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Future Animal Improvement Programs Applied to Global Populations. Topics. Brief history of past improvement programs National and global goals Genetic x environment interaction International genomic evaluation Exchange of GEBVs or genotypes Use of new reproductive tools. Step 1: - PowerPoint PPT Presentation
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2007
Paul VanRaden Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA
2009
Future Animal Improvement Future Animal Improvement Programs Applied to Global Programs Applied to Global
Populations Populations
EAAP / Interbull joint session, August 2009 (2) Paul VanRaden200
9
TopicsTopics
Brief history of past improvement programs
National and global goals Genetic x environment interaction International genomic evaluation
• Exchange of GEBVs or genotypes
Use of new reproductive tools
EAAP / Interbull joint session, August 2009 (3) Paul VanRaden200
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Step 1:Collect Data
EAAP / Interbull joint session, August 2009 (4) Paul VanRaden200
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Cows TestedCows Tested1908-20081908-2008
0
5
10
15
20
25
1908 1920 1930 1940 1950 1960 1970 1980 1990 2000 2008
Year
Nu
mb
er
of
Co
ws
(m
illio
ns
)
0
5
10
15
20
25
30
35
40
45
Pe
rce
nt
on
off
icia
l te
st
Dairy Cows
DHI Cows
% on test
EAAP / Interbull joint session, August 2009 (5) Paul VanRaden200
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Step 2: Analyze DataStep 2: Analyze DataBull proof (pounds) from 1916Bull proof (pounds) from 1916
Dtr Milk Dtr Fat Dam Milk Dam Fat
1 6976 276 4422 171
2 8602 292 5976 217
3 7631 280 1923 84
4 6640 248 4011 147
5 7121 253 5492 198
6 6901 298 6123 248
7 6622 236 5048 190
Avg 7580 282 5426 206
EAAP / Interbull joint session, August 2009 (6) Paul VanRaden200
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Traits Evaluated by U.S. and InterbullTraits Evaluated by U.S. and Interbull
Trait USA ITB Trait USA ITB
Milk, fat 1936 1995 Calving 2000 2005
Protein 1978 1995 Stillbirth 2006 2005
Conf. 1978 1999 Fertility 2003 2007
Cell count 1994 2001 M speed ??? 2009
Longevity 1994 2004 ??? ??? ???
EAAP / Interbull joint session, August 2009 (7) Paul VanRaden200
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Step 3: Select AnimalsStep 3: Select Animals
EAAP / Interbull joint session, August 2009 (8) Paul VanRaden200
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Number of U.S. Bull AssociationsNumber of U.S. Bull Associations
0
40
80
120
160
200
240
280
1908 1918 1928 1938 1948 1958 1968 1978 1988 1998 2008
Year
Nu
mb
er
of
As
so
cia
tio
ns
Bull associations
AI associations
EAAP / Interbull joint session, August 2009 (9) Paul VanRaden200
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Percent Bulls with Foreign SirePercent Bulls with Foreign SirePowell et al, 2009 JDS (abstract)Powell et al, 2009 JDS (abstract)
0
20
40
60
80
100
1986 1988 1990 1992 1994 1996 1998 2000 2002
Bull birth year
USA CAN NLD DEU FRA ITA OTHER
EAAP / Interbull joint session, August 2009 (10) Paul VanRaden200
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Global Scale, Global IndexGlobal Scale, Global IndexPowell and VanRaden, 2002 JDS 85:1863Powell and VanRaden, 2002 JDS 85:1863
Advantages• Much simpler foreign marketing• Focus on international economics• Weighted average of national goals
Disadvantages• Less national progress if corr < 1.0• Removes “home field” advantage
(removes protectionism)
EAAP / Interbull joint session, August 2009 (11) Paul VanRaden200
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Current EBV ExchangeCurrent EBV Exchange
EAAP / Interbull joint session, August 2009 (12) Paul VanRaden200
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Tropical Breeding ProgramsTropical Breeding Programs
Traits needed by tropical cattle• Tolerate heat and humidity• Consume low cost forage or pasture• Resist parasites and disease
Parameters needed for prediction• Corr (tropical, temperate) performance• Corr among tropical environments• Can 1 tropical breed fit many markets?• Is Taurus / Indicus recombination loss too
large to use synthetics? (Rutledge, 2001)
EAAP / Interbull joint session, August 2009 (13) Paul VanRaden200
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Genotype by Environment InteractionGenotype by Environment InteractionZwald et al, 2003 JDS 86:376Zwald et al, 2003 JDS 86:376
Model environment or country?• GxE exists within large countries• Little GxE for neighbor countries• Requires central control of all data
Factors affecting global GxE• Temperature, rainfall, herd yield,
herd size, persistency, calving age, seasonal calving
EAAP / Interbull joint session, August 2009 (14) Paul VanRaden200
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Genotype by Environment within USAGenotype by Environment within USA
