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RosBREED
Annual Project Report
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
Dedicated to the
genetic improvement
of U.S. rosaceous
crops
www.rosbreed.org
RosBREED Advisory Panel
Annual Meeting
January 11, 2018
San Diego, CA
Content Description Page
Agenda 3
Team Leaders 4
Team Members 5
International Partners and Nature of Partnership 6
Advisory Panel Members – Industry 7
Advisory Panel Members – Scientific 8
Advisory Panel Members – Extension 9
Project Overview 10
Crops, Breeders, and Diseases Targeted 11
Objective 1 12
Objective 2 13
Objective 3 14
Objective 4 15
Objective 5 16
DNA Test Tables 17
Obj 1 YR 3 Deliverables, Challenges, & YR 4 Planned Deliverables 20
Obj 2 YR 3 Deliverables, Challenges, & YR 4 Planned Deliverables 22
Obj 3 YR 3 Deliverables, Challenges, & YR 4 Planned Deliverables 24
Obj 4 YR 3 Deliverables, Challenges, & YR 4 Planned Deliverables 26
Obj 5 YR 3 Deliverables, Challenges, & YR 4 Planned Deliverables 29
RosBREED Breeders’ Annual Report for Year 3 - Summary 31
Break-Out Session Discussion Questions 33
Table of Contents
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
2
AgendaThu, Jan 11, 2018
Skyline/Lindbergh Rooms (Ninth Floor)
Hilton San Diego Airport, 1960 Harbor Island Dr., San Diego, Calif.
Start End
Audience/
group
Presenter/
moderator Title
7:30 8:00 Continental breakfast
8:00 All Amy Iezzoni Introductions and Agenda
8:30 All Amy Iezzoni Project overview
8:50 All Team LeadersObj. 1: Incorporate durable disease resistance into
breeding parents
9:20 All Team LeadersObj. 2: Combine disease resistance and
horticultural quality
9:40 All Team LeadersObj. 3: Advance selections with improved
confidence
10:00 10:30 Break
10:30 All Team LeadersObj. 4: Increase routine use of DNA information in
rosaceous crop breeding
11:00 All Team Leaders Obj. 5: Utilize stakeholder input
11:30 All Amy Iezzoni Budget
11:45 All Amy Iezzoni Charge for afternoon breakout groups
12:00 1:30 Lunch
1:30 2:45
Breakout
groups by
crop
Group 1 Pome Fruit (Skyline/Lindbergh Rooms)
Group 2 Stone Fruit (Chart Room – 1st floor)
Group 3 Berry and Rose (Port Room – 1st floor)
2:45 3:15 Break
3:15 4:00 AllBreakout group
moderatorsReport-outs & discussion – next steps/action items
4:00 5:00 All Cameron Peace Round table
5:00 Dinner on your own or in working groups
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
3
Team Leaders
Project DirectorAmy Iezzoni
Michigan State University
517.353.0391
Stone Fruit Breeding
Ksenija Gasic
Clemson University
Statistical Genetics
Vance Whitaker
University of [email protected]
Pome Fruit Breeding
James Luby
University of Minnesota
DNA Testing
Nahla Bassil
USDA-ARS National Clonal Germplasm
Berry Fruit Breeding
Chad Finn
USDA-ARS, Corvallis, OR
Socio-Economics
Chengyan Yue
University of Minnesota
Rose Breeding
Stan Hokanson
University of Minnesota
Co–PD, DNA-Informed Breeding
Cameron Peace
Washington State University
Pathology
Jay Norelli
USDA-ARS, Kearneysville, WV
Extension
Jim McFerson
Washington State [email protected]
Data Management
Dorrie Main
Washington State University
Extension Evaluation
Michael Coe
Cedar Lake Research Group, Portland, OR
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
4
RosBREED Team Members
Rex Bernardo (Univ. of Minnesota)
Stan Hokanson (Univ. of Minnesota)
Susan Brown (Cornell Univ.)
Craig Hardner (Univ. Queensland, Australia)
David Byrne (Texas A&M Univ.)
Kelly Ivors (Cal. Poly. State Univ.)
Matt Clark (Univ. of Minnesota)[email protected]
Amy Lawton-Rauh (Clemson Univ.)
Carlos Crisosto (Univ. of California-Davis)
Desmond Layne (Washington State Univ.)
Thomas Davis (Univ. of New Hampshire)
Vicki McCracken (Washington State Univ.)
Lisa Wasko DeVetter (Wash. State Univ.)
Gregory Reighard (Clemson Univ.)[email protected]
Kate Evans (Washington State Univ.)
Chris Saski (Clemson Univ.)[email protected]
Karina Gallardo (Washington State Univ.)
Guido Schnabel (Clemson Univ.)[email protected]
Tom Gradziel (Univ. of California-Davis)
Margaret Worthington (Univ. of Arkansas)[email protected]
James Hancock (Michigan State Univ.)[email protected]
Eric van de Weg (Wageningen Univ. &
Research Centre, [email protected]
RosBREED Project Assistants
Audrey Sebolt (Michigan State Univ.)
517.353.0432
Joan Schneider (Michigan State Univ.)
517.353.0360
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
Breeder Collaborators
Patrick Moore (Washington State Univ.)
William Shane (Michigan State Univ.)
5
International Partners and Nature of Partnership
1. Centro di Ricerca per la Frutticoltura, Rome, Italy: Ignazio Verde provides expertise in peach
genomics, genetics, and QTL discovery.
2. Department of Plant Breeding and Genetics, East Malling Research, East Malling, UK: Richard
Harrison provides expertise in strawberry genetics and genomics. Felicidad Fernandez provides
expertise in cherry and pear breeding and genetics.
3. INRA – Breeding & Genetics teams: The INRA breeding teams provide parallel expertise in apple,
peach, strawberry and cherry breeding and genetics.
a. Unité de Génétique et Amélioration des Fruits et Légumes (UGAFL), INRA CR Beauouze, France
INRA – Angers: Francois Laurens and team member Charles-Eric Durel provide expertise in
apple breeding and genetics and collaborate by using common SNP markers. Linkages are
formed with the molecular genetics laboratory of Pauline Lasserre.
b. Unité de Recherche des Espèces Fruitières (UREF), INRA CR, Villenave d'Ornon, France INRA
– Bordeaux: Béatrice Denoyes-Rothan provides expertise in strawberry breeding and genetics
and collaborates by placing the RosBREED SNP markers on the INRA octoploid strawberry map.
Elisabeth Dirlewanger provides expertise in Prunus genetics and comparative mapping in the
Rosaceae. José Quero-Garcia provides expertise in sweet cherry breeding and genetics and we
are collaborating by using common SNP markers.
c. Unité de Génétique et Horticulture (GENHORT), INRA CR, Avignon, France
INRA – Avignon: Benedicte Quilot-Turion provides expertise in peach molecular genetics and
collaborates by using common SNP markers. Linkages are formed with the peach breeding team
of Thierry Pascal and Patrick Lambert.
4. Institut für Pflanzengenetik, Leibniz University Hannover, Germany: Thomas Debener provides
expertise in rose genetics and genomics including access to a large collection of unpublished ESTs.
5. CREA - Research Centre for Viticulture and Enology, Roma, Italy: Riccardo Velasco provides
expertise in genomics and supports RosBREED through the sharing of refinements in the apple
genome sequence.
6. Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Cabrils, Spain: Pere Arús provides
expertise in peach genetics and genomics. Amparo Monfort provides expertise in strawberry genetics
and genomics as part of the international strawberry SNP consortium.
7. Instituto de Investigación y Formación Agraria y Pesquera, Málaga, Spain: Iraida Amaya
provides expertise in strawberry genetics, genomics, germplasm and breeding.
8. Plant & Food Research, Palmerston North, New Zealand: Sue Gardiner provides expertise in apple
and pear genetics and marker-assisted breeding. David Chagné provides expertise in apple and pear
genetics, including genome-wide selection.
9. University of Chile, Santiago, Chile: Herman Silva and Lee Meisel provide expertise in Rosaceae
functional genomics and metabolomics through the sharing of peach, sweet cherry, and strawberry
sequence data.
6
Professional Interests of RosBREED Advisory Panel Members
RosBREED has three Advisory Panels, representing industry, scientific, and
extension interests. Panel members broadly represent the diversity of Rosaceae
by crop, region, and professional expertise.
RosBREED Industry Advisory Panel
• Jim Allen: Vice President
New York Apple Sales, Glenmont, NY (www.newyorkapplesales.com/)
• Jen Baugher: Marketing Associate
Adams County Nursery, Aspers, PA (www.acnursery.com)
• Chalmers Carr III: CEO
Titan Peach Farms, Inc., Ridge Spring, SC (www.titanfarms.com)
Board of Directors, South Carolina Peach Council (www.scpeach.org)
• Robert Curtis: Senior Director, Agricultural Affairs
Almond Board of California, Modesto, CA (www.Almonds.com)
• Bill Dodd: President
Ohio Fruit Growers Marketing Association, Newcomerstown, OH
(www.ohioapples.com/ohio_apples_fgma.htm)
ex-President Board of Trustees, US Apple Association
• Carlos Fear: Director of Consumer Lab and Molecular Genetics
Driscoll’s Strawberry Associates, Watsonville, CA (www.driscolls.com)
• Bob Gix: Horticulturist
Blue Star Growers, Cashmere, WA
Co-Chair, Fresh Pear Research Subcommittee, Pears USA (www.usapears.com)
• Bruce Grim: Director
Washington Marketing Associations, Wenatchee, WA (www.themarketingassociations.org)
ex-President, Board of Trustees, US Apple Association
• Cynthia Haskins: President/CEO
New York Apple Association, Inc. (www.nyapplecountry.com)
• Philip Korson: President
Cherry Marketing Inst., Inc., Lansing, MI (www.choosecherries.com)
• John Lott: President
Bear Mountain Orchards, Inc., Aspers, PA
• Mercy Olmstead: Senior Research Manager
Research and Education, California Strawberry Commission, Watsonville, CA
(www.calstrawberry.com)
• Michele Scheiber: Director of Breeding
Star Roses and Plants, West Grove, PA
7
RosBREED Scientific Advisory Panel
• Pere Arús: Head, Plant Genetics Dept., Institut de Recerca i Tecnologia Agroalimentàries
(IRTA), Cabrils, Spain
Research areas: molecular tools for plant genetics; comparative genomics and application of
molecular markers in Rosaceae breeding. (www.irta.cat/ca-ES/Persones/Pagines/105.aspx)
• Joe Arvai: Max McGraw Professor of Sustainable Enterprise and Director, Erb Institute,
University of Michigan, Ann Arbor, MI
Research areas: Behavioral decision research and decision support systems
(www.snre.umich.edu/profile/joseph_Arvai)
• Frederick Bliss: Professor Emeritus, Univ. of California, Davis and Sr. Director (ret.), R&D
Special Projects, Seminis Vegetable Seeds, Woodland, CA
Research areas: genomics, genetics, and breeding of fruit and vegetable crops; research
administrator in public and private sectors; commercialization of breeding products
• Robin Buell: Professor, Dept. of Plant Biology, Michigan State Univ., East Lansing, MI
Research areas: genomic aspects of plant biology and plant pathogens; high throughput
sequencing, functional genomics, comparative genomics, and bioinformatics
(www.plantbiology.msu.edu/faculty/faculty-research/robin-buell/)
• Lailiang Cheng: Professor, Professor, Dept. of Horticulture, Cornell Univ., Ithaca, NY
Research areas: plant nutrition, fruit physiology, molecular, cellular, and whole plant response
to abiotic stress in apple, cherry, grape; undergraduate and graduate education
(http://hort.cals.cornell.edu/people/lailiang-cheng)
• Susan Gardiner: Principal Scientist, The Horticultural and Food Research Inst. of New
Zealand (Plant & Food Research [PFR])
Research areas: leads Gene Mapping Team integrated with PFR breeders in several
Rosaceae crops, including, apple, apple rootstock, pear, peach/nectarine and apricot
• Kim Hummer: Supervisory Research Horticulturist, USDA-ARS National Clonal Germplasm
Repository, Corvallis, OR
Research areas: conservation and genetics of fruit, nut, and specialty crops; ploidy in
strawberry species..
