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Plant Research Intl, Netherlands

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Presentation on theme: "Plant Research Intl, Netherlands"— Presentation transcript:

1 Plant Research Intl, Netherlands
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 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 Univ. of Arkansas John Clark USDA-ARS Nahla Bassil Gennaro Fazio Chad Finn Univ. of Minnesota Jim Luby Chengyan Yue Oregon State Univ. Alexandra Stone Plant Research Intl, Netherlands Eric van de Weg Marco Bink

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

3 The RosBREED Project

4 RosBREED The RosBREED Project
PI: Amy Iezzoni, Michigan State University 4 years, Sep 2009 – Aug 2013 Funded by SCRI (USDA-NIFA’s Specialty Crop Research Initiative) $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners) RosBREED

5 RosBREED The RosBREED Project
U.S.-wide and international collaboration 10 Teams 32 members of 3 Advisory Panels (Stakeholder, Extension, Scientific) Administration Pedigree-Based Analysis Industry Genomics Breeders’ Toolbox Socio-Economics Genotyping Extension Breeding MAB Pipeline RosBREED

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

7 RosBREED The RosBREED Project Vision
Integration of modern genomics tools with traditional breeding approaches will transform crop improvement in Rosaceae, significantly improving profitability and sustainability of U.S. rosaceous crop industries and contributing to increased consumption and enjoyment of these fruit, nut, and floral products. RosBREED

8 Socio-economics information
The RosBREED Approach Socio-economics information Objectively define SELECTION TARGETS IMPROVED CULTIVARS Optimize SELECTION STRATEGIES DNA information RosBREED

9 The Need for RosBREED

10 The Chasm good intentions skeptical dismissal Genomics Breeding

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

12 Objectives & Major Activities

13 RosBREED Project Objectives
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 RosBREED

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

15 Advances in Enabling MAB

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

17 Challenges faced when determining priorities
Technical challenges Socio-economic challenges Blue, red and green is what we identify as “technical” challenges the purple yellow pink and orange is more related to socio-economics Cumulative of mean 1-10 score Cumulative of mean 1-10 score RosBREED

18 RosBREED Phenotype Databases
for Valuable Fruit Traits of Reference Germplasm 1 2 3 4 5 Reference Germplasm Sets Public: 480 individuals Standardized Phenotyping at multiple locations (www.rosbreed.org) Data collected 2010 & 2011 Available at Genome Database for Rosaceae (www.rosaceae.org/resources/fruit-evaluation) Now playing: Apple Coming soon: Peach, Cherry, Strawberry RosBREED

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

20 Pedigree-Based Analysis Team
Software training RosBREED

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

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

23 MAB Pipeline RosBREED

24 RosBREED MAB Pipeline “Fast-tracked pipelining” of available jewels
Tables of functional genotypes Peach fruit texture type Apple fruit storability RosBREED

25 MAB Pipeline “How To” diagrams RosBREED

26 Breeders’ Toolbox Modules
“Crop Reference & Breeding Pedigree Germplasm Databases” “Marker-Locus-Trait Association Warehouse” * * * * “Technology Portfolio” “Selection Target Identifier” * “Cross Assist” * * * “Genome Database Resources” “Seedling Select”

27 RosBREED Breeders’ Toolbox Cross Assist (prototype)
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 Cross Assist (prototype) Identifies efficient crossing schemes by mobilizing all available data RosBREED

28 Extension 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 ! ! ! ! RosBREED

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) just a day prior to ASHS 2012 in Miami, Florida ! ! RosBREED

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

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

32 RosBREED MAB posters Apple #145 Peach #144 Cherry #146
Tues 1:15-2:00, Kona Ballroom


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