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MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Raymond Jussaume Vicki McCracken.

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Presentation on theme: "MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Raymond Jussaume Vicki McCracken."— Presentation transcript:

1 MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Raymond Jussaume Vicki McCracken Nnadozie Oraguzie Mykel Taylor Cornell Susan Brown Kenong Xu Clemson Ksenija Gasic Gregory Reighard Texas A&M Dave Byrne Univ. of CA-Davis Tom Gradziel Carlos Crisosto Univ. of New Hamp. Tom Davis Univ. of Minnesota Jim Luby Chengyan Yue Oregon State Univ. Alexandra Stone Plant Research Intl, Netherlands Eric van de Weg Marco Bink USDA-ARS Nahla Bassil Gennaro Fazio Chad Finn Univ. of Arkansas John Clark

2 Outline of Presentation The RosBREED Project The Need for RosBREED Objectives and Major Activities Advances in Enabling MAB

3 The RosBREED Project

4 PI: Amy Iezzoni, M ICHIGAN S TATE U NIVERSITY 4 years, S EP 2009 – A UG 2013 Funded by SCRI (USDA-NIFAs Specialty Crop Research Initiative) $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners) The RosBREED Project

5 U.S.-wide and international collaboration 10 Teams 32 members of 3 Advisory Panels (S TAKEHOLDER, E XTENSION, S CIENTIFIC ) The RosBREED Project S OCIO -E CONOMICS I NDUSTRY B REEDING P EDIGREE -B ASED A NALYSIS A DMINISTRATION B REEDERS T OOLBOX G ENOMICS G ENOTYPING MAB P IPELINE E XTENSION

6 Centered on breeders & breeding programs The RosBREED Project Project Director, Amy Iezzoni -breeder (tart cherry) -geneticist -genomicist -leader

7 The RosBREED Project Vision

8 DNA information Socio-economics information The RosBREED Approach

9 The Need for RosBREED

10 The Chasm

11 Bridging the Chasm Genome scan capability Public reference germplasm sets New QTLs Comprehensive fruit phenotypic database PBA training MAB Pipeline

12 Objectives & Major Activities

13 1)Enhance new cultivar adoption, enlarge market potential, increase consumption – socio-economics knowledge of trait values 2) Establish sustainable infrastructure for MAB in Rosaceae – genome scanning capability, new QTLs (jewels) 3) Integrate socio-econ and genomics resources into breeding – breeding information management system 4) Conduct MAB in demo breeding programs, fruit quality focus – MAB implementation 5) Enhance sustainability of cultivar development – MAB tech transfer to breeders & engage other stakeholders Project Objectives

14 TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT GENOME SCANS GENOME RESOURCES INTERFACE New QTLs discovered PBA: crop - wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Trial MASS BREEDERS TOOLBOX DEVELOPMENT Socio-economics information DNA information Efficient routine breeding operations Better fruit! MAB PIPELINING Overview of Activities Seedling selection scheme REFERENCE GERMPLASM CHOICE STANDARDIZED PHENOTYPING

15 Advances in Enabling MAB

16 Socio-Economics Team will determine trait values Breeder survey 2010 Producer survey Fall Winter 2012 Market Intermediary survey Fall Winter 2011 Household data analysis 2010; consumer survey 2012 What trait is my next breeding target? We like disease resistant apple trees! I like tasty strawberries! We like firm tart cherries that pit well! Processors

17 Challenges faced when determining priorities Cumulative of mean 1-10 score Technical challengesSocio-economic challenges

18 Phenotype Databases for Valuable Fruit Traits of Reference Germplasm Reference Germplasm Sets Public: 480 individuals Standardized Phenotyping at multiple locations ( ) Data collected 2010 & 2011 Available at Genome Database for Rosaceae ( ) Now playing: Apple Coming soon: Peach, Cherry, Strawberry

19 Pedimap for visualizing pedigrees (with IBD, alleles, traits) FlexQTL TM for discovering QTLs Fruit firmness in apple Pedigree-Based Analysis Team Flow of a specific linkage block

20 Pedigree-Based Analysis Team Software training

21 Genomics Genotype obtained for screened sweet cherry germplasm SNP failed Illumina Infinium® arrays: Peach: 9K Apple: 8K Cherry: 6K SNP chip SNP genotyping Cherry array success Example use: peach mapping Peach & Cherry genome scan strategy Apple genome scan strategy

22 Genotyping High quality DNA extraction 3 x 1000 samples PCR for SSRS (QTL-flanking & CG) Genotype calling - SSRs - 9K, 8K, 6K SNP genome scans

23 MAB Pipeline

24 Fast-tracked pipelining of available jewels Tables of functional genotypes Peach fruit texture type Apple fruit storability

25 MAB Pipeline How To diagrams

26 Breeders Toolbox Modules

27 Breeders Toolbox Step 1. Specify data source Step 2. Select up to 5 target traits Step 3. Enter trait weights, heritabilities, and max. co-parentage, or use defaults, or Calculate from data Step 4. Click Generate Parents List (prototype) Identifies efficient crossing schemes by mobilizing all available data Cross Assist

28 Our outreach is all about staying connected with our stakeholders and project participants Various ways: Website Quarterly Newsletters Presentations at professional meetings Community Breeders Page Extension

29 Extension: Coming soon… Participation in grower meetings near you! ( ) TITLE: Tell us what you want! Quantifying your priorities for new cultivars Visits to U.S. Rosaceae breeding programs ( ) - to enable MAB, share successful approaches RosBREED Participatory Workshop (30 July 2012) - j ust a day prior to ASHS 2012 in Miami, Florida

30 Evaluation of Outreach Surveys and interviews to: - Gather project feedback - Monitor changes in Rosaceae breeding programs

31 Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDAs National Institute of Food and Agriculture

32 3 posters


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