Include GxE regressions in national models• Heat tolerance• High / low input herds
Extrapolate to more extreme environments outside USA• Coefficients of regressions larger• Changes in rank will be magnified
EAAP / Interbull joint session, August 2009 (15) Paul VanRaden200
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Heat ToleranceHeat ToleranceRavagnolo and Misztal, 2000Ravagnolo and Misztal, 2000
0
10
20
30
40
50
60
0 4 10 16 21 27 32 38 43
Temperature (°C)
Yie
ld (
Kg
)
Bull 1
Bull 2
EAAP / Interbull joint session, August 2009 (16) Paul VanRaden200
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Step 4: GenomicsStep 4: Genomics
Actual results
International genomic evaluation• Simple conversion formulas• Exchange of genomic EBVs via G-
MACE• Multi-country exchange of genotypes
Future chips
EAAP / Interbull joint session, August 2009 (17) Paul VanRaden200
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Actual 50K ResultsActual 50K Results
Correlation of predicted Mendelian sampling from Nov 2004 and actual from Aug 2009 is about .5
Bull with highest predicted Net Merit in Nov 2004 is now ranked 4th of 1925 for NM$ phenotype (Man O Man)
Highest predicted Net Merit in Jan 2009 now 2nd for NM$ phenotype (Freddie)
EAAP / Interbull joint session, August 2009 (18) Paul VanRaden200
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Genotype Exchange OptionsGenotype Exchange Options
Country pairs exchange genotypes• Each computes GEBVs using joint data• Small countries get GEBV from large
All countries combine genotypes• One or many copies of genotype file?• Centralized or decentralized GEBV service?• How many genotypes must each submit?• How many phenotypes must each submit?• Are GEBVs on 25 scales really needed?
EAAP / Interbull joint session, August 2009 (19) Paul VanRaden200
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Genomic Evaluation - GMACEGenomic Evaluation - GMACE
Exchange GEBVs (not genotypes)• Each country computes GEBVs separately• GMACE accounts for any data sharing• GEBVs from different countries have
residual correlations due to common bulls
Similar to conventional MACE
Less benefit than combining genotypes
EAAP / Interbull joint session, August 2009 (20) Paul VanRaden200
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Multi-Country Combined GenotypesMulti-Country Combined Genotypes
Evaluation options• Foreign data included via MACE, then
single-trait genomic evaluation, OR• Domestic and foreign data evaluated using
multi-country genomic model
Advantages of multi-trait model• Phenotypic and genomic both multi-trait• Domestic data weighted more than foreign• More accurate ranking than G-MACE
EAAP / Interbull joint session, August 2009 (21) Paul VanRaden200
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Multi-Country ComputationMulti-Country Computationwith combined genotype fileswith combined genotype files
USA-CAN, 2 trait model• 10,129 HO with data, 11,815 without• Block-diagonal solver converged in
250 iterations (similar to single-trait)• 11 hours using 2 processors
Global Brown Swiss, 9 countries• All 8,073 proven bulls simulated• 30 hours using 9 processors
EAAP / Interbull joint session, August 2009 (22) Paul VanRaden200
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Proven Bull ReliabilityProven Bull ReliabilitySimulated BS bulls on home country scaleSimulated BS bulls on home country scale
Traditional Genomic
Country Nat’l MACE Nat’l Multi-trait
DEU 81 82 84 84
CHE 91 91 91 92
USA 80 81 83 88
CAN 71 86 72 90
EAAP / Interbull joint session, August 2009 (23) Paul VanRaden200
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Young Bull ReliabilityYoung Bull Reliability120 simulated BS bulls sampled in USA120 simulated BS bulls sampled in USA
Traditional Genomic
Country Nat’l MACE Nat’l Multi-trait
DEU 4 11 64 69
CHE 14 17 65 73
USA 20 20 55 70
CAN 1 14 9 61
EAAP / Interbull joint session, August 2009 (24) Paul VanRaden200
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Holstein SimulationHolstein Simulation Results ResultsWorld population, single-trait methodsWorld population, single-trait methods
40,360 older bulls to predict 9,850 younger bulls in Interbull file
50,000 or 100,000 SNP; 5,000 QTL
Reliability vs. parent average REL• Genomic REL = corr2 (EBV, true BV) • 81% vs 30% observed using 50K• 83% vs 30% observed using 100K
EAAP / Interbull joint session, August 2009 (25) Paul VanRaden200
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Lower and Higher Density ChipsLower and Higher Density Chips
384 marker low-cost assay• 96 parentage + 288 selected for Net Merit $• Available in fall 2009
600,000 marker chip• Expected to be available in 2010
3 billion full sequence of individual• Blackstar (most related to HO breed)• Already done by USDA Bovine Functional
Genomics Lab
EAAP / Interbull joint session, August 2009 (26) Paul VanRaden200