• Dan Kluepfel: USDA-ARS & Professor, Dept. of Plant Pathology, UC Davis, CA
Research areas: bacterial diseases of almonds and walnuts, specifically crown gall.
(http://plantpathology.ucdavis.edu/?story=1033)
• Brad Rickard: Assoc. Professor, Dept. of Agricultural Sciences, Cornell Univ., Ithaca, NY
Research areas: economic implications of policies, innovation, and industry-led initiatives
applied to agricultural and food markets (http://dyson.cornell.edu/people/profiles/rickard.php)
• Carolyn Ross: Assoc. Professor, Dept. of Food Science, Wash. State Univ., Pullman, WA
Research areas: sensory analysis and consumer preferences of fruit and fruit products,
including fresh and processed apple, pear, and cherry and wine.
(http://sfs.wsu.edu/personnel/faculty-staff/ross-c/)
• Phil Simon: Research Geneticist, USDA-ARS and Professor, Dept. of Horticulture, Univ. of
Wisconsin-Madison, Madison, WI
Research areas: vegetable breeding and genetics; biochemistry of culinary and nutritive
factors, terpenoids, and sugars in carrots and garlic.
(www.ars.usda.gov/pandp/people/people.htm?personid=5186)
• Chang-Lin Xiao: Supervisory Research Plant Pathologist. USDA-ARS, Parlier CA
Research areas: biology, epidemiology, and management of diseases of fruit crops with an
emphasis on postharvest diseases.
(www.ars.usda.gov/pandp/people/people.htm?personid=47587)
8
RosBREED Extension Advisory Panel
• David Eddy: Editor, American/Western Fruit Grower, MeisterMedia, Willoughby OH
Professional interests: Ag journalism, print and electronic communication
(www.growingproduce.com/author/david-eddy/)
• Peter Hirst: Professor, Dept. of Horticulture, Purdue Univ., West Lafayette, IN
Professional interests: tree fruit production systems and physiology, physiological genetics of
flowering and fruit development in Rosaceae; state Extension specialist; undergraduate and
graduate education
(https://ag.purdue.edu/hla/Pages/Profile.aspx?strAlias=hirst&intDirDeptID=16)
• David Karp: Associate, Agricultural Experiment Station, UC Riverside, Riverside, CA
Professional interests: freelance food journalist and photographer
• Ron Perry: Professor, Dept. of Horticulture, Michigan State Univ., East Lansing, MI
Professional interests: extension and research in cherry and apple orchard systems
(http://www.hrt.msu.edu/ronald-perry/pg7)
• Clark Seavert: Professor & Director of the NW Agribusiness Executive Seminar Department
of Agricultural & Resource Economics, Oregon State Univ., Corvallis, OR
Professional interests: assessment and advancement of technologies that increase
profitability and feasibility in commercial agriculture, with the aim of aligning business model
innovation strategies to existing and future technologies.
(http://arec.oregonstate.edu/seavert)
• Chris Watkins: Professor, Dept. of Horticulture, Cornell Univ., Assoc. Director for Cornell
Cooperative Extension, Ithaca, NY
Professional interests: postharvest physiology and management of apple, pear, peach, and
cherry; state-wide agricultural extension activities
(http://hort.cals.cornell.edu/people/christopher-watkins)
9
RosBREED is a multi-state, multi-institution project dedicated to the genetic
improvement of U.S. rosaceous crops by targeted applications of genomics
knowledge and tools to accelerate and increase the efficiency of breeding
programs.
This Coordinated Agricultural Project is funded through the USDA-NIFA Specialty
Crop Research Initiative by a combination of federal and matching funds, grant
2014-51181-22378.
What is RosBREED?
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
The perfect cultivar of apple, cherry, peach, strawberry, rose, and other rosaceous
crops, one which consistently exceeds consumer expectations with satisfying
appearance, aroma, flavor, shelf life, and texture AND also meets industry needs
for durable disease resistances and productivity, remains elusive.
Yet, such rosaceous cultivars are possible. The components exist – but they must
be combined.
What stakeholder and consumer needs does
RosBREED address?
Combining horticultural quality, durable disease resistances, and productivity into
new cultivars can be achieved through the coordinated application and
implementation of new scientific advances.
What is our vision?
• Consumers are satisfied, repeat customers
• Rosaceous crop industries are more profitable and sustainable
• Plant breeding programs are more efficient and effective
What does success look like?
10
Combining Disease Resistance
with Horticultural Quality
in New Rosaceous Cultivars
Targeted Crops, Breeders, & Diseases
Tart cherry (scion & rootstock): Cherry leaf
spot, Armillaria root rot
• Michigan State Univ. (Amy Iezzoni)
Rose: Black spot
• Univ. of Minnesota (Stan Hokanson)
• Texas A&M Univ. (Dave Byrne)
Strawberry: Root and Crown rots, Bacterial
angular leaf spot
• Michigan State Univ. (James Hancock)
• USDA-ARS Corvallis (Chad Finn)
• Univ. of Florida (Vance Whitaker)
• Univ. of New Hampshire (Tom Davis)
• Washington State Univ. (Pat Moore)
Apple: Apple scab, Blue mold, Fire blight
• Washington State Univ. (Kate Evans)
• Univ. of Minnesota (James Luby)
• Cornell Univ. (Susan Brown)
• USDA-ARS Kearneysville (Jay Norelli)
Peach (scion & rootstock): Bacterial spot,
Brown rot, Armillaria root rot
• Clemson Univ. (Ksenija Gasic)
• Univ. of Arkansas (Margaret
Worthington)
• Texas A&M (David Byrne)
• Univ. of California Davis (Tom Gradziel)
• Michigan State Univ. (William Shane)
Pear: Fire blight
• USDA-ARS Kearneysville (Jay Norelli)
Sweet cherry: Powdery mildew
• Washington State Univ. (Cameron
Peace)
Blackberry: Fruit sweetness. This is the
overwhelming need as there is not a major
disease threat
• Univ. of Arkansas (Margaret
Worthington)
• USDA-ARS Corvallis (Chad Finn)
11
OBJECTIVE 1
Incorporate Durable Disease Resistance in Breeding Parents
U.S. Rosaceae breeders, collaborating with pathologists, will identify and incorporate disease
resistance alleles into breeding parents. Use of these parents will enable new disease resistant
cultivars to be developed more rapidly, as these parents will donate multiple resistance alleles
to their progeny.
Obj. 1: Develop donor parents with multiple alleles for disease resistance
Pyramiding
disease A resistances
X
CombiningValidationDiscovery1a 1b
X
Phenotype & Genotype
QTL analysis
DNA tests
Multiple resistance
alleledonor
X
disease B resistances
Methods Overview: Participating teams of U.S. Rosaceae breeders and pathologists will:
1a Identify alleles and develop and validate DNA tests for disease resistance by QTL analysis
1b Incorporate these alleles by marker-assisted introgression into breeding parents, which we
call “multiple resistance allele donors”. These 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.
Timeline: 1a was initiated in Year 1 and will be completed at the end of Year 4. 1b started in Year
1 for apple, Year 2 for peach, strawberry and tart cherry with resistance alleles pyramided or
combined from at least two sources is to be completed by the end of Year 5.
Jay Norelli Guido Schnabel Kelly Ivors
12
OBJECTIVE 2
Combine Disease Resistance and Horticultural Quality
Methods Overview: New large-effect fruit quality alleles will be discovered by:
2a Leveraging syntenic genomic locations of QTLs, and
2b Using a genome-wide pedigree-based analytical approach,
2c Alleles within regions contributing to desired phenotypes will be identified by haplotype
blocking (haploblocking) to expand selection decisions from individual loci and traits to many
linked loci and traits.
2d Marker-assisted parent and seedling selection will combine disease resistance with superior
horticultural quality in the next generation of breeding families.
Timeline: 2a–2c was initiated in Year 1, with completion in Year 3. 2d will be accomplished in
Years 1-5 (apple, peach, strawberry, cherry) or Years 4-5 (rose, blackberry, pear).
Development of cultivars that combine excellent horticultural quality and disease resistance will
be enabled with knowledge of desirable alleles and their locations in the genome.
Dorrie Main Carlos Crisosto Amy Lawton-Rauh
13
New selections will be advanced toward commercial release with improved confidence due to
more accurate predictions of fruit quality performance, which includes estimates of non-genetic
factors (e.g., cultural practices, climate) and alleles at small-effect loci across the entire genome.
Obj. 3: Advance selections with improved confidence
Non-genetic effects Superior selectionsGenome-wide selection
3bPrediction models
Selection populations
Genetic background effects estimated
3c
Compare with traditional selection
Collate trial data
Determinegenomic replication
Non-genetic effects
Performance predictions
Validate
Engage stakeholders
Predict performance under alternative conditions
Id. superior selections
3a
5a
Methods Overview: 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.
3a 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.
3b Genomic relationship matrices using dense SNP arrays 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.
3c In case studies, performance stability of elite selections under alternative growing conditions
will be predicted using 3a and 3b results, validated, and used to streamline selection
advancement and engage stakeholders in the latter stages of their breeding programs.
Timeline: 3a and 3b
was initiated in Year
1 with data compilation
and analysis completed
in Year 4. 3c will be
conducted in Year 4.
Rex Bernardo Craig HardnerVance Whitaker
OBJECTIVE 3
Advance Selections with Improved Confidence
14
Methods Overview:
4a Cutting-edge DNA diagnostic tools will be developed and crop-specific
DNA testing services will be made available.
4b DNA Information will be integrated into enhanced decision support
software.
4c Cost-benefit analyses will be conducted to identify tangible dollar values
for DNA-informed breeding applications.
4d Breeders and allied scientists will receive technical training in use of
DNA information in breeding.
Timeline: 4a was initiated in Year 1 and tool development will continue until
the end of Year 5. Routine DNA testing will transition to commercial service
providers after Year 3. 4b was discontinued in Year 3 due to sustained
USDA mandated 7% budget cuts. 4c cost: benefit analyses began in Year 1
and new adoption case studies will begin in Year 2; all will be completed in
Year 4. 4d technical training will be ongoing for all five years.
Cameron Peace Jim McFerson Vicki McCrackenChengyan Yue Karina Gallardo
OBJECTIVE 4
Increase Routine Use of DNA Information
The development of cost-effective and accessible DNA diagnostic tools will enable DNA-informed
breeding to be widely adopted by rosaceous crop breeders, leading to increased breeding
efficiency.
Nahla Bassil
Chris Saski
15
The impact of new cultivars will be maximized with industry stakeholder input into cultivar trait
priorities and improved predictability of commercial performance. Due to the geographic and
crop diversity within RosBREED, stakeholder input and recommendations will be specific for
individual crop breeding programs.
OBJECTIVE 5
Utilize Stakeholder Input
Methods Overview:
5a Stakeholder decisions on new cultivar adoption will be systematically investigated in two
breeding programs.
5b Stakeholders are being engaged in project outcomes, evaluation, and adjustments.
Timeline: 5a will be initiated in Year 2, with surveys conducted in Years 2 to 4. 5b stakeholder
activities will follow an annual timeline for all five years of recurring (and some ad hoc) meetings
Vicki McCracken
Jim McFerson Des Layne
Greg Reighard
Vance Whitaker Lisa Wasko DeVetter
Karina Gallardo Chengyan Yue Ksenija Gasic
16
Table 1. Diseases and physiological disorders of apple, cherry, strawberry, peach, pear and
rose where predictive DNA tests for major resistance loci are being sought. Stage of progress
towards use of a DNA test is indicated.
