of Florida. Acta Hort (accepted)
  • Type: Journal Articles Status: Accepted Year Published: 2016 Citation: Yue C, Zhao S, Gallardo K, McCracken V, Luby J, McFerson J. 2016. U.S. growers willingness to pay for improvement in Rosaceous fruit traits. Agricultural and Resource Economics Review (accepted).
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Chagn� D, Kirk C, Vanderzande S, Edge-Garza D, Roniotis J, Patocchi A, Costa F, Volv R, Gardiner S, Norelli J, Sargent D, Padmarasu S, Peace C, Bassil N. 2016. Validation of genetic markers for fruit quality and disease resistance in apple breeding germplasm using the openArray� technique. 8th International Rosaceae Genomics Conference, June 21-24, Angers, France. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Hardner C, Vanderzande S, Cai L, Oraguzie N, Quero-Garcia J, Campoy J, Barreneche T, Wunsch A, Giovannini D, Liverani A, Hampson C, Kumar S, Hayes B, Peace C. 2016. Using SNP arrays to leverage historic data sets for improved prediction accuracy and estimation of GxE of fruit maturity in sweet cherry. 8th International Rosaceae Genomics Conference, June 21-24, Angers, France. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Osorio Luis, Gezan S, Whitaker V. 2016. Integration of genomic selection into the University of Florida strawberry breeding program. 8th International Rosaceae Genomics Conference, June 21-24, Angers, France. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Mansur Z and Byrne DH. 2015. Improving the postharvest quality of peaches. Poster presentation for the Texas Plant Protection Conference, College Station, TX. Dec. 8-9, 2015.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: McFerson J. 2016. Synergy and success: Industry stakeholders and the Rosaceae Genomics Conference. 8th International Rosaceae Genomics Conference, June 21-24, Angers, France. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Peace C, Edge-Garza D, Rowland T, Ru S, Piaskowski J, Sandefur P. 2016. From QTLs to routine DNA-Informed Breeding: prospects, advances, and needs. 8th International Rosaceae Genomics Conference, June 21-24, Angers, France. Oral presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Verma S, Roach J, Mangandi J, Lee S, Salinas N, Bassil N, Bink MCAM, van de Weg E, Peace C, Iezzoni I, and Whitaker V. 2016. DNA-informed strawberry breeding in RosBREED. Plant and Animal Genome Conference XXIV, San Diego, CA. W346.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Yan M, Dong Q, Byrne DH, Klein P. 2016. Map construction in diploid rose using GBS. Plant and Animal Genome Conference XXIV, San Diego, CA. W663.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Noh Y, Mangandi J, Verma S, Whitaker VM, Lee S. 2016. Application of high-throughput markers for Phytophthora crown rot resistance breeding in strawberry. American Phytopathology Society Southern Division Meeting, February 20-22, 2016, Gulf Coast Research and Education Center, Florida.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bassil N, Yin M, Carter K, Nyberg A, Clark M, Peterson M, Finn C, Clark J, Peace C, Iezzoni A. 2016. A blackberry DNA test to verify parentage in RosBREED. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Bassil N, Bell R, Nyberg A, Schaefer K, Postman J, Peace C, Iezzoni A. 2016. An improved Pyrus SSR fingerprinting DNA test to confirm parentage in RosBREED. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Blissett L, Luby J, Bernardo R. 2016. Accuracy of genome wide prediction with and without heterozygote effects in apple. 5th International Symposium on Quantitative Genetics. Madison, WI, June 12-17. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Cai L, Subodh S, Lawton-Rauh A, Voorrips R, Peace C, Iezzoni A. 2016. Haploblock structure in sweet cherry using a pedigree-based approach. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Edge-Garza D, Vanderzande S, Wannemuehler S, Tillman J, Luby J, Gardiner S, Chagn� D, Peace C. 2016. Conversion of DNA tests to high-throughput technologies supporting apple breeding decisions. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Howard N, Luby J, Tong C, Vanderzande S. 2016. Two large effect QTL identified and characterized for soft scald incidence in apple. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Hokanson S, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C. 2016. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Vanderzande S, Cai L, Howard N, Bink M, Iezzoni A, Peace C, van de Weg E. 2016. A pipeline for the curation of genetic data for pedigree-based QTL studies, demonstrated on RosBREEDs apple data set. 8th International Rosaceae Genomics Conference, Angers, France. June 21-24. Poster presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Gallardo K, Yue C, McCracken V, Luby J, McFerson J. 2016. Are WTP estimates for fruit quality similar between producers and consumers? Results of a choice experiment on five rosaceous fruit crops. Agricultural and Applied Economics Association 2016 annual conference, Boston, MA, July 31-August 2. