Genomic Selection for Fusarium Head Blight Resistance in Barley

Transcription

1 Genomic Selection for Fusarium Head Blight Resistance in Barley Kevin Smith University of Minnesota Aaron Lorenz, U Nebraska Jean Luc Jannink USDA Ithaca, NY Shiaoman Chao USDA Fargo, ND, Vikas Vikram University of Minnesota Richard Horsley North Dakota State University U.S. Wheat & Barley Scab Initiative

2 FHB QTL Bi-Parental Mapping (7H) 2(2H) 3(3H) (4H) 5(1H) 6(6H) 7(5H) Chevron Frederickson Harbin CI4196 Zhedar 2 Gobernadora Russian 6 FHB Breeding Challenge

3 FHB and DON QTL Association Mapping Trait Chrom cm bin r 2 Robust QTL identified in both CAP I and CAP II DON and FHB sometimes coincident Relatively small allelic effects FHB 2H FHB 4H FHB 6H FHB 6H DON 1H DON 2H DON 3H DON 4H DON 4H DON 4H DON 5H DON 6H FHB Breeding Challenge

4 In traditional marker-assisted selection choice of markers is somewhat arbitrary Here? Here? Here? Why Genomic Selection?

5 Training population Line Yield Mrk 1 Mrk 2 Mrk p Line Line Line Line Line n Selection candidates Line Yield Mrk 1 Mrk 2 Mrk p Line A Line B Line C Line D Line n Model training y p b x i j i j j 1 Prediction GEBV p bˆ x i j i j j 1 Basic framework GEBV = genomic estimated breeding value Parent selection Line GEBV Mrk 1 Mrk 2 Mrk p Line A Line B Line C Line D Line n Why Genomic Selection?

6 Implementing Genomic Selection Why switch now? Relatively slow progress via phenotypic selection Large cost of phenotyping Limited throughput (plot area, time, people) FHB genetics (quantitative, small effects) Decreasing cost of genotyping USDA Genotyping Laboratories Promising results from simulation and cross validation of GS Implementing Genomic Selection

7 Genomic Selection for Fusarium Head Blight Resistance in Barley Conventional Phenotypic Selection Fitting and Validating Models Implementing Selection Evaluating Selection Accuracy & Gain

8 Current Scheme Phenotypic Selection Yr 1 Yr 2 Yr 3-4 Yr 5-9 Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE 4 Year Breeding Cycle Phenotypic Selection

9 Current Scheme Field Screening for FHB Yr 1 Yr 2 Yr 3-4 Yr 5-9 Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE Insert Winter Nursery Picture In 2010 evaluated over 13,000 single row plots for FHB severity Phenotypic Selection

10 Phenotypic Selection Costs (per sample/plot) Seedling Disease Assay Single Plant Off-Season Nursery.. FHB Severity (head rows) DON.. Yield.. Malting Quality. $2 $4 $5 $10 $15 $100 Phenotypic Selection

11 Genomic Selection for Fusarium Head Blight Resistance in Barley Conventional Phenotypic Selection Fitting and Validating Models Implementing Selection Evaluating Selection Accuracy & Gain

12 Model Cross-Validation Studies Model for estimating marker effects Number of markers Size of training population Composition of training population Train Model Predict Individual

13 More markers are better, but 384 is enough Training population 691 six-row barley lines from CAP

14 Large populations are better (at least 300) Mean Training population 691 six-row barley lines from CAP

15 Training population composition effects model accuracy

16 Genomic Selection for Fusarium Head Blight Resistance in Barley Conventional Phenotypic Selection Fitting and Validating Models Implementing Selection Evaluating Selection Accuracy & Gain

17 Current Scheme Genomic Selection Yr 1 Yr 2 Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery Breeding Cycle Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery Yr 1 Yr 2 Genomic Selection Yr 3-4 Yr 5-9 F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial Evaluation 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial Plant Brew 5 th year trial 6 th year trial RELEASE Yr 3 Yr 4-8 RELEASE Implementing Genomic Selection

18 FHB Genomic Selection Project U.S. Wheat & Barley Scab Initiative Parents UM Busch Ag NDSU Crosses UM B A NDSU UM B A B A NDSU UM NDSU 1440 progeny = 6 cross types x 10 crosses per type x 24 progeny per cross 384 SNPs selected from BOPA1&2 optimized for PIC and genome distribution Training Data set CAPI, II, II from three programs Ridge Regression Model Shiaoman Chao, Jean-Luc Jannink, Aaron Lorenz, Rich Horsley, Blake Cooper, Gary Hanning, Implementing Genomic Selection

19 GS Predicted Values Lacey Quest Tradition MIN MAX AVE Freq Wt X DON_f FHB Aa Bg Dp protein hd ht plump st yield G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W G10W Implementing Genomic Selection

20 Genomic Selection for Fusarium Head Blight Resistance in Barley Conventional Phenotypic Selection Fitting and Validating Models Implementing Selection Evaluating Selection Accuracy & Gain

21 Evaluation of Cycle 1 Fall 2009 Winter 2009/10 Summer 2010 Fall 2010 Winter 2010/11 Summer 2011 Crosses among parents (UM, BA, NDSU) F1 F2 F3 GS (384 SNP markers) F4 New Zealand Off Season Nursery Yield Trials, FHB Screening, Malting Quality Evaluating Selection Accuracy & Gain

22 2011 Trials (2 Loc) 140% 130% 120% 110% 100% 90% 80% 70% 60% 50% 40% GS Predicted FHB R = 0.54 Evaluating Selection Accuracy & Gain

23 2011 Trials (2 Loc) 140% 130% 120% 110% 100% 90% 80% 70% 60% 50% 40% GS Predicted FHB Robust Quest Evaluating Selection Accuracy & Gain