Progress towards the use of DNA tests for diseases and physiological disorders
Crop Disease/PathogenLocus/Loci
Discovered
Valuable
Alleles
Identified
DNA Test
Developed
(Test Name)
DNA Test
in Use
Apple Blue mold M. sieversii PI yes Md-Pe3-SSR yes
Apple Foliar powdery mildew M. sieversii (LG8) yes Md-Plw-SSR yes
Apple Scab LG1 yes
CHVf1,
VfSNP1,
RviHC
yes
Peach Bacterial spot - fruit Clayton LG1 and LG6 yes Ppe-Xap6 yes
Strawberry Phytophthora cactorum FaRPc2 LG7D yes Pc2-HRM yes
Strawberry Xanthomonas fragariae FaRXf1 LG6D yes Xf1-HRM yes
Sweet cherryPowdery mildew – leaf
and fruit LG5 yes
Pav-G5PM-
SSRyes
Tart cherry Cherry leaf spot LG4 yes SSR-CLS028 yes
Peach Bacterial spot - fruit LG1 yes Ppe-Xap in progress
StrawberryColletotrichum
gloeosporioidesFaRCg1 LG6B yes Cg1-HRM in progress
Strawberry Colletotrichum acutatum FaRCa1 LB6B yes Ca1-HRM in progress
Apple ScabHoneycrisp (+Wildung)
LG1 & HC LG15yes in progress
Apple Scab Vh2, Wh4 and Vh8 yes in progress
Apple Fire blightEnterprise LG7 and LG
13yes in progress
AppleSoft scald/soggy
breakdownHoneycrisp LG2 & LG16 yes in progress
Apple Zonal leaf chlorosis Honeycrisp LG7 yes in progress
Pear Fire blightMoonglow, Roi Charles
de Würtemburg LG2yes in progress
Apple Fire blight Splendour (three loci)in
progress
Rose Black spot Brite Eyes™ (LG5-1)in
progress
Pear Fire blight (Old Home) in progress
Pear Fire blight (Illinois 76) in progress
Peach Fruit brown rot in progress
Peach Bacterial spot – leaf in progress
Peach/CherryArmillaria root rot (plum,
P. maackii) in progress
RoseBlack spot (Lemon Fizz,
High Voltage)in progress
Tart cherryCherry leaf spot (sweet
cherry, North Star)in progress
StrawberryVerticillium (UNH
germplasm)in progress
Strawberry Macrophomina phaseolina
(MI germplasm)in progress
17
Table 2. Maturity date and fruit quality traits for which predictive DNA tests are available or
being developed. Stage of progress towards use of a DNA test is indicated.
Progress towards the use of DNA tests for maturity date and fruit quality traits
Crop Trait Locus/Loci
Discovered
Valuable
Alleles
Identified
DNA Test
Developed
(Test Name)
DNA
Test in
Use
Apple Fruit texture (ethylene) MdACS1 (LG15) yesMd-ACS1-indel,
ACS1SNP1yes
Apple Fruit texture (ethylene) MdACO1 (LG10) yesMd-ACO1-indel,
ACO1SNP1yes
Apple Fruit texture (firmness) MdPG1 (LG10) yesMd-PG1SSR10Kd,
PG1SNP1yes
Apple Fruit texture (firmness) MdExp7 (LG1) yes Md-Exp7-SSR yes
Apple Fruit texture (crispness) Ma (LG16) yesMa-indel,
Ma1SNP1yes
Apple Fruit texture (acidity) Ma (LG16 + LG8) yes Ma × A Acidity yes
Apple Fruit sweetness Md-LG1Fru (LG1) yes Md-LG1Fru-SSR yes
Apple Bitter pit susceptibility Bp1 (LG16) yes BP16-indel yes
Apple Fruit skin blush Rf (LG9) yes Md-Rf-SSR yes
Apple Fruit flesh color MYB110 (LG17) yes Md-S3-indel yes
Peach Fruit skin blush MYB10 (LG3) yes Ppe-Rf-SSR yes
Peach Fruit acidity/flavorD (LG5) and G7Flav
(LG7)yes Ppe-Acid yes
Peach Peach vs. nectarine G (LG5) yes indelG yes
Peach Yellow vs. white flesh Y (LG1) yes CCD4-SSR yes
Peach Fruit texture type F-M and “SMF” (LG4) yes Ppe-Texture yes
Peach Maturity timing G4Mat (LG4) yes G4Mat-SNP yes
Strawberry Fruity aroma FaFAD1 (LG3B) yes qFaFAD1 yes
Strawberry Sherry aroma FaOMT (LG7B) yes FaOMT-SI/NO yes
Sweet Cherry Fruit size & firmness LG2 yes Pav-G2-SSR yes
Sweet Cherry Fruit color type LG3 yes Pav-Rf-SSR yes
Sweet Cherry Fruit maturity time LG4 yes Pav-Fht-SSR yes
Sweet Cherry Fruit cracking LG5 yesPav-G5Crack-
SSRyes
Tart Cherry Fruit flesh color LG3 yes LG3_13.146 yes
Apple Soft scald LG2 yes in progress
Peach Fruit size LG4, LG6 in progress
Strawberry Fruit sweetness (SSC) LG6A in progress
Sweet Cherry Fruit sweetness LG2 in progress
Blackberry Fruit sweetness (SSC) in progress
Peach Postharvest fruit quality in progress
Tart Cherry Fruit firmness in progress
Tart Cherry Fruit freestone in progress
18
Table 3. Productivity traits for which predictive DNA tests are available or being developed.
Stage of progress towards use of a DNA test is indicated.
Progress towards the use of DNA tests for productivity traits
Crop Trait Locus/Loci Discovered
Valuable
Alleles
Identified
DNA Test
Developed
(Test Name)
DNA Test
in Use
Apple Cross-compatibility S locus (LG17) yes S-geno-SNP yes
Strawberry Perpetual flowering FaPFRU (LG4A) yes Bx215 yes
Sweet Cherry Self-fertility S locus (LG6, S4´ allele) yes Pav-S4-indel yes
Sweet Cherry Self-fertilityLG3 (Cristobalina
source)yes EMPaS02b yes
Sweet Cherry Cross-compatibility S locus (LG6) yes Pav-S-common yes
Tart Cherry Self-fertility S locus (LG6) yes (various) yes
Tart Cherry Bloom timing LG4 yes in progress
Peach Bloom timing LG3, LG4 in progress
19
Ob
ject
ive
Sub
-O
bje
ctiv
eYe
ar 3
Acc
om
plis
hm
en
tsTo
Wh
om
Imp
act
1 Inco
rpo
rate
Du
rab
le
Dis
ease
Res
ista
nce
in
Bre
edin
g P
aren
ts
1a.
Dis
ease
resi
stan
ce
alle
le d
isco
very
an
d v
alid
atio
n
Dis
ease
ph
eno
typ
ic d
ata
-co
llect
ed f
or
55
39
ind
ivid
ual
s se
greg
atin
g fo
r d
isea
sere
sist
ance
Cro
pB
reed
ing
Team
s an
d P
ath
olo
gy T
eam
Thes
e p
lan
tm
ater
ials
an
d t
hei
r p
hen
oty
pic
an
d g
eno
typ
ic d
ata
are
resu
ltin
gin
dis
cove
ry
of
loci
ass
oci
ated
wit
h
dis
ease
res
ista
nce
an
d
enab
le d
evel
op
men
t o
f D
NA
tes
ts f
or
bre
edin
g ap
plic
atio
n
Gen
om
e-w
ide
gen
etic
dat
afo
r ap
ple
, sw
eet
cher
ry, p
each
, pea
r, a
nd
ro
se p
op
ula
tio
ns
ph
eno
typ
ed f
or
dis
ease
res
ista
nce
–o
bta
ined
, qu
alit
y-ch
ecke
d,
and
pro
vid
ed f
or
anal
ysis
DN
A-I
nfo
rmed
B
reed
ing
Team
Maj
or-
effe
ctlo
cus
dis
cove
ry:
27
dis
ease
res
ista
nt
maj
or
loci
iden
tifi
ed a
nd
val
idat
ed in
U
.S. b
reed
ing
germ
pla
sm s
ince
pro
ject
beg
an (
Tab
le 1
, pag
e 1
7).
New
ly d
isco
vere
d lo
ci in
Ye
ar 3
incl
ud
e ro
se b
lack
sp
ot
(LG
5-1
), s
wee
t ch
erry
fru
it p
ow
der
y m
ildew
(LG
5),
an
d
zon
al le
af c
hlo
rosi
s d
iso
rder
(fr
om
Ho
ney
cris
p)
linke
d t
o f
ruit
ski
n c
olo
r lo
cus
DN
A t
est
dev
elo
pm
ent:
8 D
NA
tes
ts d
evel
op
ed f
or
resi
stan
ce lo
ci s
ince
pro
ject
beg
an
(Tab
le 1
, pag
e 1
7).
New
DN
A t
ests
dev
elo
ped
in Y
ear
3 in
clu
de
swee
t ch
erry
fru
it
po
wd
ery
mild
ew a
nd
tw
o s
traw
ber
ry d
isea
ses
DN
A-I
nfo
rmed
B
reed
ing
Team
, DN
A
Test
ing
Team
, Cro
p
Bre
edin
g Te
ams
New
str
awb
erry
po
pu
lati
on
sse
greg
atin
g fo
r d
isea
se r
esis
tan
ce c
ho
sen
fo
r lo
cus
dis
cove
ry
–ge
ner
ated
:•
4 p
op
ula
tio
ns
segr
egat
ing
for
resi
stan
ce t
o F
usa
riu
m, M
acro
ph
om
ina,
an
d V
erti
cilli
um
(1 U
C D
avis
, 3 c
om
bin
ing
MI a
nd
OR
par
ents
wit
h a
wild
acc
essi
on
res
ista
nce
so
urc
e)
•1
ped
igre
e-co
nn
ecte
d g
erm
pla
sm s
et (
n=6
2)
segr
egat
ing
for
Ver
tici
lliu
m r
esis
tan
t(N
H)
Stra
wb
erry
Bre
edin
g Te
am a
nd
Pat
ho
logy
Te
am
New
Pru
nu
s ro
ots
tock
ger
mp
lasm
to s
earc
hfo
r A
rmill
aria
res
ista
nce
–o
bta
ined
an
d
ph
eno
typ
ing
init
iate
d (
op
en-p
olli
nat
ed s
eed
fro
m 9
1 a
cces
sio
ns
in U
SDA
-AR
S P
run
us
germ
pla
sm c
olle
ctio
n)
Sto
ne
Fru
it B
reed
ing
Team
an
d P
ath
olo
gy
Team
1b
. Pyr
amid
an
d
com
bin
e d
isea
se
resi
stan
ce
alle
les
Off
spri
ng
crea
ted
fro
m c
ross
es t
o p
yram
id o
r co
mb
ine
dis
ease
res
ista
nce
alle
les
–o
bta
ined
:E.
g., S
traw
ber
ry a
t U
F: 4
00
0 o
ffsp
rin
g ge
ner
ated
to
co
mb
ine
resi
stan
ces
for
anth
racn
ose
an
d P
hyt
op
hth
ora
cro
wn
ro
t, a
nd
an
thra
cno
se w
ith
bac
teri
al a
ngu
lar
leaf
spo
t; a
nd
42
0 o
ffsp
rin
g ge
ner
ated
to
pyr
amid
sca
b r
esis
tan
ces
Cro
p B
reed
ing
Team
sTh
ese
pro
gen
ies
will
p
rovi
de
ind
ivid
ual
s th
at b
reed
ers
can
use
as
par
ents
to
dev
elo
p
cult
ivar
s w
ith
mo
re
du
rab
le d
isea
se
resi
stan
ce d
ue
to t
he
pre
sen
ce o
f re
sist
ance
fr
om
mu
ltip
le lo
ci
Gen
oty
pin
g to
iden
tify
off
spri
ng
wit
h m
ult
iple
res
ista
nce
loci
–in
itia
ted
:•
Stra
wb
erry
res
ista
nce
s to
Co
lleto
tric
hu
m,
Ph
yto
ph
tho
ra,
Xan
tho
mo
nas
an
d b
acte
rial
angu
lar
leaf
sp
ot
•A
pp
le r
esis
tan
ces
to s
cab
an
d b
lue
mo
ld
Cro
p B
reed
ing
Team
s an
d D
NA
-In
form
ed
Bre
edin
g Te
am
Tab
le 1
: Ob
ject
ive
1 –
Del
iver
able
s fo
r Ye
ar 3
20
Tab
le 1
: Ob
ject
ive
1 –
Year
3 C
hal
len
ges
(blu
e)
and
Yea
r 4
Pla
nn
ed D
eliv
erab
les
(pu
rple
)
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
1 Inco
rpo
rate
D
ura
ble
D
ise
ase
R
esi
stan
ce in
B
ree
din
g P
are
nts
1a.