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Abdelghafar A, Gasic K, Reighard G. 2016. QTL mapping for phytochemical compounds in peach [Prunus persica (L.) Batsch]. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Antanaviciute L, Arus P, Bassi D, Rossini L, Gasic K. 2016. High density, multi-population consensus genetic linkage map for peach (Prunus persica L. Batsch). American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Luo F, Sandefur P, Evans K, Norelli J, Peace C. 2016. Introgressing multiple disease resistance alleles into elite apple cultivars by DNA-informed breeding. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Frett T, Clark J, Sandefur P, Smith B, Bluhn B, Jecman A, Fresnedo-Ramirez J, van de Weg E, Bink M, Peace C, Gasic K, Verma S. 2016. Evaluating bacterial Spot [Xanthomonas Arboricola Pv. Pruni (Xap)] Resistance for molecular characterization and incorporation of marker-assisted breeding (MAB) into the University of Arkansas peach and nectarine breeding program. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Frett T, Clark J, Salgado A, Fresnedo-Ramirez J, Sandefur P, Gasic K, Peace C, Bink M, van de Weg E, Verma S. 2016. Pedigree-based quantitative trait loci analysis for fruit quality and phenological traits in the University of Arkansas peach and nectarine breeding program. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Frett T, Clark J, Sandefur P, Jecman A, Gasic K, Peace C, Lee S. 2016. Implementing marker-assisted selection (MAS) for bacterial spot [Xanthomonas Arboricola Pv. Pruni (Xap)] resistance in the University of Arkansas peach and nectarine breeding program. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Olmstead M, Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Hokanson S, Luby J, Main D, McFerson J, Norelli J, Whitaker V, Yue C, Sebolt A. 2016. Successful networking to create international collaborations in the Rosaceae community. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Bassil N, Hummer K, Finn, C. 2016. Lessons learned from DNA-based tool development and use in a Genebank. ISHS VIII International Strawberry Symposium, Quebec City, Canada. Aug 13-18. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Bassil N, Jung S, Cheng C, Lee T, Zheng P, Humann J, Evans K, Peace C, DeVetter L, Gasic K, Olmstead M, Coe M, Main D. 2016. Resources available for Fragaria research through the Genome Database for Rosaceae. ISHS VIII International Strawberry Symposium, Quebec City, Canada. Aug 13-18. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Lee S, Noh Y, Roach JA, Mangandi J, Verma S, Whitaker VM, Cearley KR. 2016. A high-throughput genotyping system combining rapid DNA extraction, high-resolution melting assay and allele specific endpoint genotyping: octoploid strawberry as a model for Rosaceae crops. ISHS VIII International Strawberry Symposium, Quebec City, Canada. Aug 13-18. Oral presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Whitaker VM, Lee S, Osorio LF, Verma S, Roach J, Mangandi J, Noh Y, Gezan S, Peres N. 2016. Advances in strawberry breeding at the University of Florida. ISHS VIII International Strawberry Symposium, Quebec City, Canada. Aug 13-18. Oral presentation
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Fu W, Antanaviciute L, Burrell R, Schnabel G, Gradziel T, Gasic K. 2016. RosBREED: enabling marker-assisted breeding for brown rot (Monilina spp.) resistance in peach. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11, Poster presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Lewter J, Clark J, Antanaviciute L, Gasic K, Burrell III R, Cristosto C, Mansur Z, Byrne D. 2016. RosBREED: Enabling marker-assisted selection for post-harvest deterioration in peach. Development of a standardized phenotyping protocol for blackberry. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11, Poster presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Wannemuehler S, Yue C, Oraguzie N, Luby J, Gallardo RK, McCracken VA. 2016. Cost-benefit analysis of DNA marker selection in sweet cherry breeding. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11, Poster presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Yin M, Clark M, Peterson M, Bassil N, Finn C, Clark J. 2016. Development of a Standardized Phenotyping Protocol for Blackberry. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11, Poster presentation.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Yin M, Carter K, Nyberg A, Clark M, Peterson M, Finn C, Clark J, Bassil N. 2016. Parentage verification of blackberry seedling populations with a microsatellite fingerprinting set. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11, Poster presentation.