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Embryo SelectionEmbryo Selection
In vitro embryos from heifers before puberty• Further reduce generation interval
Frozen, genotyped embryo market• Cost of genotyping < cost of ET• Could replace AI if accuracy high
Very rapid generation turnover• Velogenetics not yet feasible
EAAP / Interbull joint session, August 2009 (27) Paul VanRaden200
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Best Chromosome 1 Best Chromosome 1 Co-Op Boliver LishaCo-Op Boliver Lisha
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
EAAP / Interbull joint session, August 2009 (28) Paul VanRaden200
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Best Chromosome 2 Best Chromosome 2 Kellercrest Earnit HankKellercrest Earnit Hank
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
EAAP / Interbull joint session, August 2009 (29) Paul VanRaden200
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Best Chromosome 3 Best Chromosome 3 Wesselcrest Sidney AricWesselcrest Sidney Aric
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
Boliver
-40
-20
0
20
40
60
80
100
Lisha
-40
-20
0
20
40
60
80
100
120
140
160
Hank
-60
-40
-20
0
20
40
60
80
100
120
140
160
Aric
-60
-40
-20
0
20
40
60
80
100
120
140
160
Cactus
-40
-20
0
20
40
60
80
100
120
Walkman
-60
-40
-20
0
20
40
60
80
100
120
Snow
-60
-40
-20
0
20
40
60
80
100
120
140
Ringo
-60
-40
-20
0
20
40
60
80
100
120
140
Taffy
-60
-40
-20
0
20
40
60
80
100
120
140
Merit
-60
-40
-20
0
20
40
60
80
100
120
Elegant
-60
-40
-20
0
20
40
60
80
100
120
140
Lon
-60
-40
-20
0
20
40
60
80
100
120
140
Planet
-40
-20
0
20
40
60
80
100
120
Wizard
-60
-40
-20
0
20
40
60
80
100
120
Moses
-40
-20
0
20
40
60
80
100
120
140
160
Diddley
-40
-20
0
20
40
60
80
100
120
140
Bram
-60
-40
-20
0
20
40
60
80
100
120
Tuple
-40
-20
0
20
40
60
80
100
Classic
-60
-40
-20
0
20
40
60
80
100
120
Skyler
-40
-20
0
20
40
60
80
100
120
140
Calypso
-150
-100
-50
0
50
100
150
Gaston
-40
-20
0
20
40
60
80
100
Cri
-60
-40
-20
0
20
40
60
80
100
Howie
-60
-40
-20
0
20
40
60
80
100
120
Impressive
-100
-50
0
50
100
150
Luther
-60
-40
-20
0
20
40
60
80
100
120
Mic
-40
-20
0
20
40
60
80
100
120
Blade
-40
-30
-20
-10
0
10
20
30
40
50
60
70
Tabbon
-100
-80
-60
-40
-20
0
20
40
60
80
100
Sherry
-40
-20
0
20
40
60
80
100
EAAP / Interbull joint session, August 2009 (31) Paul VanRaden200
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Best Chromosomes 1-30Best Chromosomes 1-30Genomics Extraordinaire, +3148 Net Merit $Genomics Extraordinaire, +3148 Net Merit $
-40
0
40
80
120
160
X 2 4 6 8 10 12 14 16 18 20 22 24 26 28
Chromosome
Net
Mer
it $
EAAP / Interbull joint session, August 2009 (32) Paul VanRaden200
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Step 5: CrossbreedingStep 5: Crossbreeding
Composite population• Select best alleles from any breed• Increase genetic SD, long term gain
Perpetual F1 crossbred • For example, JE x HO F1 embryos
inserted into JE x HO F1 cows• Maximize heterosis and uniformity• Similar to breeding of hybrid corn
EAAP / Interbull joint session, August 2009 (33) Paul VanRaden200
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Step 6: TransgenicsStep 6: TransgenicsBrophy et al, 2003, Wall et al, 2005Brophy et al, 2003, Wall et al, 2005
Insert polled gene into horned cow • Faster than traditional breeding• Are resulting animals transgenic? • Similar events occur naturally
Insert desired genes from different species• Large investment needed to prove safe• Global marketing will be difficult because
of within-country politics
EAAP / Interbull joint session, August 2009 (34) Paul VanRaden200
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EAAP / Interbull joint session, August 2009 (35) Paul VanRaden200
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Breeding CompaniesBreeding Companies
Poultry, swine• Closed, private breeding populations • Central control and vertical integration
Dairy, beef cattle• Open exchange of breeding stock• Producers choose using genetic rankings
Almost no patents or intellectual property
EAAP / Interbull joint session, August 2009 (36) Paul VanRaden200
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ConclusionsConclusions
Local data collection and selection programs have become international
Global genomic evaluations possible• Conversion formulas for young bulls• G-MACE to exchange GEBVs• Multi-country genomic evaluation
increases reliability
Advanced technologies require more investment and organization
EAAP / Interbull joint session, August 2009 (37) Paul VanRaden200
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AcknowledgmentsAcknowledgments
Interbull Genomics Task Force for ideas on global evaluation• Pete Sullivan, Georgios Banos, Esa
Mantysaari, Mario Calus, Vincent Ducrocq, Zengting Liu, Hossein Jorjani, and João Dürr
Tabatha Cooper for preparing slides on individual chromosome selection