Dis
ease
resi
stan
ce
alle
le d
isco
very
an
d v
alid
atio
n
Dis
ease
ph
eno
typ
ic d
ata
of
pla
nt
mat
eria
ls f
or
20
18
sea
son
–
ob
tain
ed [
pea
r fi
re b
ligh
t, a
pp
le s
cab
, str
awb
erry
ro
ot
and
cr
ow
n r
ots
, Arm
illa
ria
]
Cro
pB
reed
ing
Team
s an
d P
ath
olo
gy T
eam
Thes
e p
lan
tm
ater
ials
an
d t
hei
r p
hen
oty
pic
an
d
gen
oty
pic
dat
a w
ill c
on
tin
ue
tole
ad t
o d
isco
very
of
loci
ass
oci
ated
wit
h d
isea
se r
esis
tan
ce a
nd
en
able
d
evel
op
men
t o
f D
NA
tes
ts f
or
bre
edin
g ap
plic
atio
n
Gen
om
e sc
an d
ata
of
dis
ease
-ph
eno
typ
ed f
amili
es –
ob
tain
ed [
stra
wb
erry
, tar
t ch
erry
, ro
se]
Cro
p B
reed
ing
Team
san
d D
NA
Tes
tin
g Te
am
Pea
rfi
re b
ligh
tge
net
ic m
ap f
rom
th
e fi
re b
ligh
t p
op
ula
tio
ns
for
trai
t lo
cus
dis
cove
ry a
nd
val
idat
ion
–co
nst
ruct
edC
rop
Po
std
ocs
Larg
e-ef
fect
tra
it lo
cus
dis
cove
ryfo
r d
isea
ses
and
so
urc
es
wh
ere
ph
eno
typ
ing
and
gen
oty
pin
g co
mp
lete
d –
dis
cove
red
fo
r 7
dis
ease
s an
d r
esis
tan
ceso
urc
es (
Tab
le 1
, pag
e 1
7)
Cro
pB
reed
ing
Team
s an
d C
rop
Po
std
ocs
DN
A t
ests
–d
evel
op
ed a
nd
dep
loye
d f
or
18
res
ista
nce
loci
(T
able
1, p
age
17
)D
NA
-In
form
edB
reed
ing
Team
Use
of
thes
e D
NA
tes
ts w
ill e
nab
le t
he
pyr
amid
ing
and
co
mb
inin
g o
f re
sist
ance
alle
les
in n
ew e
lite
pla
nt
mat
eria
ls
1b
. Pyr
amid
an
d
com
bin
e d
isea
se
resi
stan
ce a
llele
s
New
off
spri
ng
crea
ted
fro
m c
ross
es t
o p
yram
id a
nd
co
mb
ine
dis
ease
res
ista
nce
alle
les
–o
bta
ined
fo
r ap
ple
, pea
ch, t
art
cher
ry, s
traw
ber
ry
Cro
p B
reed
ing
Team
s an
d C
rop
Po
std
ocs
Thes
e p
roge
nie
sw
ill p
rovi
de
ind
ivid
ual
s th
at b
reed
ers
can
use
as
par
ents
to
dev
elo
p c
ult
ivar
s w
ith
mo
re
du
rab
le d
isea
se r
esis
tan
ce d
ue
to t
he
pre
sen
ce o
f re
sist
ance
fro
m m
ult
iple
loci
Fam
ilies
fo
r p
yram
idin
g/co
mb
inin
g ge
no
typ
ed w
ith
dis
ease
-re
sist
ance
DN
A t
ests
to
ad
van
ce r
esis
tan
t in
div
idu
als
–o
ngo
ing
[var
iou
s cr
op
s an
d d
isea
ses]
Ob
ject
ive
Ch
alle
nge
Pla
nfo
r Ta
cklin
g1 In
corp
ora
te
Du
rab
le
Dis
eas
e
Re
sist
ance
in
Bre
ed
ing
Par
en
ts
Dif
ficu
lty
in m
app
ing
fire
blig
ht
resi
stan
t lo
ci f
rom
‘Sp
len
do
ur’
like
ly d
ue
to e
pis
tati
c ge
ne
acti
on
Use
alt
ern
ativ
e m
app
ing
app
roac
hes
incl
ud
ing
Flex
QTL
Spri
ng
flo
ral f
reez
e d
amag
e lim
ited
ab
ility
to
mak
e cr
oss
es in
pea
ch t
o p
yram
id
dis
ease
res
ista
nce
alle
les
Cro
sses
pla
nn
edfo
r sp
rin
g 2
01
8
Cu
rren
t te
st f
or
‘Mo
on
glo
w’ s
ou
rces
of
fire
blig
ht
resi
stan
cein
pea
r n
ot
pre
dic
tive
in
a la
rger
ger
mp
lasm
co
llect
ion
Map
res
ista
nce
in p
ear
and
iden
tify
pre
dic
tive
mar
kers
21
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
2 Co
mb
ine
D
ise
ase
R
esi
stan
ce a
nd
H
ort
icu
ltu
ral
Qu
alit
y
2a.
Ho
rtic
ult
ura
l q
ual
ity
alle
le
dis
cove
ry a
nd
va
lidat
ion
–R
osM
AP
Bla
ckb
erry
fam
ilies
ph
eno
typ
edfo
r fr
uit
qu
alit
y tr
aits
, in
clu
din
g sw
eetn
ess
and
ind
ivid
ual
su
gars
(O
R: n
=28
8; A
R, n
=28
8)
–co
mp
lete
d
Ber
ryFr
uit
Bre
edin
g Te
amR
osM
AP
will
pro
vid
e a
sho
rtcu
t to
id
enti
fyin
g va
luab
le t
rait
loci
by
leve
ragi
ng
kno
wle
dge
of
com
mo
n a
nce
stra
l ori
gin
ac
ross
rosa
ceo
us
gen
era,
dem
on
stra
ted
her
e b
y sw
eetn
ess
in b
lack
ber
ryC
and
idat
e sw
eetn
ess
gen
es id
enti
fied
usi
ng
Ro
sace
ae s
ynte
ny
–b
lack
ber
ry e
ffec
tive
hap
loty
pe
dis
cove
ry in
pro
gres
sD
NA
Tes
tin
g Te
am
2b
.Ho
rtic
ult
ura
l q
ual
ity
alle
le
dis
cove
ry a
nd
va
lidat
ion
–ad
van
ced
re
sou
rces
Maj
or
loci
fo
r p
each
fru
it q
ual
ity
afte
r st
ora
geb
ein
g so
ugh
t fr
om
A
dva
nce
d P
each
Cro
p R
efer
ence
Set;
gen
oty
pic
dat
a o
bta
ined
w
ith
up
dat
ed 1
6K
pea
ch a
rray
–co
mp
lete
d,
com
pile
d w
ith
p
ost
har
vest
ph
eno
typ
ic d
ata
(~ 1
bill
ion
dat
a p
oin
ts)
DN
A-I
nfo
rmed
Bre
edin
g Te
am
Ro
sace
ae b
reed
ers
will
hav
e n
ew t
rait
loci
to
le
arn
th
e al
lelic
co
mb
inat
ion
s o
f th
eir
par
ents
an
d f
rom
wh
ich
to
req
ues
t n
ew D
NA
te
sts
that
co
uld
rev
eal t
rait
-ass
oci
ated
al
lele
s in
th
eir
seed
ling
fam
ilies
Maj
or
locu
s d
isco
very
for
valu
able
ho
rtic
ult
ura
l tra
its
usi
ng
exis
tin
g d
ata
sets
: 26
DN
A t
ests
fo
r fr
uit
qu
alit
y an
d p
rod
uct
ion
tr
aits
pu
t in
to a
pp
licat
ion
sin
ce s
tart
of
pro
ject
(Ta
ble
s 2
& 3
, p
ages
18
-19
). In
Yea
r 3
th
is in
clu
des
loci
fo
r p
each
fru
it s
ize,
st
raw
ber
ry a
nd
sw
eet
cher
ry s
wee
tnes
s, a
nd
so
ft s
cald
/so
ggy
bre
akd
ow
n a
pp
le d
iso
rder
DN
A-I
nfo
rmed
Bre
edin
g Te
am
Ped
igre
e-B
ased
An
alys
is s
oft
war
e su
pp
ort
–p
rovi
ded
(fo
r u
se
wit
h d
iplo
id c
rop
s)C
rop
Bre
edin
gTe
ams
Larg
e-ef
fect
locu
s d
isco
very
for
tetr
aplo
id c
rop
s w
ith
new
ly
dev
elo
ped
so
ftw
are
–u
tiliz
ed f
or
QTL
dis
cove
ry in
tar
t ch
erry
Cro
p B
reed
ing
Team
s
2c.
Co
mp
ilelo
cus-
spec
ific
DN
A
info
rmat
ion
acr
oss
th
e ge
no
me
Div
ersi
ty-b
ased
hap
lob
lock
dis
cove
ry a
nd
an
alys
is f
or
fru
it q
ual
ity
and
gro
wth
QTL
ho
tsp
ot
aro
un
d M
alo
cus
in a
pp
le –
on
goin
gC
rop
Bre
edin
g, D
NA
-In
form
ed B
reed
ing,
an
d
DN
A T
esti
ng
Team
s
Kn
ow
led
ge o
f al
lelic
var
iati
on
acr
oss
th
e ge
no
me
in d
iscr
ete
blo
cks
will
allo
w t
he
char
acte
riza
tio
n o
f al
lele
s p
rese
nt
in d
iver
se
bre
edin
g ge
rmp
lasm
at
a re
solu
tio
n t
hat
b
reed
ers
can
eas
ily m
anag
e
Ped
igre
e-b
ased
hap
lob
lock
s d
efin
ed f
or
fru
it q
ual
ity
QTL
ho
tsp
ot
on
LG
2 in
sw
eet
cher
ry –
com
ple
ted
2d
. Co
nd
uct
mar
ker-
assi
sted
sel
ecti
on
fo
r co
mb
ined
tr
aits
Mar
ker-
assi
sted
par
ent
and
see
dlin
g se
lect
ion
acc
ord
ing
to
Ro
sBR
EED
’s t
hre
e D
NA
Tes
tin
g P
ort
als’
cro
p g
rou
ps
–co
mp
lete
d,
all 2
0 d
emo
nst
rati
on
bre
edin
g p
rogr
ams
use
d D
NA
info
rmat
ion
fo
r b
reed
ing
dec
isio
ns
Cro
pB
reed
ing
Team
sB
reed
ers
will
ben
efit
fro
m D
NA
info
rmat
ion
fo
r p
aren
t an
d s
eed
ling
sele
ctio
n.