  • Type: Other Status: Published Year Published: 2015 Citation: Clark JR. 2015. Peach and nectarine breeding update. Peach Field Day, Fruit Research Station, Clarksville, AR.
  • Type: Other Status: Published Year Published: 2016 Citation: Finn CE, Mackey T, Peterson M, Martin R, Strik B, Buller G, Jones P, Vance A, Moore P, Dossett M. 2016. Sweet Sunrise, Charm and ORUS 2427-4 hit the fields. Oregon Strawberry Commission. Aurora, OR.
  • Type: Other Status: Published Year Published: 2016 Citation: Finn CE, Peterson M, Mackey T, Martin R, Strik B, Jones P, Vance A, Yorgey B, Moore P, Dossett M. 2016. Releasing Columbia Giant and Kokanee. ORUS 35448-2 Next Up! Oregon Raspberry and Blackberry Commission. Woodburn, OR.
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE, Mackey T, Peterson M, Martin R, Dossett M, Strik B, Jones P, Vance A, Moore P. 2015. Charm, Sweet Bliss, Sweet Sunrise and More! USDA-ARS/OSU cooperative strawberry breeding program. Washington Strawberry Commission. Puyallup, WA.
  • Type: Other Status: Published Year Published: 2016 Citation: Finn CE, Mackey T, Peterson M, Martin R, Strik B, Jones P, Vance A, Yorgey B, Moore P, Dossett M. 2016. Sweet Sunrise Charms a Columbia Giant! Grab a Kokanee and Listen to a Cultivar Update from the Oddballs at the USDA-ARS/OSU Collaborative Breeding Program. North Willamette Valley Horticulture Association Annual Meeting. Canby, OR.
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE, Mackey T, Peterson M, Martin R, Strik B, Jones P, Vance A, Yorgey B, Moore P, Dossett M. 2015. Berry cultivars and advanced selections ready for release or trial. Lynden Small Fruit Conference, Lynden WA.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2016 Citation: Peace C, Piaskowski J, Sandefur P, Powell A, Luo F, Edge-Garza D, Rowland T, Johnson C, Vanderzande S. 2016. DNA test cards: delivering trait-predictive discoveries to breeders. American Society for Horticultural Sciences Annual Conference, Atlanta, GA, Aug 8-11. Oral presentation.
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE, Peterson M, Mackey T, Martin R, Strik B, Buller G, Jones P, Vance A, Moore P, Dossett M. 2015. Red raspberry breeding with the USDA-ARS. Washington Red Raspberry Commission. Mt. Vernon, WA.
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE. 2015. USDA-ARS Strawberry Breeding Program Progress Report. OSU-North Willamette Research and Extension Center Strawberry Field Day, Aurora, OR
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE. 2015. USDA-ARS Raspberry and Blackberry Breeding Program Progress Report. OSU-North Willamette Research and Extension Center Caneberry Field Day, Aurora, OR
  • Type: Other Status: Published Year Published: 2015 Citation: Finn CE. 2015. USDA-ARS Blueberry Breeding Program Progress Report. OSU-North Willamette Research and Extension Center Blueberry Field Day, Aurora, OR
  • Type: Other Status: Published Year Published: 2015 Citation: Frett TJ and Clark JR. 2015 Evaluating bacterial spot resistance in peaches using some old and new techniques. Peach Field Day, Fruit Research Station, Clarksville, AR.
  • Type: Other Status: Published Year Published: 2015 Citation: Evans K. 2015. Breeding pome fruit in Washington State. Advances in Field-based High-throughput Phenotyping and Data Management: Grains and Specialty Crops, Spokane, WA.
  • Type: Other Status: Published Year Published: 2015 Citation: Evans K. 2015. Developing and implementing new technologies for and from the WSU pome fruit breeding program. Washington State Horticultural Association Show, Yakima, WA.
  • Type: Other Status: Published Year Published: 2015 Citation: Peace C, Oraguzie N, Sandefur P, Main D, Ru S, Iezzoni A, and Bliss F. 2015. Developing and deploying new sweet cherry DNA Tests. Cherry Research Review, Yakima, Wash.
  • Type: Other Status: Published Year Published: 2015 Citation: Salgado A, Clark JR, Frett T, Sandefur P, Peace C. 2015. Peach texture diversity in the Arkansas peach breeding program. Peach Field Day, Fruit Research Station, Clarksville, AR.
