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2007 Paul VanRaden, Dan Null, Katie Olson, Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal Breeders, Columbia,

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Presentation on theme: "2007 Paul VanRaden, Dan Null, Katie Olson, Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal Breeders, Columbia,"— Presentation transcript:

1 2007 Paul VanRaden, Dan Null, Katie Olson, Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal Breeders, Columbia, MO Paul.VanRaden@ars.usda.gov 2011 Reporting of Haplotypes with Recessive Effects on Fertility

2 Interbull annual meeting, Norway, August 2011 (2) Paul VanRaden 2011 Introduction  Five haplotypes with recessive effects on fertility discovered Additive effects small and in EBVs All populations already carry these  At least 19 countries have ‘health’ laws excluding carriers of defects Only countries that test are banned? Import restrictions make little sense

3 Interbull annual meeting, Norway, August 2011 (3) Paul VanRaden 2011 Recessive Defect Discovery  Check for homozygous haplotypes 7 to 90 expected but none observed 5 of top 11 confirmed as lethal 936 to 52,449 carrier sire by carrier MGS fertility records 3.0% to 3.7% lower conception rates Some slightly higher stillbirth rates  Confirmed Brachyspina same way

4 Interbull annual meeting, Norway, August 2011 (4) Paul VanRaden 2011 Haplotypes Affecting Fertility Name Chrom- osome Loca- tion Carrier FreqEarliest Known Ancestors BTAMbase% HH1562-684.5Pawnee Farm Arlinda Chief HH2193-984.6Willowholme Mark Anthony HH3892-974.7Glendell Arlinda Chief, Gray View Skyliner JH11511-1623.4Observer Chocolate Soldier BH1742-4714.0West Lawn Stretch Improver

5 Interbull annual meeting, Norway, August 2011 (5) Paul VanRaden 2011 Hapl- Additive EffectSire x MGS Interaction otypeCRNR60NR100NR140CR280 CVM -0.12-0.9-1.5-1.9-2.9 BY -0.46-2.2-2.3 -2.5 HH1 -0.35-1.1-1.6-2.0-3.1 HH2 -0.36-1.7-3.0-2.9-3.0 HH3 -0.36-3.1-3.4 -3.2 JH1 -2.22-3.7 -3.6-3.7 BH1 -0.98-2.5-3.7-2.9-3.4 Additive and Nonadditive Effects on nonreturn rates or full gestation conception

6 Interbull annual meeting, Norway, August 2011 (6) Paul VanRaden 2011 Haplo-Conception Rates typeBullService SireHeiferCow BYRamosN / A+0.1+5.2 HH1Lucius+3.1+2.5 HH2Colby+2.2+5.2+5.4 HH3O-Man+0.6+2.1+3.5 JH1Country-0.5+2.7+3.2 BH1Payoff+1.5 +3.4 Carrier Bulls with High Fertility

7 Interbull annual meeting, Norway, August 2011 (7) Paul VanRaden 2011 Using Crossovers to Fine Map Source Combined With Source Suspect Area Carrier Possible 75 marker haplotype (50K), about 5 Mbases

8 Interbull annual meeting, Norway, August 2011 (8) Paul VanRaden 2011 Crossover haplotypes Haplo- type That combined with source Within suspect area That contained suspect area SNPs in suspect area BY10663128 HH18512639 HH29381525 HH3354070 JH110221917 BH104074 Crossovers used in Fine Mapping

9 Interbull annual meeting, Norway, August 2011 (9) Paul VanRaden 2011  3 methods to detect carriers: Use all genotypes and pedigrees One at a time (ignore pedigree) Find and test for causative mutation  Without vs. with haplotyping 2.5% false positive, 0.05% false neg Similar to Georges et al (2010) Brachyspina haplotype test Detection Without Haplotyping

10 Interbull annual meeting, Norway, August 2011 (10) Paul VanRaden 2011 Haplotype False positive (%) False negative (%) Error rate (%) BY0.02.21.1 HH10.46.43.4 HH20.01.80.9 HH30.22.81.5 JH10.46.43.4 Detection with 3K Genotypes 500 carriers, 500 noncarriers, with imputation

11 Interbull annual meeting, Norway, August 2011 (11) Paul VanRaden 2011 Conclusions  Recessive defects found in each breed (HH1, HH2, HH3, JH1, BH1) Officially reported in August Most embryo losses < 60 days  Breeders should select for fertility, not against individual defects, and mate carriers to noncarriers  Crossovers used for fine mapping

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