Info
rmat
ion
on
par
ents
will
det
erm
ine
wh
ich
D
NA
tes
ts a
re s
uit
able
fo
r u
se o
n f
amili
es;
info
rmat
ion
on
gre
enh
ou
se-g
row
n f
amili
es
will
iden
tify
op
tim
al s
ets
of
seed
lings
fo
r fi
eld
-pla
nti
ng.
Use
will
en
han
ced
bre
edin
g ef
fici
ency
, acc
ura
cy, c
reat
ivit
y, a
nd
pac
e
Use
an
d e
xper
ien
ces
of
mar
ker-
assi
sted
par
ent
and
see
dlin
g se
lect
ion
–tr
acke
d (
see
rep
ort
pag
es 3
1-3
2)
Ad
min
istr
atio
n,
DN
A-
Info
rmed
Bre
edin
g, a
nd
Ex
ten
sio
n T
eam
s
Tab
le 2
: Ob
ject
ive
2 –
Del
iver
able
s fo
r Ye
ar 3
22
Tab
le 2
co
nt.
: Ob
ject
ive
2 –
Ch
alle
nge
s (b
lue
) an
d Y
ear
4 P
lan
ned
Del
iver
able
s(p
urp
le)
Ob
ject
ive
Ch
alle
nge
Pla
nfo
r Ta
cklin
g2 C
om
bin
e
Dis
eas
e
Re
sist
ance
an
d
Ho
rtic
ult
ura
l Q
ual
ity
Po
lyp
loid
y o
fb
lack
ber
ry g
eno
me
com
plic
ates
gen
oty
pin
g o
f ca
nd
idat
e ge
nes
Inve
stig
ate
use
of
Pac
Bio
for
seq
uen
cin
g ta
rget
cap
ture
lib
rari
es t
o f
acili
tate
h
aplo
typ
e id
enti
fica
tio
n
Larg
est-
effe
ct t
rait
loci
iden
tifi
ed f
or
solu
ble
so
lids
con
ten
t in
str
awb
erry
, bu
t re
sult
s ar
e ex
trem
ely
dep
end
ent
on
en
viro
nm
ent
Inve
stig
ate
GxE
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
2 Co
mb
ine
D
ise
ase
R
esi
stan
ce a
nd
H
ort
icu
ltu
ral
Qu
alit
y
2a.
Ho
rtic
ult
ura
l q
ual
ity
alle
le
dis
cove
ry a
nd
va
lidat
ion
–R
osM
AP
Can
did
ate
loci
fo
r sw
eetn
ess
–te
sted
in b
lack
ber
ry
swee
tnes
sD
NA
Test
ing
Team
, B
erry
Fru
itB
reed
ing
Team
This
cas
e st
ud
y fo
r R
osM
AP
can
did
ate
locu
s ap
pro
ach
w
ill d
eter
min
e h
ow
rea
dily
a le
ss-g
eno
mic
s-re
sou
rced
cr
op
like
bla
ckb
erry
can
be
fast
-tra
cked
to
hav
ing
trai
t-p
red
icti
ve D
NA
tes
ts b
y le
vera
gin
g sh
ared
an
cest
ry
and
res
ou
rces
of
oth
er R
osa
ceae
cro
ps
2b
.Ho
rtic
ult
ura
l q
ual
ity
alle
le
dis
cove
ry a
nd
va
lidat
ion
–ad
van
ced
re
sou
rces
New
QTL
s fo
r p
each
po
sth
arve
st f
ruit
qu
alit
yso
ugh
t fr
om
u
se o
f A
dva
nce
d P
each
Cro
p R
efer
ence
Set
–la
rge-
effe
ct lo
ci
iden
tifi
ed a
nd
alle
les
char
acte
rize
d
DN
A-I
nfo
rmed
B
reed
ing
Team
Ro
sace
ae b
reed
ers
will
hav
e n
ew t
rait
loci
to
lear
n
alle
lic c
om
bin
atio
ns
of
thei
r p
aren
ts a
nd
fro
m w
hic
h
to r
equ
est
new
DN
A t
ests
th
at c
ou
ld r
evea
l tra
it-
asso
ciat
ed a
llele
s in
th
eir
seed
ling
fam
ilies
Val
uab
le lo
cian
d a
llele
s fr
om
Ro
sBR
EED
1 d
ata
sets
–id
enti
fied
usi
ng
Ped
igre
e-B
ased
An
alys
is s
oft
war
e (T
able
s2
&
3 p
ages
18
-19
)
Cro
p P
ost
do
cs a
nd
C
rop
Bre
edin
g Te
ams
Ped
igre
e-B
ased
An
alys
is s
oft
war
ein
stru
ctio
n –
pro
vid
ed
Cro
p P
ost
do
cs a
nd
C
rop
Bre
edin
g Te
ams
2c.
Co
mp
ilelo
cus-
spec
ific
DN
A
info
rmat
ion
Div
ersi
ty b
ased
hap
lob
lock
con
stru
ctio
n a
nd
ch
arac
teri
zati
on
in
ap
ple
–in
pro
gres
sD
NA
-In
form
ed
Bre
edin
g an
d D
NA
Te
stin
gTe
ams
Kn
ow
led
ge o
f al
lelic
var
iati
on
acr
oss
cro
p g
eno
mes
in
dis
cret
eb
lock
s w
ill a
llow
th
e ch
arac
teri
zati
on
of
alle
les
pre
sen
t in
div
erse
bre
edin
g ge
rmp
lasm
at
a re
solu
tio
n t
hat
bre
eder
s ca
n e
asily
man
age
Fun
ctio
nal
uti
lity
add
ed t
o a
pp
le h
aplo
blo
cks
–in
pro
gres
s
Ped
igre
e-b
ased
hap
lob
lock
con
stru
ctio
n a
nd
uti
lity
anal
yses
fo
r LG
4 Q
TL h
ots
po
t in
ch
erry
an
d p
each
–in
pro
gres
sC
rop
Po
std
ocs
an
d
Cro
p B
reed
ing
Team
s
2d
. Co
nd
uct
mar
ker-
assi
sted
sel
ecti
on
fo
r co
mb
ined
tr
aits
Mar
ker-
assi
sted
par
ent
sele
ctio
n a
nd
mar
ker-
assi
sted
se
edlin
g se
lect
ion
gen
oty
pin
g p
rovi
ded
fo
r ap
ple
, pea
ch,
cher
ry, a
nd
str
awb
erry
bre
edin
g p
rogr
ams
–co
nd
uct
ed
Cro
pB
reed
ing
Team
sB
reed
ers
will
ben
efit
fro
m D
NA
info
rmat
ion
fo
r p
aren
t an
d s
eed
ling
sele
ctio
n. I
nfo
rmat
ion
on
par
ents
will
d
eter
min
e w
hic
h D
NA
tes
ts a
re s
uit
able
fo
r u
se o
n
fam
ilies
; in
form
atio
n o
n g
reen
ho
use
-gro
wn
fam
ilies
w
ill id
enti
fy o
pti
mal
set
s o
f se
edlin
gs f
or
fiel
d-
pla
nti
ng.
Exp
erie
nce
s w
ill u
nd
erlie
new
su
cces
s st
ori
es
of
enh
ance
d b
reed
ing
effi
cien
cy,
accu
racy
, cre
ativ
ity,
an
d p
ace
to s
har
e w
idel
y to
th
e b
reed
ing,
ind
ust
ry
stak
eho
lder
, an
d a
llied
sci
enti
st c
om
mu
nit
ies
Mar
ker-
assi
sted
par
ent
sele
ctio
n g
eno
typ
ing
pro
vid
ed f
or
rose
, bla
ckb
erry
, an
d p
ear
–co
nd
uct
ed
Use
an
d e
xper
ien
ces
of
mar
ker-
assi
sted
par
ent
sele
ctio
n a
nd
m
arke
r-as
sist
ed s
eed
ling
sele
ctio
n –
trac
ked
Ad
min
istr
atio
n,
DN
A-
Info
rmed
Bre
edin
g,
and
Ext
ensi
on
Tea
ms
23
Tab
le 3
: Ob
ject
ive
3 -
Del
iver
able
s fo
r Ye
ar 3
(gr
een
) an
d C
hal
len
ges
(blu
e)
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
3 Ad
van
ce
Sele
ctio
ns
wit
h I
mp
rove
d
Co
nfi
de
nce
3a.
Ad
d g
enet
ic
bac
kgro
un
d e
ffec
ts
Ap
ple
: P
red
icti
on
mo
del
fo
r ge
no
me-
wid
e se
lect
ion
tes
ted
on
fiv
e R
B2
ap
ple
fam
ilies
fo
r fr
uit
tex
ture
co
mp
on
ents
–co
mp
lete
d;
5 r
elat
ed a
pp
le p
op
ula
tio
ns
ph
eno
typ
ed t
o v
alid
ate
pre
dic
tio
ns
Ap
ple
bre
eder
s an
d
Stat
isti
cal G
enet
ics
Team
Off
spri
ng
will
be
sele
cted
an
d a
dva
nce
d w
ith
im
pro
ved
co
nfi
den
ce b
ased
on
kn
ow
led
ge o
f si
gnif
ican
t an
d n
on
-sig
nif
ican
t lo
ci
infl
uen
cin
g tr
ait
vari
atio
n
Ad
op
tio
n o
f ge
no
me-
wid
e p
red
icti
on
s fo
r p
aren
t se
lect
ion
in s
traw
ber
ry h
as r
esu
lted
in
red
uct
ion
of
bre
edin
g cy
cle
fro
m t
hre
e ye
ars
to t
wo
yea
rs
Pea
ch: P
red
icti
on
mo
del
fo
r ge
no
me
-wid
ese
lect
ion
–p
hen
oty
pic
an
d g
eno
typ
ic d
ata
sets
tra
nsf
erre
dto
Sta
tist
ical
Gen
etic
s Te
am,
anal
yses
un
der
way
Pea
chb
reed
ers
and
St
atis
tica
l Gen
etic
s Te
am
Stra
wb
erry
: Gen
om
e-w
ide
sele
ctio
n s
trat
egy
for
par
ent
sele
ctio
n
for
five
tra
its
–va
lidat
ed a
cro
ss 4
bre
edin
g cy
cles
an
d a
pp
lied
in U
Fl
ori
da
pro
gram
in 2
cyc
les
Stra
wb
erry
: Wit
hin
-fam
ily s
eed
ling
gen
om
e-w
ide
sele
ctio
n
exp
erim
ent
–d
esig
ned
, d
ata
colle
ctio
n in
pro
gres
s
Stra
wb
erry
bre
eder
san
d
Stat
isti
cal G
enet
ics
Team
3b
.Ad
d n
on
-gen
etic
ef
fect
sSw
eet
cher
ry G
xExM
mo
del
for
swee
t ch
erry
on
ch
erry
mat
uri
ty
dat
e–
com
ple
ted
, te
sted
; A
nal
ysis
on
fru
it s
ize
–in
itia
ted
Ap
ple
,p
each
, sw
eet
cher
ry, a
nd
str
awb
erry
b
reed
ers
and
Sta
tist
ical
G
enet
ics
Team
Off
spri
ng
will
be
sele
cted
an
d a
dva
nce
d w
ith
im
pro
ved
co
nfi
den
ce b
ased
on
kn
ow
led
ge o
f in
flu
ence
of
no
n-g
enet
ic f
acto
rs c
om
par
ed
to g
enet
ic f
acto
rs, i
ncl
ud
ing
effe
cts
of
clim
ates
/lo
cati
on
s an
d m
anag
emen
t p
ract
ices
Esti
mat
ion
of
no
n-g
enet
ic e
ffec
ts f
or
fru
it s
wee
tnes
sfr
om
pea
ch –
init
iate
d
Esti
mat
ion
of
no
n-g
enet
ic e
ffec
ts f
or
fru
it s
wee
tnes
s an
d a
cid
ity
fro
m a
pp
le –
init
iate
d
Co
llati
on
of
mu
lti-
envi
ron
me
nt
per
form
ance
an
d S
NP
dat
a se
tsfo
r p
each
an
d a
pp
le –
in p
rogr
ess
Ob
ject
ive
Ch
alle
nge
Pla
nfo
r Ta
cklin
g3 A
dva
nce
Se
lect
ion
s w
ith
Im
pro
ved
C
on
fid
en
ce
Co
st o
fh
igh
-den
sity
gen
oty
pin
g is
to
o h
igh
fo
r se
edlin
g ge
no
mic
sel
ecti
on
ap
plic
atio
ns
Met
ho
ds
for
red
uci
ng/
imp
uti
ng
SNP
s ar
e b
ein
g ex
plo
red
, w
ith
pre
limin
ary
dat
a in
dic
atin
g 1
50
0 S
NP
s m
igh
t b
e su
ffic
ien
t
Nee
dto
co
mb
ine
SNP
dat
a fr
om
th
ree
arra
ys (
8K
, 20
K, a
nd
48
0K
)U
se a
su
bse
t o
fse
qu
ence
d in
div
idu
als
to e
stab
lish
a f
ou
nd
atio
nal
dat
abas
e en
ablin
g p
ipel
ine
to c
om
bin
e d
ata
sets
24
Tab
le 3
co
nt.