  • Type: Other Status: Published Year Published: 2016 Citation: Lee S, Whitaker, VM, Noh Y, Mangandi J, Roach JA, Verma S, Cearley K. 2016. Application of molecular tools to develop superior strawberry cultivars. Florida Strawberry Growers Association 34th Agritech Conference, Plant City, FL.
  • Type: Other Status: Published Year Published: 2016 Citation: Olmstead M, Iezzoni A, Piaskowski J, Peace C, Schnabel G, Sebolt A, Wilson A. 2016. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 6 Issue 2.
  • Type: Other Status: Published Year Published: 2015 Citation: Olmstead M, McFerson J, Iezzoni A, Peace C, Sebolt A, Wisniewski M, Yue C. 2015. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 6 Issue 1.
  • Type: Other Status: Published Year Published: 2015 Citation: Olmstead M, Andersen K, Gasic K, McFerson J, Iezzoni A, Johnson C, Peace C, Sebolt A, Whitaker V. 2015. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 5 Issue 4.
  • Type: Other Status: Published Year Published: 2016 Citation: Blackberry cultivars can now be distinguished using a DNA test
  • Type: Other Status: Published Year Published: 2016 Citation: Breeding new crisp juicy apple cultivars is more efficient and accurate using DNA tests
  • Type: Other Status: Published Year Published: 2016 Citation: The MSU tart cherry breeding program uses predictive tests to develop superior new cultivars
  • Type: Other Status: Published Year Published: 2016 Citation: The OR-WA sweet cherry breeding program uses predictive DNA test to develop superior new cultivars
  • Type: Other Status: Published Year Published: 2016 Citation: Peach breeders use predictive DNA tests to develop superior new cultivars
  • Type: Other Status: Published Year Published: 2016 Citation: Breeding new flavorful, disease resistant strawberry cultivars is more efficient and accurate using DNA tests


Progress 09/01/14 to 08/31/15

Outputs
Target Audience:Target audiences include Rosaceae tree fruit, berry and rose breeders, pathologists and other allied scientists, Rosaceae crop nurseries, producers, processors, marketers, and consumers. Changes/Problems:Due to unexpected problems with available plant materials, the following performance-evaluation activities will be delayed from Year 1 to Year 2: scab evaluations of apple families (Cornell Univ.) (Obj. 1), fire blight evaluations of apple families (Wash. State Univ.) (Obj. 1), and post-harvest fruit quality evaluations of peach families (Texas A&M Univ.) (Obj. 2). As not all the participating breeders have industry advisory committees, RosBREED will work with each breeder individually to provide supporting content for breeder engagement with their industry clientele (Obj. 5). What opportunities for training and professional development has the project provided?Project participants include two post-doctoral associates fully supported by RosBREED and numerous technicians, graduate students, and undergraduate students partially funded by the project across the breeding programs. These trainees and technicians are participating in RosBREED activities of performance evaluation, DNA profiling, and implementation of DNA-informed breeding strategies. These personnel are gaining knowledge, experience, and skills in accurate measurement of fruit and disease characteristics, determination of trait inheritance, design and implementation of genetic tests, and breeding program planning and management. The major project-wide face-to-face training opportunity was the Annual Project Participant Workshop held 9-11 February 2015. In addition, these participants are members of project Teams and undertake targeted training such as a workshop held for peach postharvest performance evaluation. Twelve of the project participants will be delivering a poster or oral presentation at the 2015 American Society for Horticultural Science Conference. How have the results been disseminated to communities of interest?Communities of interest received project results via presentations at industry and scientific meetings, industry trade publications, scientific publications, project newsletters, the project website (http://www.rosbreed.org), the Genome Database for Rosaceae (www.rosaceae.org), and social media sites [Facebook (www.facebook.com/rosbreed2) and Twitter (@rosbreed)]. Results were disseminated to and input received from 25 Advisory Panel members at meeting held in San Diego, CA on 8 January 2015. The Advisory Panel, comprising 31 stakeholders representing research, extension, and industry, is a key information channel to industry and scientific colleagues and clientele. What do you plan to do during the next reporting period to accomplish the goals?Year 2 of this five-year project will continue to involve activities for all objectives, focusing on: (1) identification and validation of alleles for disease resistance and the generation of breeding parents with combined resistance alleles from multiple sources for each disease; (2) discovery of new large-effect genomic regions influencing fruit quality, expansion of genetic knowledge to the effects of selection of large-effect genomic regions on adjacent regions and concomitant performance effects, and increased breeding efficiency due to the routine implementation of DNA information in parent and seedling selection; (3) generation of preliminary predictive models to capture the effects of genetic background and non-genetic factors; (4) development of cutting-edge DNA-based diagnostic tools, provision of accessible crop-specific DNA testing services, preliminary cost-benefit analysis of the tangible dollar values for DNA-informed breeding applications in two case studies, and technical training in DNA information application for Rosaceae breeding; and, (5) systematic investigation of industry stakeholder decisions on new cultivar adoption in two case studies, engagement of industry stakeholders and allied scientists through the development and delivery of project content, presence at industry and scientific meetings and conferences, and interaction with the project's 31-member Advisory Panel.