24 2011 Trials (2 Loc) 140% 130% 120% 110% 100% 90% 80% 70% 60% 50% 40% GS Predicted FHB Robust Quest Evaluating Selection Accuracy & Gain

25 2011 Trials (2 Loc) 140% 130% 120% 110% 100% 90% 80% 70% 60% 50% 40% GS Predicted FHB Robust Quest Evaluating Selection Accuracy & Gain

26 Current Scheme Genomic Selection Crossing A x B Crossing A x B Yr 1 F1 Inbreeding F1 Inbreeding Yr 1 F2 F3 F2 F3 Genomic Selection Yr 2 F4 Winter Nursery F4 Winter Nursery Yr 2 Phenotypic Selection Yr 3-4 Yr 5-9 F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial Evaluation 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial Plant Brew 5 th year trial 6 th year trial RELEASE Yr 3 Yr 4-8 RELEASE Evaluating Selection Accuracy & Gain

27 % 50% 60% 70% 80% 90% 100% 110% 120% 130% 140% 150% 160% 170% 180% 190% 200% 210% 220% Phenotypic versus Genomic Selection Evaluating Selection Accuracy & Gain FHB Yield % 50% 60% 70% 80% 90% 100% 110% 120% 130% 140% 150% 160% 170% 180% 190% 200% 210% 220% Phenotypic Genomic

28 Summary Enhancing FHB resistance in barley is a good target for genomic selection approach. We can reduce breeding cycle to 1 year. Training populations of 500 or more and 384 markers should be sufficient to both increase gain per year and reduce overall cost of selection.

29 Join me.? Focus on phenotyping Assemble training data sets Use a database Work closely with genotyping centers. Collect data to measure gain/impact

30 Acknowledgements Barley Project Ed Schiefelbein Guillermo Velasquez Karen Beaubien Ahmad Sallam Stephanie Navarra Vikas Vikram Leticia Kumar Celeste Falcon Danelle Dykema Jon Massman Other Institutions Richard Horsley, NDSU; Shiaoman Chao, USDA; Blake Cooper and Gary Hanning, Busch Ag. Res., Inc Flavio Capettini, ICARDA Jean-Luc Jannink, USDA Aaron Lorenz, University of Nebraska University of Minnesota Ruth Dill-Macky Brian Steffenson Yanhong Dong Galen Thompson SMALL GRAINS INITIATIVE U.S. Wheat & Barley Scab Initiative Minnesota Agricultural Experiment Station American Malting Barley Association

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32 Barley Breeding Cycle Winter Greenhouse F1 Greenhouse SSD Off-Season Nursery Fall (Greenhouse) Crossing block Single Seed Decent (SSD) Summer Field F2 s Head Rows Yield Trials

33 Unfavorable Linkages with FHB Resistance 2(2H) 6(6H) Heading Date FHB Russian 6 Chevron Frederickson Zhedar 2 CI 4780 Grain Protein FHB Chevron Frederickson Hor211 Spike Morphology FHB Frederickson Zhedar 2 CI 4780 FHB Breeding Challenge

34 The Genomic Selection Cycle Advance lines informative for model improvement Test varieties and release Advance lines with highest GEBV Phenotype (lines have already been genotyped) Model Training Cycle Updated Model Genomic Selection Line Development Cycle Make crosses and advance generations Train prediction model Genotype selection candidates Modified from Heffner, Sorrells, and Jannink Crop Sci. New Germplasm Why Genomic Selection?

35 Current Scheme Yr 1 Yr 2 Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery F2-F3 Limited Selection Visual head selection Greenhouse seedling disease assays Traditional MAS single QTL Yr 3-4 Yr 5-9 F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE Phenotypic Selection

36 Current Scheme Crossing A x B Single Plant Selection Yr 1 F1 Inbreeding F2 F3 Yr 2 Yr 3-4 Yr 5-9 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE Insert Winter Nursery Picture

37 Current Scheme Crossing A x B Yr 1 F1 Inbreeding F2 F3 Replicated Preliminary Yield Trials ( 3 locations) Yr 2 Yr 3-4 Yr 5-9 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE Phenotypic Selection

38 Current Scheme Crossing A x B Yr 1 F1 Inbreeding F2 F3 Replicated 2nd Year Yield Trials ( 5 locations) Yr 2 Yr 3-4 Yr 5-9 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE INSERT 2 nd YEAR TRIAL PIC Phenotypic Selection

39 Current Scheme Yr 1 Yr 2 Yr 3-4 Yr 5-9 Crossing A x B F1 Inbreeding F2 F3 F4 Winter Nursery F4:5 Plant Rows Evaluation Winter Nursery Increase 1 st year trial 2 nd year trial AMBA 3 rd year trial Pilot Malt 4 th year trial 5 th year trial Plant Brew 6 th year trial RELEASE USDA Malt Quality Lab Yield Trials Industry (AMBA) Pilot Malt Trials Plant Scale Brewing Phenotypic Selection

40 Selection Accuracy as Effected by Training Population

41 Evaluation of Cycle 1 6 populations randomly selected lines Cross n Correlation Heritability All Evaluating Selection Accuracy & Gain

42 Evaluation of Cycle 1 Selected Breeding Lines Location Correlation Accuracy Saint Paul 0.38 Crookston Locations lines selected from among 25 crosses for low DON and high yield Correlation (r) between GEBV : Observed Phenotype Accuracy = r/h H 2 = heritability Evaluating Selection Accuracy & Gain

43 Genotyping Logistics Harvest F2 (field) Plant F3 (greenhouse) Harvest Plant Tissue DNA Extraction/Genotyping GS Predictions / Parent Selection Crossing July 30 August 16 August 30 Sept 20 Sept 27 Oct 4 Implementing Genomic Selection