: Ob
ject
ive
3 –
Year
4 P
lan
ned
Del
iver
able
s
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
3 Ad
van
ce
Sele
ctio
ns
wit
h I
mp
rove
d
Co
nfi
de
nce
3a.
Ad
d g
enet
ic b
ackg
rou
nd
eff
ects
A
pp
le:
Thre
ege
no
me-
wid
e se
lect
ion
m
od
els
(sta
nd
ard
mo
del
, mo
del
fit
tin
g h
eter
ozy
gou
s SN
P e
ffec
ts, m
od
el w
ith
la
rge-
effe
ct Q
TLs
as f
ixed
eff
ects
) –
dev
elo
ped
an
d c
om
par
ed u
sin
g fi
ve
fam
ilies
Po
me
Fru
it B
reed
ing
Team
an
d
Stat
isti
cal G
enet
ics
Team
Off
spri
ng
will
be
sele
cted
an
d a
dva
nce
d w
ith
im
pro
ved
co
nfi
den
ce b
ased
on
kn
ow
led
ge o
f si
gnif
ican
t an
d n
on
-sig
nif
ican
t lo
ci in
flu
enci
ng
trai
t va
riat
ion
Pea
ch: P
red
icti
on
mo
del
s –
test
ed o
n
trai
nin
g p
op
ula
tio
n;
sele
ctio
n
po
pu
lati
on
s –
gen
oty
ped
an
d
ph
eno
typ
ed
Sto
ne
Fru
it B
reed
ing
Team
an
d
Stat
isti
cal G
enet
ics
Team
Stra
wb
erry
:Wit
hin
-fam
ily s
eed
ling
gen
om
e w
ide
sele
ctio
n m
eth
od
s u
sin
g lo
w-d
ensi
ty g
eno
typ
ing
to r
edu
ce c
ost
–
eval
uat
ed
Stra
wb
erry
Bre
edin
g Te
am a
nd
St
atis
tica
l Gen
etic
s Te
am
3b
. Ad
d n
on
-gen
etic
eff
ects
GxE
xMp
erfo
rman
ce p
red
icti
on
s –
com
ple
ted
fo
r sw
eetn
ess
and
acid
ity
in a
pp
le, s
wee
tnes
s in
pea
ch, a
nd
fru
it
size
in s
wee
t ch
erry
Stat
isti
calG
enet
ics
Team
an
d
inte
rnat
ion
ally
co
llab
ora
tin
g p
artn
ers
Off
spri
ng
will
be
sele
cted
an
d a
dva
nce
d w
ith
im
pro
ved
co
nfi
den
ce b
ased
on
kn
ow
led
ge o
f in
flu
ence
of
no
n-g
enet
ic f
acto
rs c
om
par
ed t
o
gen
etic
fac
tors
, in
clu
din
g ef
fect
s o
f cl
imat
es/l
oca
les
and
man
agem
ent
pra
ctic
es
3c.
Ad
van
ce s
up
erio
r se
lect
ion
sG
eno
typ
e ad
van
ced
sel
ecti
on
sto
p
red
ict
per
form
ance
–in
itia
ted
DN
A T
esti
ng,
Sta
tist
ical
Gen
etic
s,an
d
Cro
p B
reed
ing
Team
sSe
lect
ion
s w
ill b
e ad
van
ced
to
war
d
com
mer
cial
rel
ease
or
dis
card
ed w
ith
im
pro
ved
co
nfi
den
ce b
ased
on
kn
ow
led
ge o
f si
gnif
ican
t an
d n
on
-sig
nif
ican
t lo
ci a
s w
ell a
s n
on
-gen
etic
fac
tors
infl
uen
cin
g tr
ait
vari
atio
n
25
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
4 Incr
eas
e
Ro
uti
ne
Use
of
DN
A
Info
rmat
ion
4a.
DN
A t
est
and
fi
nge
rpri
nti
ng
set
dev
elo
pm
ent
and
ge
rmp
lasm
sc
reen
ing
serv
ices
DN
A t
ests
fo
r n
ewtr
ait
loci
of
dis
ease
res
ista
nce
s an
d f
ruit
qu
alit
y co
mp
on
ents
–d
evel
op
ed,
adap
ted
, co
nve
rted
, ref
ined
, o
r co
nfi
rmed
(cu
rren
tly
19
+ te
sts
are
bei
ng
use
d b
y ro
sace
ou
s cr
op
b
reed
ers)
–fo
r ex
amp
le,
2 n
ew t
ests
fo
r p
each
blu
sh a
nd
sw
eet
cher
ry f
ruit
po
wd
ery
mild
ew r
esis
tan
ce w
ere
dev
elo
ped
in
Yea
r 3
(T
able
s 1
, 2 &
3 p
ages
17
-19
)
Cro
pB
reed
ing
Team
s an
d
com
mer
cial
ser
vice
p
rovi
der
s o
f D
NA
-bas
ed
dia
gno
stic
s
Dem
on
stra
tio
n b
reed
ers
hav
e ac
cess
to
D
NA
-bas
ed d
iagn
ost
ics
serv
ices
an
d s
pec
ific
to
ols
; les
son
s le
arn
ed f
or
com
mer
cial
p
rovi
der
s
DN
A t
ests
fo
r m
ult
iple
lo
ciu
sin
g a
KA
SPm
ini-
arra
y –
in
dev
elo
pm
ent
in p
each
, tes
ts f
or
2 a
pp
le t
rait
loci
co
nve
rted
to
K
ASP
fo
r se
edlin
g se
lect
ion
Sto
ne
Fru
it B
reed
ing
Team
, DN
ATe
stin
g Te
am
Gen
om
e-w
ide
dia
gno
stic
too
l fo
r ch
erry
–u
pd
ated
an
d
com
mer
cial
ized
wit
h a
dd
itio
n o
f +9
00
0 m
ore
SN
Ps
add
ed t
o 6
K
Illu
min
a® I
nfi
niu
m a
rray
Ch
erry
bre
eder
s
DN
A-b
ased
dia
gno
stic
ser
vice
sfo
r O
bj.
1 a
nd
2 –
pro
vid
ed t
o
bre
eder
s. T
hre
e D
NA
Tes
tin
g P
ort
als
of
Ber
ry &
Ro
se, A
pp
le &
C
her
ry, a
nd
Pea
ch c
olle
ctiv
ely
gen
oty
ped
~2
5,0
00
ind
ivid
ual
s w
ith
an
oth
er ~
30
,00
0 in
div
idu
als
gen
oty
ped
in U
Flo
rid
a st
raw
ber
ry
bre
edin
g p
rogr
am
Cro
p B
reed
ing
Team
s
An
nu
al I
nte
rnat
ion
al P
artn
er M
eeti
ng
–h
eld
14
Jan
20
17
. In
clu
ded
1
2 in
tern
atio
nal
co
llab
ora
tin
g p
artn
ers
fro
m 7
inst
itu
tio
ns
in 6
co
un
trie
s –
gen
om
e sc
an a
nd
DN
A t
est
nee
ds
coo
rdin
ated
DN
A T
esti
ng
Team
, alli
ed
scie
nti
sts,
Ro
sace
ae
bre
eder
s
Too
ls f
or
up
stre
am g
enet
ic r
esea
rch
an
d
pra
ctic
al b
reed
ing
dev
elo
ped
/ad
van
ced
effi
cien
tly
4b
. So
ftw
are
sup
po
rtC
ross
Ass
ist
and
See
dlin
gSe
lect
soft
war
e: O
bje
ctiv
e re
mo
ved
in
Year
3 a
s co
nse
qu
ence
of
sust
ain
ed U
SDA
man
dat
ed 7
% b
ud
get
cuts
na
DN
A T
est
Effe
cts
soft
war
e: M
ixed
-mo
del
met
ho
d in
ASR
eml-
R t
o
calc
ula
te e
ffec
ts o
f D
NA
tes
ts, g
enet
ic b
ackg
rou
nd
, an
d
envi
ron
men
tal
mai
n e
ffec
ts (
year
, lo
cati
on
) –
com
ple
ted
DN
A-I
nfo
rmed
Bre
edin
g Te
amD
NA
tes
ts u
sed
wit
h g
reat
er c
on
fid
ence
b
ecau
se o
f im
pro
ved
acc
ura
cy o
f p
red
icti
on
s
4c.