Impacts
What was accomplished under these goals? DNA-based diagnostics is ramping up the efficiency, accuracy, speed, and creativity of specialty crop breeding. RosBREED supports U.S. breeding programs of apple, peach, strawberry, cherry and related crops in the Rosaceae family with DNA diagnostic tools to develop superior new cultivars. New cultivars must meet consumer expectations for appearance, aroma, flavor, shelf life and texture and also meet industry needs for durable disease resistances and productivity. This goal has remained elusive using traditional breeding practices that rely on tedious, time- and resource-intensive performance evaluations at all stages. RosBREED has created a coordinated, sustained effort in research, training, and extension to accelerate the application of DNA information in U.S rosaceous crop breeding programs. Eight crops are directly included: apple, blackberry, peach, pear, rose, strawberry, sweet cherry, and tart cherry. Sixteen key diseases are targeted: apple scab, blue mold, and fire blight; peach bacterial spot and brown rot; pear fire blight; Armillaria root rot in Prunus; rose black spot; sweet cherry powdery mildew; tart cherry leaf spot; strawberry bacterial angular leaf spot and five root and crown rot diseases. U.S. Rosaceae breeders, collaborating with pathologists, physiologists, and geneticists, are identifying genetic factors underlying superior fruit quality and genetic sources of disease resistance, and then using the resulting diagnostic DNA profiles to more efficiently incorporate these desirable traits into breeding parents and the next generation of desirable, profitable cultivars. Socio-economic analyses of DNA information use are identifying the most cost-efficient tools for rosaceous crop breeders that will enable more effective use of resources, including the huge biodiversity within rosaceous crops and their wild relatives. The long-term goal is improved consumption, profitability, and sustainability of U.S. rosaceous crops via a continual supply of new disease-resistant cultivars with superior horticultural quality. Obj. 1 - Incorporate durable disease resistance into breeding parents: Standardized protocols to evaluate disease susceptibility were established for the 16 targeted diseases. Almost 5000 individuals across all participating programs were evaluated for disease resistance using these protocols. Plant materials and their performance and genome-scan data are leading to the discovery of new genomic regions associated with disease resistance, enabling development and refinement of DNA tests to increase breeding effectiveness. To date, nine disease resistance genomic regions were discovered and DNA tests developed for them. A total of 124 new breeding families were made via crossing to combine genetic factors for resistance to single and multiple pathogens. Seventy-five apple individuals were confirmed to have multiple genetic sources of scab resistance using DNA tests. Breeders can use such individuals as breeding parents to more rapidly develop new cultivars that have more durable disease resistance than current cultivars with only single resistance factors. Obj. 2 - Combine disease resistance and horticultural quality: Numerous advances have been made regarding cultivar-generating breeding families. An online tool was completed for leveraging knowledge of shared ancestry across rosaceous crops. Use of this tool has already identified interesting new regions for blackberry and pear, crops with less prior genomics research than others such as peach and apple. Genome-wide chromosome characterization of U.S. breeding resources of cherry, apple, and peach was initiated to compile our knowledge of all known valuable genetic factors. The resulting descriptions of the genome-wide structure of historic selections and the locations and effects of genetic factors influencing horticultural quality and disease resistance will provide the foundation for DNA profiling to reveal genetic potential in breeding germplasm individuals. The compositions of the "Crop Reference Sets" of blackberry and pear were chosen; these will be used to identify and confirm the location and effects of valuable genetic factors influencing fruit sweetness. A standardized evaluation protocol for peach postharvest fruit quality was developed for the 2015 fruiting season. DNA profiling of breeding parents was conducted in several U.S. breeding programs of apple, peach, cherry, and strawberry. Use of DNA-based knowledge about potential breeding parents is enabling breeders to design crosses more likely to generate superior offspring. Thousands of seedlings in U.S. breeding programs of apple and sweet cherry were DNA-tested for up