2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Future Animal Improvement Programs Applied.

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Presentation transcript:

2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Future Animal Improvement Programs Applied to Global Populations

EAAP / Interbull joint session, August 2009 (2)Paul VanRaden 2009 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

EAAP / Interbull joint session, August 2009 (3)Paul VanRaden 2009 Step 1: Collect Data

EAAP / Interbull joint session, August 2009 (4)Paul VanRaden 2009 Cows Tested

EAAP / Interbull joint session, August 2009 (5)Paul VanRaden 2009 Step 2: Analyze Data Bull proof (pounds) from 1916 Dtr MilkDtr FatDam MilkDam Fat Avg

EAAP / Interbull joint session, August 2009 (6)Paul VanRaden 2009 Traits Evaluated by U.S. and Interbull TraitUSAITBTraitUSAITB Milk, fat Calving Protein Stillbirth Conf Fertility Cell count M speed???2009 Longevity ???

EAAP / Interbull joint session, August 2009 (7)Paul VanRaden 2009 Step 3: Select Animals

EAAP / Interbull joint session, August 2009 (8)Paul VanRaden 2009 Number of U.S. Bull Associations

EAAP / Interbull joint session, August 2009 (9)Paul VanRaden 2009 Percent Bulls with Foreign Sire Powell et al, 2009 JDS (abstract)

EAAP / Interbull joint session, August 2009 (10)Paul VanRaden 2009 Global Scale, Global Index Powell 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 VanRaden 2009 Current EBV Exchange

EAAP / Interbull joint session, August 2009 (12)Paul VanRaden 2009 Tropical 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 VanRaden 2009 Genotype by Environment Interaction Zwald 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 VanRaden 2009 Genotype 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 VanRaden 2009 Heat Tolerance Ravagnolo and Misztal, 2000

EAAP / Interbull joint session, August 2009 (16)Paul VanRaden 2009 Step 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 VanRaden 2009 Actual 50K Results Actual 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 4 th 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 VanRaden 2009 Genotype 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 VanRaden 2009 Genomic 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 VanRaden 2009 Multi-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 VanRaden 2009 Multi-Country Computation with 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 VanRaden 2009 Proven Bull Reliability Simulated BS bulls on home country scale TraditionalGenomic CountryNat’lMACENat’lMulti-trait DEU CHE91 92 USA CAN

EAAP / Interbull joint session, August 2009 (23)Paul VanRaden 2009 Young Bull Reliability 120 simulated BS bulls sampled in USA TraditionalGenomic CountryNat’lMACENat’lMulti-trait DEU CHE USA CAN114961

EAAP / Interbull joint session, August 2009 (24)Paul VanRaden 2009 Holstein Simulation Results World 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 = corr 2 (EBV, true BV) 81% vs 30% observed using 50K 83% vs 30% observed using 100K

EAAP / Interbull joint session, August 2009 (25)Paul VanRaden 2009 Lower and Higher Density Chips  384 marker low-cost assay 96 parentage 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 VanRaden 2009 Embryo 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 VanRaden 2009 Best Chromosome 1 Co-Op Boliver Lisha

EAAP / Interbull joint session, August 2009 (28)Paul VanRaden 2009 Best Chromosome 2 Kellercrest Earnit Hank

EAAP / Interbull joint session, August 2009 (29)Paul VanRaden 2009 Best Chromosome 3 Wesselcrest Sidney Aric

EAAP / Interbull joint session, August 2009 (31)Paul VanRaden 2009 Best Chromosomes 1-30 Genomics Extraordinaire, Net Merit $

EAAP / Interbull joint session, August 2009 (32)Paul VanRaden 2009 Step 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 VanRaden 2009 Step 6: Transgenics Brophy 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 VanRaden 2009

EAAP / Interbull joint session, August 2009 (35)Paul VanRaden 2009 Breeding 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 VanRaden 2009 Conclusions  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 VanRaden 2009 Acknowledgments  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