Eco
no
mic
s o
f D
NA
in
form
atio
n u
seTe
mp
late
s to
cal
cula
te b
reed
ing
cost
: ben
efit
for
wid
e ra
nge
of
DN
A-i
nfo
rmed
bre
edin
g ap
plic
atio
ns,
via
cas
e st
ud
ies
on
app
le (
U
Min
n)
–co
mp
lete
d,
pro
vid
ed t
o b
reed
ers
U.S
. Ro
sace
aeb
reed
ers
Kn
ow
led
geo
f re
lati
ve c
ost
s an
d b
enef
its
of
vari
ou
s u
ses
of
DN
A in
form
atio
n in
bre
edin
g an
d e
xper
ien
ces
of
new
ad
op
ters
will
in
crea
se im
pac
t o
f D
NA
info
rmat
ion
use
in
bre
edin
g
Cal
cula
tio
ns
of
eco
no
mic
s o
f D
NA
use
wh
ere
ben
efit
mo
del
ed is
d
ecre
ase
in s
eed
ling
nu
mb
er in
fie
ld p
er c
ult
ivar
rel
ease
–co
mp
lete
d o
n a
pp
le (
U M
inn
)
Cas
e st
ud
ies
of
new
ad
op
tio
n o
f D
NA
info
rmat
ion
use
–co
mp
lete
d
(MSU
pea
ch, W
SU s
traw
ber
ry),
man
usc
rip
t in
pro
gres
s
Tab
le 4
: Ob
ject
ive
4 D
eliv
erab
les
for
Year
3
26
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
4 Incr
eas
e
Ro
uti
ne
Use
of
DN
A
Info
rmat
ion
4d
. Tec
hn
ical
trai
nin
g in
ro
uti
ne
use
of
DN
A in
form
atio
n in
b
reed
ing
On
line
trai
nin
g re
sou
rces
via
th
ree
new
Co
mm
un
ity
Bre
eder
A
rtic
les
incl
ud
ing
intr
od
uct
ion
of
“Hap
loty
pe
mo
saic
s” –
pro
vid
ed;
“Fo
r B
reed
ers”
web
pag
e –
up
dat
ed (
ww
w.r
osb
reed
.org
/bre
edin
g)
U.S
. Ro
sace
aeb
reed
ers
and
alli
ed s
cien
tist
s
Ro
sace
aecr
op
bre
eder
s b
enef
it f
rom
use
of
DN
A in
form
atio
n t
o a
chie
ve g
reat
er
effi
cien
cy, a
ccu
racy
, an
d s
up
erio
r cu
ltiv
ar
rele
ases
; kn
ow
led
ge o
f su
cces
ses
and
lim
itat
ion
s in
DN
A-i
nfo
rmed
bre
edin
g ad
op
tio
n id
enti
fies
str
ateg
ies
and
w
eakn
esse
s to
fo
cus
futu
re e
ffo
rts
Co
mp
iled
info
rmat
ion
on
ava
ilab
le D
NA
tes
ts a
nd
info
rmat
ion
re
veal
ed –
4 n
ew D
NA
tes
t ca
rds
[2 s
wee
t ch
erry
, 1 a
pp
le, 1
st
raw
ber
ry]
-> t
ota
l 13
Ass
essm
ent
inst
rum
ent
toth
oro
ugh
ly a
sses
s b
reed
ing
pro
gram
o
pp
ort
un
itie
s, a
ttit
ud
es, s
tatu
s, c
hal
len
ges,
an
d n
ext
step
s in
usi
ng
DN
A in
form
atio
n –
des
crib
ed (
CB
Pag
e ar
ticl
e D
ec 2
01
6),
ref
ined
, u
sed
to
fac
ilita
te t
rain
ing
com
mu
nic
atio
ns
wit
h U
.S R
osa
ceae
b
reed
ers
An
nu
alu
pd
ate
by
Exte
rnal
Eva
luat
or
on
ad
op
tio
n o
f D
NA
-in
form
ed b
reed
ing
by
U.S
. ro
sace
ou
s cr
op
bre
eder
s in
clu
din
g p
itfa
lls a
nd
lim
itat
ion
s –
pro
vid
ed (
see
rep
ort
pag
es 3
1-3
2)
Ad
min
istr
atio
n,
DN
A-
Info
rmed
Bre
edin
g, a
nd
Ex
ten
sio
n T
eam
s
Tab
le 4
: O
bje
ctiv
e 4
Del
iver
able
s fo
r Ye
ar 3
co
nt.
(gr
een
) an
d C
hal
len
ges
(blu
e)
Ob
ject
ive
Ch
alle
nge
Pla
nfo
r Ta
cklin
g4 In
cre
ase
R
ou
tin
e U
se o
f D
NA
In
form
atio
n
Pru
nu
sC
rop
Po
std
oc
at
Cle
mso
n U
left
un
exp
ecte
dly
N
ew P
ost
do
ch
ired
; M
SU p
ost
do
c as
sist
s w
ith
tas
ks a
nd
tra
inin
g o
f th
e n
ew P
ost
do
c
Tim
e n
eed
ed f
or
“up
stre
am r
esea
rch
” to
ols
an
d in
form
atio
n (
gen
om
esc
an
dev
elo
pm
ent,
QTL
dis
cove
ry, D
NA
tes
t d
evel
op
men
t, e
tc.)
gre
atly
lim
its
tim
e av
aila
ble
fo
r C
rop
Po
std
ocs
to
co
nd
uct
th
eir
role
of
liais
ing
wit
h U
.S. R
osa
ceae
b
reed
ers
Gen
om
esc
an w
ork
sh
ou
ld b
e m
uch
less
in Y
ear
4; o
ther
pro
ject
sci
enti
sts
hel
p w
ith
co
mm
un
icat
ion
s w
ith
co
mm
un
ity
bre
eder
s; C
rop
Po
std
ocs
fo
cus
on
th
eir
iden
tifi
ed
rese
arch
str
engt
hs
27
Tab
le 4
co
nt.
: Ob
ject
ive
4 Y
ear
4 P
lan
ned
Del
iver
able
s
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
4 Incr
eas
e
Ro
uti
ne
Use
of
DN
A
Info
rmat
ion
4a.
DN
A t
est
and
fi
nge
rpri
nti
ng
set
dev
elo
pm
ent
and
ge
rmp
lasm
scr
een
ing
serv
ices
New
DN
A t
ests
fro
m d
isco
veri
es in
Ob
j. 1
an
d 2
–d
evel
op
ed (
see
tar
gets
in T
able
s 1
, 2 a
nd
3,
pag
es 1
7-1
9)
DN
A T
esti
ng
Team
Dem
on
stra
tio
n b
reed
ers
hav
e su
stai
ned
acc
ess
to D
NA
-b
ased
dia
gno
stic
s se
rvic
es, s
pec
ific
to
ols
,an
d
info
rmat
ion
on
th
eir
germ
pla
sm
Use
of
new
hap
lob
lock
fra
mew
ork
to
ref
ine
DN
A
test
s an
d c
on
vert
SN
P a
rray
info
rmat
ion
fo
r p
aren
ts/e
lites
in
to p
erfo
rman
ce-r
elev
ant
info
rmat
ion
–in
itia
ted
Cro
p B
reed
ing
Team
s
DN
A t
esti
ng
serv
ices
pro
vid
edan
d t
ran
siti
on
ing
to f
ee-b
ased
–al
mo
stco
mp
lete
Cro
p B
reed
ing
and
DN
A
Test
ing
Team
s
4b
. So
ftw
are
sup
po
rtO
bje
ctiv
e re
mo
ved
na
na
4c.
Eco
no
mic
s o
f D
NA
in
form
atio
n u
seC
ost
: ben
efit
cas
e st
ud
ies
(U M
inn
ap
ple
) –
anal
yses
co
mp
lete
d a
nd
co
mm
un
icat
edU
.S. R
osa
ceae
bre
eder
sK
no
wle
dge
of
rela
tive
co
sts
and
ben
efit
s o
f va
rio
us
use
s o
f D
NA
info
rmat
ion
in b
reed
ing
and
exp
erie
nce
s o
f n
ew
ado
pte
rs w
ill in
crea
se im
pac
t o
f D
NA
info
rmat
ion
use
in
bre
edin
g
New
ad
op
tio
n c
ase
stu
die
s (M
SU p
each
, WSU
st
raw
ber
ry)
–an
alys
es c
om
ple
ted
an
d
com
mu
nic
ated
4d
. Tec
hn
ical
trai
nin
g in
ro
uti
ne
use
of
DN
A
info
rmat
ion
in b
reed
ing
On
line
reso
urc
es: t
rain
ing
mo
du
les
in s
pec
ific
to
pic
s –
dev
elo
ped
an
d d
eliv
ered
via
web
site
of
“Fo
r B
reed
ers”
(w
ww
.ro
sbre
ed.o
rg/b
reed
ing)
U.S
. Ro
sace
aeb
reed
ers
Ro
sace
aecr
op
bre
eder
s b
enef
it f
rom
use
of
DN
A
info
rmat
ion
to
ach
ieve
gre
ater
eff
icie
ncy
, acc
ura
cy, a
nd
cr
eati
vity
cu
lmin
atin
g in
su
per
ior
cult
ivar
rel
ease
;
kno
wle
dge
of
succ
esse
s an
d li
mit
atio
ns
in D
NA
-in
form
ed
bre
edin
g ad
op
tio
n id
enti
fies
str
ateg
ies
and
wea
knes
ses
to f
ocu
s fu
ture
eff
ort
s
On
e-o
n-o
ne
com
mu
nic
atio
n c
on
tin
ued
, al
l U.S
. b
reed
ers
asse
ssed
fo
r ch
alle
nge
s an
d
op
po
rtu
nit
ies
to t
hei
r D
NA
-in
form
ed b
reed
ing
ado
pti
on
; co
mm
on
ch
alle
nge
s an
d o
pp
ort
un
itie
s ad
dre
ssed
in o
nlin
e co
nte
nt,
idio
syn
crat
ic o
nes
ad
dre
ssed
acc
ord
ing
to c
ost
:ben
efit
an
d a
s re
sou
rces
allo
w
[Ari
sin
gfr
om
on
e-o
n-o
ne
com
mu
nic
atio
n a
bo
ve]
Succ
essf
ul a
do
pti
on
of
DN
A-i
nfo
rmed
bre
edin
g b
y U
.S. r
osa
ceo
us
cro
p b
reed
ers
–q
uan
tifi
ed;
Pit
falls
an
d li
mit
atio
ns
–id
enti
fied
Ad
min
istr
atio
n,
DN
A-
Info
rmed
Bre
edin
g, a
nd
Ex
ten
sio
n T
eam
s
28
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
5 Uti
lize
St
ake
ho
lde
r In
pu
t
5a.
Cu
ltiv
arad
op
tio
n
case
stu
die
sP
rod
uce
r su
rvey
s fo
r ca
se s
tud
ies
of
cult
ivar
rel
ease
–co
nd
uct
ed
for
pea
ch (
33
res
po
nd
ents
); in
pro
gres
s fo
r st
raw
ber
ry, d
ata
anal
ysis
on
goin
g
U.S
. pea
ch a
nd
str
awb
erry
bre
eder
sIn
sigh
t in
to d
ecis
ion
-mak
ing
rece
ived
fro
m
pea
ch a
nd
str
awb
erry
ind
ust
ry m
emb
ers
abo
ut
new
elit
e se
lect
ion
s w
ill in
form
cu
ltiv
ar d
evel
op
men
t an
d r
elea
se s
trat
egie
s
5b
. Sta
keh
old
eren
gage
men
tYe
ar 2
Ad
viso
ry P
anel
mee
tin
g (J
an 2
01
7):
co
mm
un
icat
ion
of
pro
ject
act
ivit
ies,
ou
tco
mes
, im
pac
ts, c
hal
len
ges,
rec
eip
t, a
nd
ad
dre
ssin
g o
f fe
edb
ack
–co
nd
uct
ed
Ad
viso
ry P
anel
mem
ber
s,
Pro
ject
par
tici
pan
ts, R
B
Exec
Co
mm
itte
e
Ro
sBR
EED
pro
ject
incr
ease
s ef
fect
iven
ess;
ex
tern
al a
nd
inte
rnal
sta
keh
old
ers
valu
e p
roje
ct o
utc
om
es
Up
dat
e w
ebsi
te a
nd
dis
trib
ute
New
slet
ter
–ac
com
plis
hed
All
stak
eho
lder
sA
war
enes
s o
fan
d s
up
po
rt f
or
Ro
sBR
EED
en
han
ced
; D
NA
-in
form
ed b
reed
ing
wid
ely
acce
pte
d b
y in
du
stry
sta
keh
old
ers;
Ex
ten
sio
n A
P m
emb
ers
Dav
e Ed
dy
and
Dav
id
Kar
p c
on
tin
ue
regu
lar
con
trib
uti
on
s to
N
ewsl
ette
rs a
nd
th
eir
wid
er c
ircl
es o
f in
flu
ence
; ro
bu
st d
ata
sets
of
stak
eho
lder
an
d b
reed
er a
ttit
ud
es a
bo
ut
DN
A
info
rmat
ion
use
d t
o a
dju
st p
roje
ct a
ctiv
itie
s
Pro
ject
ou
tco
mes
an
d im
pac
ts c
om
mu
nic
ated
thro
ugh
elec
tro
nic
m
edia
an
d p
rese
nta
tio
ns
at in
du
stry
mee
tin
gs –
con
du
cted
(n
um
ero
us
chan
nel
s &
ven
ues
)
Ind
ust
ryst
akeh
old
ers
Bre
eder
en
gage
men
t in
Yea
r 2
wit
h s
take
ho
lder
sab
ou
t D
NA
-in
form
ed b
reed
ing
and
sta
keh
old
erin
pu
t –
ob
tain
ed a
nd
su
mm
ariz
ed (
see
rep
ort
on
pag
es 3
1-3
2)
RB
Exe
cuti
veC
om
mit
tee,
Ex
tern
al E
valu
ato
r, T
eam
Le
ader
s
Pro
po
sal f
or
maj
or
thre
e-se
ssio
n s
ymp
osi
um
on
SC
RI (
and
h
igh
ligh
tin
g R
osB
REE
D) a
t A
mer
Soc
Ho
rtic
Scia
nn
mtg
, W
ash
ingt
on
DC
, Ju
ly 2
01
8 –
dev
elo
ped
, ac
cep
ted
Tab
le 5
: Ob
ject
ive
5 D
eliv
erab
les
for
Year
3 (
gree
n)
and
Ch
alle
nge
s (b
lue
)
Ob
ject
ive
Ch
alle
nge
Pla
nfo
r Ta
cklin
g5 U
tiliz
e
Stak
eh
old
er
Inp
ut
5a.