to six traits; those seedlings predicted to be inferior were culled. Such early evaluation and culling of seedlings for several traits in 2015 is estimated to have provided a future net resource savings of approximately $200,000 that can be reallocated to more effectively achieving breeding targets rather than spending years managing inferior seedlings. Obj. 3 - Advance selections with improved confidence: Foundational advances were made in two novel DNA-based approaches in breeding selection, complementary to those targeted above, here focusing on elite candidate cultivars elevated to multi-location performance trials. Pedigree, performance, and DNA-based data of training populations for genome-wide selection in strawberry and apple, were compiled and analyzed. These preliminary genome-wide predictions have provided insight into families more likely to yield genetic gain from the accumulation of major and minor genetic factors. Also, eight institutions in Europe, Australia, and Chile each provided historical datasets of performance evaluation for elite selections in multiple locations under various crop management regimes. Compiling these datasets and interrogating them is an unprecedented use of genome-wide data and should result in DNA profiles that predict performance of cultivar candidates under growing conditions not yet experienced. Such predictions were already made for the trait of apple crispness in an early test of this approach. Obj. 4 - Increase routine use of DNA information: Rosaceae breeders were provided with access to crop-specific DNA testing facilities, removing a roadblock to routine adoption of DNA-informed breeding. New DNA tests were developed for pear and blackberry parentage testing and for trait predictions of pear fire blight, apple, cherry, and peach fruit quality, and strawberry angular leaf spot. Enhancement of decision-support software Cross Assist and Seedling Select was initiated. Case studies were initiated for cost-benefit analysis of DNA information use in breeding. Rosaceae breeders were provided with access to information to increase their understanding and adoption of routine DNA-informed breeding strategies. This includes a revised community breeders' webpage (www.rosbreed.org/breeding/community-breeders), two articles distributed in quarterly newsletters, a brochure, and "DNA test cards" to describe available DNA testing tools and services for peach breeders. Obj. 5 - Utilize stakeholders input: Case studies of strawberry and peach cultivar releases were initiated with detailed plans developed by socio-economists, peach and strawberry breeders, and industry stakeholder groups. Briefs describing DNA test application and impact were developed and circulated to Rosaceae commodity group leaders. The RosBREED Executive Committee met with 25 (of 31) Advisory Panel members in San Diego on 8 January 2015. Recommendations from this large expert panel were discussed at the annual project-wide meeting in February 2015. Advisory Panel members were also engaged throughout the year, enhancing project communications by contributing to the RosBREED quarterly newsletter, industry briefs, and brochures.

Publications

  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Minas I, Font i Forcada C, Dangl G, Gradziel T, Dandekar A, Crisosto C. 2015. Discovery of non-climacteric and suppressed climacteric bud sport mutations originating from a climacteric Japanese plum cultivar (Prunus salicina Lindl.). Fron Plant Science 6:316.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C. 2015. RosBREED: Combining disease resistance with horticultural quality in new rosaceous cultivars. Plant & Animal Genome XXIII, San Diego, CA. W335.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Peace C, Bassil N, Coe M, Finn C, Gasic K, Hokanson S, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C, Iezzoni A. 2015. RosBREED: A pedigree of amazing germplasm, traditional genetics, international collaboration, and DNA-based technologies. CROPS 2015: Genomics Enabled Crop Breeding & Improvement, Huntsville, AL.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Roach J, Verma S, Peres N, Jamieson A, van de Weg E, Bassil N, Whitaker V. 2015. FaRXf1: a locus conferring resistance to Xanthomonas fragariae in octoploid strawberry. VIII North American Strawberry Symposium, Ventura, CA.
  • Type: Other Status: Other Year Published: 2014 Citation: Olmstead M, Norelli J, Iezzoni A, Peace C, Sebolt A. 2014. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 5 Issue 1.
  • Type: Other Status: Other Year Published: 2015 Citation: Olmstead M, DeVetter L, Iezzoni A, Ivors K, Peace C, Sebolt A. 2015. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 5 Issue 2.
