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Cameron Peace, Nahla Bassil, Michael Coe, Chad Finn, Ksenija Gasic, Stan Hokanson, Jim Luby, Dorrie Main, Jim McFerson, Jay Norelli, Mercy Olmstead, Vance Whitaker, Chengyan Yue, and Amy Iezzoni
Genomics Research Advances
Amazing Germplasm
DNA-Based Technologies
Traditional Genetics
Cultivar Development Pipeline
International Collaboration
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Outline of Presentation
Cultivar Development Pipeline × Genomics Research Advances
International Collaboration × DNA-Based Technologies
Amazing Germplasm × Traditional Genetics
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The Rosaceae Family
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Amazing Germplasm!
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Features of Rosaceous Crops• Product quality is paramount• Clonally propagated• Perennial • Often long juvenility
• Often obligate outcrossers• Often high heterozygosity• Sometimes polyploid
• Few generations in cultivation, much diversity in primary genepools huge genetic gains possible
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Traditional Genetics• Crossing & selecting mostly by phenotype• Quantitative genetics rarely used
• Breeders often rely on serendipity
• Challenges: large plant sizes, long juvenility,disease resistances combined with superior quality
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Cultivar Development Pipelines• Need for much public breeding (some crops/regions not commercially viable?)
• Cultivar development pipelines are functional but inefficient
• Many exciting releases
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Strong Spirit of Collaboration
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International Research Community Hub
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Rosaceae Community Collaboration
US–EurRosaceae Mapping
ConsortiumTechnology
Roadmap for Tree Fruit Production
White Paper:US Rosaceae
Genomics, Genetics, & Breeding Initiative
Rosaceae Specialty Crops Planning Workshop
US RosEXEC
U.S.
RGC4CHILE
RGC3NEW Z’LAND
RGC2U.S.
SNP arrays
Whole genome sequences
RGC5S. AFRICA
ITALY
International Rosaceae Genomics Conferences
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Genomics Research Advances
• Powerful genomics resourcesand many discoveries
• Little translation to breeding application
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Genomics Research Advances
Cultivar Development Pipeline
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Genomics-Assisted Breeding
Genomics resources(e.g., whole genome sequences)
More efficient development of new cultivars
Decision support
DNA information
The Chasm!
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The Chasm!Decision support
DNA information
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Some Reasons for the ChasmDecision support
DNA information Reported QTLs themselves:
• Trait low priority / low value• Weak linkage• Different germplasm• Unknown functional alleles• Unknown genetic action• Unknown linkage relationships• Unknown environment effects• Unknown management effects
No suitable DNA testing services
Not believed to be cost efficient
No training in routine DNA testing
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Bridging the ChasmDecision support
DNA information
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• Funded by USDA Specialty Crop Research Initiative
• $7.2 M federal
• Sep 2009 –Aug 2014
• Project Directors:Amy IezzoniCameron Peace
“RosBREED 1”
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RosBREED 1 Outcomes
• Socio-economic values for levels of breeding traits
• Genomics resources and DNA information:SNP array genome scans, QTLs
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RosBREED 1 Outcomes
• Practical tools for breeding use:DNA tests for many breeding-relevant traits
• DNA information about breeding germplasm:genetic potential of parents, seedlings, selections, cultivars
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DNA Tests in 2009
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DNA Tests Now
JUN JUL
APR MAY JUN JUL AUG SEP
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RosBREED 1 Outcomes• Trained the next generation of breeders!
… and many of the current generation
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RosBREED 1 Outcomes
• DNA-informed breeding is now conventional!
Agree that “Genetic marker information will be included in 2014 in how my organization addresses plant breeding & selection”
62%
U.S.-wide survey of Rosaceae breeders (early 2014):
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MSUAmy Iezzoni (PD)
Jim HancockBill Shane
Clemson Univ Ksenija Gasic
Steve KresovichAmy Lawton-RauhGregory Reighard
Chris SaskiGuido Schnabel
Texas A&MDave Byrne
Univ CA-DavisTom Gradziel
Carlos Crisosto
Univ MinnesotaRex Bernardo
Stan HokansonJim Luby
Chengyan YueUniv Queensland
Craig Hardner
USDA-ARSNahla BassilRichard BellChad FinnJay Norelli
Univ ArkansasJohn Clark
Univ FloridaMercy OlmsteadVance Whitaker
WSUCameron Peace (coPD)
Lisa DeVetterKate Evans
Karina Gallardo Des LayneDorrie Main
Vicki McCracken Pat Moore
Nnadozie Oraguzie
Cal Poly StateKelly Ivors
Univ New HampshireTom Davis
Cornell UnivSusan Brown
• Funded by USDA Specialty Crop Research Initiative
• $10.0 M federal
• Sep 2014 –Aug 2019
• Project Directors:Amy IezzoniCameron Peace
“RosBREED 2”
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RosBREED 2 Vision
U.S. rosaceous crop breeding programswill exploit genetic resources,
applying modern genomics toolsto efficiently, accurately, creatively, and rapidly deliver new cultivars with market-essential horticultural quality
and producer-required disease resistancesto enhance consumer demandand mitigate stakeholder risk
for rosaceous fruit, nut, and floral products.
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RosBREED 2 Breeding Programs
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RosBREED 2 Breedging Germplasm Levels
Innovative, superior,
risk-mitigating new cultivars
Creative, efficient, accurate, rapid
breeding
Accessible natural diversity
PRODUCTIONMARKETING
Seedling selectionParent selection
Elite selection performance
Germplasm development
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RosBREED 2 Transdisciplinary Approach
Objectives
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Objective 1
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Objective 2
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Objective 3
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Objective 4
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Objective 5
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Haploblocking
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HaploblockingDivide each chromosome into segments that are non-recombining in historical, selected germplasm– haploblocks
BLIGHTRESISTANCE
POST-ZYGOTICSEGR. DISTORTION
SWEETNESS
Characterize effects and ancestryof each variant – haplotypes
SIZE
extremely positivestrongly positivepositivemildly positiveneutralmildly negativenegativestrongly negativeextremely negative
over-representedneutralunder-represented
Target tight linkages to break, if desired
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The Pedigree of RosBREED
Enhanced breeding efficiency, accuracy, speed, & creativity
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The Children of RosBREED
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RosBREED is supported by the USDA-NIFA-Specialty Crop Research Initiative by a combination of federal and matching funds (grant number 2014-51181-22378).
Acknowledgements
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Questions?
www.rosbreed.org