Lo
w s
urv
ey r
esp
on
se r
ate.
Rep
on
ses
wer
e m
ost
ly f
rom
op
erat
ion
s <5
0
acre
sP
each
: co
mp
lem
ent
mai
l su
rvey
res
po
nse
sw
ith
au
die
nce
su
rvey
at
SE p
each
gro
wer
s m
eeti
ng
Stra
wb
erry
: On
line
stra
wb
erry
su
rvey
tar
geti
ng
FL p
rod
uce
rs g
arn
ered
mo
re r
esp
on
ses,
su
rvey
s p
lan
ned
fo
r 5
gro
wer
mee
tin
g in
PN
W
5b
. Nee
d a
dd
itio
nal
per
son
nel
to
cap
ture
succ
ess
sto
ries
an
d p
ut
them
in
form
at f
or
lay
aud
ien
ces
New
Ph
D s
tud
ent
wit
h jo
urn
alis
m/p
lan
t b
reed
ing
and
gen
etic
s b
ackg
rou
nd
an
d a
du
al
futu
re c
aree
r in
tere
st r
ecru
ited
to b
egin
at M
SU o
n M
arch
1, 2
01
8 a
nd
join
Ext
ensi
on
Tea
m
29
Tab
le 5
co
nt.
: Ob
ject
ive
5 Y
ear
4 P
lan
ned
Del
iver
able
s
Ob
ject
ive
Sub
-Ob
ject
ive
Wh
atTo
Wh
om
Imp
act
5 Uti
lize
St
ake
ho
lde
r In
pu
t
5a.
Cu
ltiv
arad
op
tio
n
case
stu
die
sC
ase
stu
die
s o
f p
each
an
d s
traw
ber
ry c
ult
ivar
rel
ease
–P
each
: An
alys
is o
f d
ata
colle
cted
via
20
16
mai
l su
rvey
w
ill b
e co
mp
lem
ente
d w
ith
dat
a co
llect
ed a
t th
e SE
p
each
gro
wer
s m
eeti
ng
in S
avan
nah
, GA
12
Jan
20
18
.-
Stra
wb
erry
: An
alys
is o
f d
ata
colle
cted
via
mai
l an
d
on
line
surv
eys
in p
rogr
ess.
Als
o c
olle
ctin
g re
leva
nt
info
rmat
ion
on
res
earc
h p
rio
riti
es a
t 5
reg
ion
al
stra
wb
erry
gro
wer
mee
tin
gs in
WA
an
d O
R
-D
ata
anal
ysis
init
iate
d
U.S
. pea
ch a
nd
st
raw
ber
ryb
reed
ers
Insi
ght
into
dec
isio
n-m
akin
g re
ceiv
edfr
om
pea
ch a
nd
st
raw
ber
ry in
du
stry
mem
ber
s ab
ou
t n
ew e
lite
sele
ctio
ns
will
info
rm c
ult
ivar
dev
elo
pm
ent
and
rel
ease
str
ateg
ies;
m
eth
od
olo
gica
l ap
pro
ach
an
d r
esu
lts
pro
vid
e in
sigh
ts f
or
oth
er b
reed
ing
pro
gram
s an
d c
rop
s
5b
. Sta
keh
old
eren
gage
men
tYe
ar 4
Ad
viso
ry P
anel
mee
tin
g (J
an 2
01
8):
co
mm
un
icat
ion
of
pro
ject
act
ivit
ies,
ou
tco
mes
, im
pac
ts, c
hal
len
ges,
rec
eip
t an
d a
dd
ress
ing
of
feed
bac
k –
con
du
cted
Ad
viso
ry P
anel
m
emb
ers,
Pro
ject
p
arti
cip
ants
, RB
Exe
c C
om
mit
tee
Ro
sBR
EED
pro
ject
incr
ease
s ef
fect
iven
ess;
ext
ern
al a
nd
in
tern
al s
take
ho
lder
s va
lue
pro
ject
ou
tco
mes
; aw
aren
ess
of
and
su
pp
ort
fo
r R
osB
REE
D e
nh
ance
d;
DN
A-i
nfo
rmed
b
reed
ing
wid
ely
acce
pte
d b
y in
du
stry
sta
keh
old
ers;
ro
bu
st
dat
a se
ts o
f st
akeh
old
er a
nd
bre
eder
att
itu
des
ab
ou
t D
NA
in
form
atio
n u
sed
to
ad
just
pro
ject
act
ivit
ies
Pro
ject
ou
tco
mes
an
d im
pac
ts c
om
mu
nic
ated
thro
ugh
el
ectr
on
ic m
edia
an
d p
rese
nta
tio
ns
at in
du
stry
m
eeti
ngs
–co
nd
uct
ed
Ind
ust
ryst
akeh
old
ers
Jarg
on
-fre
e o
ne-
pag
ers
of
succ
ess
sto
ries
usi
ng
bre
edin
g p
rogr
am-s
pec
ific
lan
guag
e an
d c
on
sist
ent
form
at –
dev
elo
ped
an
d d
istr
ibu
ted
Cro
p B
reed
ing
Team
s
Bre
eder
en
gage
men
t in
Yea
r 4
wit
h s
take
ho
lder
sab
ou
t D
NA
-in
form
ed b
reed
ing
and
th
eir
stak
eho
lder
inp
ut
–o
bta
ined
an
d s
um
mar
ized
Exte
rnal
Eva
luat
or,
R
osB
REE
D E
xecu
tive
Co
mm
itte
e, T
eam
Le
ader
s
30
RosBREED Demonstration Breeders Annual Reports for Year 3
(9/1/2016 – 8/31/2017)
Progress in DNA-Informed Breeding
Summarized by Michael Coe, Cedar Lake Research Group LLC
Respondents: 16 breeders or breeder teams representing 20 rosaceous crop breeding programs
Status
• During project year three, 18 of 20 RosBREED breeding programs engaged their regional
stakeholders in formal or informal communications about DNA-informed breeding practices
or opportunities. Formal presentations or publications for growers and other industry
stakeholders were reported by 16 of the programs. Eighteen of the 20 programs reported
informal discussions with stakeholder groups or individuals, focused on DNA-informed
breeding opportunities.
• Industry stakeholders continued to express interest in and support for application of DNA-
informed selective breeding, with many focusing on current needs for improved disease
and insect resistance. Stakeholders continued to raise questions about genetic
engineering methods such as gene editing and how these differ from or relate to selective
breeding programs that may use DNA tests to inform selection. In addition to requests for
more information about applications, costs and timelines of DNA-informed methods,
stakeholders provided specific recommendations for traits and crops that should be the
focus of new DNA tests, including increased emphasis on pear and caneberries as well as
specific disease resistance, phenology and taste/aroma traits.
Themes in Breeders’ Recommendations about Stakeholder Engagement
• Existing RosBREED extension materials were viewed as useful, and more were
requested: DNA test cards, RosBRIEFs, the RosBREED website, newsletter, and slide
sets. Other suggestions: video animations to explain DNA informed breeding in practice;
additional downloadable material on RosBREED “by the numbers” from the newsletter.
• Continued direct engagement with industry and breeders, including visits to breeding
programs and outreach to specific stakeholder groups, is important. It would help to
develop more non-technical articles, videos, slides, and shared “talking points” with an
emphasis on topics of interest such as progress on disease resistance. Crop-specific and
region-specific communication is important.
Breeder-Industry stakeholder engagement
about DNA-informed breeding in Year 3
Addressing Breeders’ Needswww.rosbreed.org
HOME PAGE
“FOR BREEDERS” PAGE
31
RosBREED Breeders’ Annual Report for Year 3
Cont.
Status
• All 20 programs reported some use of DNA information in the past year.
• Fourteen programs reported using DNA information in the past year for verifying or
understanding germplasm identity, relatedness, or parentage;12 programs reported using
DNA information for parent selection or planning crosses; 8 programs reported using DNA
for seedling selection or culling; 15 programs reported using DNA information in year three
for upstream research and development of direct relevance to their breeding program.
• A new rating scale for was instituted this year, asking for a summary of program use of
DNA information over time (not just during the past year). Each of four categories of use
are rated on a 5-point scale from “never used” to “the program does this on an ongoing,
routine basis and is involved in developing new tests or applications.”
• Thirteen of 20 demonstration programs were rated as using DNA information on a routine
basis (RosBREED’s goal; levels 3 or 4 on the scale) for at least one DNA use category.
Breeders’ Recommendations
• Further training and documentation/tutorials for use of FlexQTL and other software tools;
more intuitive, efficient software for data management, visualization and analysis
• Expanded training for DNA-informed breeding more generally, including funding and
commercialization issues
• Continued development of phenotyping tools (e.g. FieldBook), markers and DNA tests for
trait loci of near-term value to specific breeding programs and crop groups; more
information about available vendors, services and costs; lower costs for genome scans
• Increased synergy between programs, across crops and public/private sector programs
Breeding program use of DNA information
• Continue to develop complementary slides, brochures, handouts, and online materials that
can be used separately or together, using similar style and content so as to reinforce each
other and the RosBREED “brand.”
• Continue to identify and publicize crop-specific success stories about DNA-informed
applications in the context of overall breeding program activities; do not oversell.
• Continue to identify and publicize non-crop-specific RosBREED 2 success stories, such as
success stories about students and technical staff members from RosBREED 1 – where
they are now, how they were affected by RosBREED experiences, and success stories
about scientific accomplishments due to synergistic RosBREED 2-led activities.
• Continue outreach through the website, newsletter, events, conferences, interactions with
stakeholders, etc.
• Respond to Demonstration Breeder recommendations and needs.
Action items developed based on
Demonstration Breeders’ reports
32
Discussion Questions for Break-out Session
Instructions: While in your crop group, please discuss the five questions below and
summarize your answers for the reporting session (3:15 pm).
Genomics Research and Use of DNA Information by Breeding Programs
1. What are the key emerging opportunities for DNA-informed breeding that are arising
from worldwide Rosaceae genomics research? Is RosBREED best utilizing the
outcomes, expertise, and datasets of this worldwide research? How can we better
synergize?
2. How can DNA information be effectively integrated into what are mostly traditional
breeding programs within the timeframe of RosBREED 2?
Breeding-Industry Interface
3. What’s new (or gaining in importance) in industry that breeders need to know about and
that RosBREED can help address?
4. At this point, is RosBREED providing a satisfactory return on investment by USDA and
industry stakeholders? If not, how do you suggest we adjust activities?
Project Outreach
5. Given that the primary extension audiences are U.S. Rosaceae breeding and industry
stakeholders, how effectively are we using avenues to achieve the goals described in
the other four discussion questions? How can these avenues be more effectively
employed?
• RosBREED website
• Newsletter periodical
• RosBRIEFs
• Social media
• Annual RosBREED Advisory Panel meetings
• Professional meetings (Amer Soc Hort Sci, Natl Assoc Plant Breeders, Rosaceae
Genomics Conf)
• Commodity group meetings
• Individual breeding program interactions with their industries and other breeders
(page 31-32)
• Others?
33