  • Type: Other Status: Other Year Published: 2014 Citation: Layne, D. 2014. RosBREED2: Disease resistance plus horticultural quality is the goal. Published in: Growing Produce magazine. www.growingproduce.com/fruits/rosbreed-2-program-focuses-on-disease-resistance-and-quality
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Harshman J, Evans K. 2015. Survey of moldy core incidence in germplasm from the three U.S. apple breeding programs. J Amer Pomol Soc 69: 51-57.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C. 2015. RosBREED2: Progress and future plans to enable DNA-informed breeding in the Rosaceae. XIV Eucarpia Fruit Breeding and Genetics Symposium June 14-18. Bologna.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Koehorst-van Putten H, van Dijk T, Bassil N, Davis TM, van de Weg E. 2015. An ultra-dense SNP linkage map for the octoploid, cultivated strawberry and its application in genetic research. XIV Eucarpia Fruit Breeding and Genetics Symposium June 14-18. Bologna .
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Byrne DH, Anderson N, Mansur Z. 2015. Smooth delight and smooth zest nectarines: Four new low-chill stone fruit cultivars. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Verma S, Mangandi J, Roach J, Peres N, Whitaker V. 2015. QTL detection and allele mining for Phytophthora cactorum resistance in University of Florida strawberry breeding germplasm. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Andersen K, Sebolt A, Stegmeir T, Iezzoni A. 2015. Development of single sequence repeat marker PcdG4RS for the differentiation of cherry rootstocks. Poster presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Byrne DH, Anderson N, Mansur Z. 2015. Zest peaches and smooth Texan nectarines, new medium-chill stone fruit cultivars. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Iezzoni A, Peace C, Bassil N, Coe, M, Finn C, Gasic K, Hokanson S, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C. 2015. RosBREED2: More traits, additional crops, expanded germplasm, new science. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 20115 Citation: Mansur ZJ, Hartmann TP, Carpenedo S, Byrne DH. 2015. Heritability and phenotypic correlations among bloom, flower density and fruit set. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Roach J, Verma S, Peres N, Jamieson A, Van de Weg E, Bassil N, Whitaker V. 2015. FaRXf1: a locus conferring resistance to Xanthomonas fragariae in octoploid strawberry. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Salinas N, Daeil K, Perrotte J, Gaston A, Potier A, Hancock J, Gunduz K, Mathey M, Mookerjee S, van Dijk T, van de Weg E, Peace C, Denoyes B, Finn C, Bassil N. 2015. Usefulness of FaPFRU-associated perpetual flowering markers in the cultivated octoploid strawberry. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Verma S, Mangandi J, Roach J, Peres N, Bassil N, Van de Weg E, Whitaker V. 2015. Pedigree-based QTL detection for disease resistance and fruit quality traits: an overview of the University of Florida strawberry breeding population. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Salinas N, Tennessen J, Vining K, Liston A, van de Weg E, Sargent D, Finn CE, Jackson E, Schlueter J, Schlueter S, Bassil N. 2015. Comparison of three genotyping by sequencing pipelines for variant identification and linkage mapping in the cultivated octoploid strawberry. Poster presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Bassil N, Finn C, Clark J, Peace C, Iezzoni A. 2015. Development of a multiplexed fingerprinting set in blackberry. XI International Rubus and Ribes Symposium, Asheville, NC.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Iezzoni A, Peace C, Bassil N, Coe M, Finn C, Gasic K, Luby J, Main D, McFerson J, Norelli J, Olmstead M, Whitaker V, Yue C. 2015. RosBREED2: Progress and future plans to enable DNA-informed breeding in the Rosaceae. XI International Rubus and Ribes Symposium, Asheville, NC.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Bassil N, Davis T, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin E, Rosyara U, Putten H, Monfort A, Sargent D, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E. 2015. Development and preliminary evaluation of a 90 K Axiom� SNP array for the allo-octoploid cultivated strawberry Fragaria � ananassa. BMC Genomics 16:155
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Ru S, Main D, Evans K, Peace C. 2015. Current applications, challenges, and perspectives of marker-assisted seedling selection in Rosaceae tree fruit breeding. Tree Genet Genomes 11:8.
  • Type: Journal Articles Status: Published Year Published: 2014 Citation: Clark MD, Bus VGM, Luby JJ, Bradeen JM. 2014. Characterization of the defense response to Venturia inaequalis in Honeycrisp apple, its ancestors, and progeny. Eur J Plant Path 140:69-81.
  • Type: Theses/Dissertations Status: Published Year Published: 2015 Citation: Basundari, F. 2015. Marker-assisted seedling selection in sour cherry for cherry leaf spot resistance and fruit color. M.S. Thesis, Plant Breeding, Genetics, and Biotechnology Graduate Program, Michigan State Univ.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Frett T, Clark J, Smith B, Bluhm B, Sandefur P, Peace C, Jecman A, Salgado A, Gasic K. 2015. Evaluating Bacterial Spot [Xanthomonas arboricola pv. Pruni (Xap)] Resistance for Molecular Characterization and Incorporation of Marker-assisted Breeding (MAB) into the University of Arkansas Peach and Nectarine Breeding Program. Poster presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014. Research on berry cultivars and their development. October 21, 2014, Washington Red Raspberry Commission Annual Meeting, Video Teleconference.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014.Research on strawberry cultivars and their development. December 11, 2014. Washington Strawberry Commission Annual Meeting, WSU-Puyallup.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014. USDA blackberry and raspberry breeding program in the Pacific Northwest. December 17, 2014, Oregon Raspberry and Blackberry Commission Annual Meeting, Woodburn, OR.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014. USDA berry breeding program and new releases from other programs. January 15, 2015. North Willamette Valley Horticulture Association Annual Meeting, Canby, OR.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014 USDA-ARS small fruit cultivars and advanced selections. January 29, 2015. Lower Mainland Horticulture Improvement Association, Abbotsford, BC, Canada.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014. USDA blackberry and raspberry breeding program in the Pacific Northwest. February 17, 2015. Oregon Caneberry Workshop, Woodburn, OR.
  • Type: Other Status: Under Review Year Published: 2015 Citation: Olmstead M, DeVetter L, Gasic K, Iezzoni A, McFerson J, Peace C, Sebolt A. 2015. RosBREED: Combining disease resistance and horticultural quality in new rosaceous cultivars Newsletter. Volume 5 Issue 3.
  • Type: Other Status: Other Year Published: 2014 Citation: Finn, C. 2014. USDA strawberry breeding program in the Pacific Northwest. January 19, 2015. Oregon Strawberry Commission Annual Meeting, Aurora, OR.
  • Type: Other Status: Other Year Published: 2015 Citation: Finn, C. 2014. Raspberry and blackberry breeding. February 27, 2015. North American Raspberry and Blackberry Association, Fayetteville, AR.
  • Type: Other Status: Other Year Published: 2014 Citation: Frett, TJ, Clark, JR. 2015. Evaluating Bacterial Spot Resistance. 34th Annual Horticulture Industries Show. January 16-17, 2015. Fort Smith, AR.
  • Type: Other Status: Other Year Published: 2015 Citation: Howard, N. Marker-assisted breeding efforts at the UMN apple breeding program: Current efforts and future prospects. January 8, 2015, Minnesota Apple Growers Assn Annual Conference, La Crosse, WI
  • Type: Other Status: Other Year Published: 2015 Citation: Norelli, J, Evans, K. Incorporating fire blight resistance into Washington apple cultivars. January 29, 2015. Washington Tree Fruit Research Commission: Apple Crop Protection Review, Pasco, WA.
  • Type: Other Status: Other Year Published: 2015 Citation: Salgado A, Clark J, Frett T, Sandefur P, Peace C. 2015. Integrating phenotypic and genotypic data for flesh texture and marker-assisted breeding in peach. Southern Region American Society of Horticultural Sciences. Atlanta, GA.
  • Type: Conference Papers and Presentations Status: Accepted Year Published: 2015 Citation: Yan M, Dong Q, Byrne DH, Klein P. 2015. Applying genotyping by sequencing technology on Rosa spp. Presentation at the American Society for Horticultural Science conference in New Orleans, LA, August, 2015.
  • Type: Journal Articles Status: Published Year Published: 2015 Citation: Hancock JF, Callow PW, Mathey MM, Mackey T, Gunduz K, Mookerjee S, Lichun C, Salinas N, Bassil NV, Hummer KE, Finn CE. 2015. Phenotypic variability in a panel of strawberry cultivars from North America and the European Union. J Amer Pomol Soc 69: 85-101.