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

Slides:

Advertisements

Similar presentations

J. B. Cole, 1,* P. M. VanRaden, 1 D. J. Null, 1 T. S. Sonstegard, 2 M. McClure, 2 C. P. Van Tassell, 2 H. A. Adams, 3 and H. A. Lewin 4 1 Animal Improvement.

Advertisements

2007 Paul VanRaden 1, Jeff O’Connell 2, George Wiggans 1, Kent Weigel 3 1 Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2 University of Maryland.

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Phenotypes.

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA Applications.

Genomic evaluation of Ayrshire dairy cattle and new haplotypes affecting fertility and stillbirth in Holstein, Brown Swiss and Ayrshire breeds T.A. Cooper*,

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA New applications.

2007 Paul VanRaden and Jeff O’Connell Animal Improvement Programs Lab, Beltsville, MD U MD College of Medicine, Baltimore, MD

2015 John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Genomic improvement.

Wiggans, 2013RL meeting, Aug. 15 (1) Dr. George R. Wiggans, Acting Research Leader Bldg. 005, Room 306, BARC-West (main office);

Mating Programs Including Genomic Relationships and Dominance Effects

Mating Programs Including Genomic Relationships and Dominance Effects Chuanyu Sun 1, Paul M. VanRaden 2, Jeff R. O'Connell 3 1 National Association of.

Effects of complex vertebral malformation gene on production and reproduction M. T. Kuhn*, J. L. Hutchison, and C. P. Van Tassell Animal Improvement Programs.

WiggansARS Big Data Workshop – July 16, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

Changes in the use of young bulls K. M. Olson* 1, J. L. Hutchison 2, P. M. VanRaden 2, and H. D. Norman 2 1 National Association of Animal Breeders, Columbia,

2007 Paul VanRaden Animal Improvement Programs Lab, Beltsville, MD 2011 Avoiding bias from genomic pre- selection in converting.

Wiggans, 2013China Emerging Markets Program Seminar Dr. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

Wiggans, 2013SRUC Imputation (1) Dr. George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD ,

2007 Paul VanRaden, Curt Van Tassell, George Wiggans, Tad Sonstegard, and Jeff O’Connell Animal Improvement Programs Laboratory and Bovine Functional Genomics.

Wiggans, th WCGALP (1) G.R. Wiggans*, T.A. Cooper, D.J. Null, and P.M. VanRaden Animal Genomics and Improvement Laboratory Agricultural Research.

Comparison of Holstein service-sire fertility for heifer and cow breedings with conventional and sexed semen H. D. Norman*, J. L. Hutchison, and P. M.

An Efficient Method of Generating Whole Genome Sequence for Thousands of Bulls Chuanyu Sun 1 and Paul M. VanRaden 2 1 National Association of Animal Breeders,

2007 Paul VanRaden and Mel Tooker Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA

John B. Cole 1, Daniel J. Null *1, Chuanyu Sun 2, and Paul M. VanRaden 1 1 Animal Genomics and Improvement 2 Sexing Technologies Laboratory Navasota, TX.

2007 Paul VanRaden, Mel Tooker, Jan Wright, Chuanyu Sun, and Jana Hutchison Animal Improvement Programs Lab, Beltsville, MD National Association of Animal.

2007 Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Mixing Different SNP Densities Mixing Different.

2007 Melvin Tooker and Paul VanRaden Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2009 Happy Bulls, Happy Cows,

2007 Paul VanRaden, George Wiggans, Jeff O’Connell, John Cole, Animal Improvement Programs Laboratory Tad Sonstegard, and Curt Van Tassell Bovine Functional.

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD New Tools for.

G. R. Wiggans and P. M. VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Using.

2005 Paul VanRaden Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA Selection for.

2007 Paul VanRaden and Jan Wright Animal Improvement Programs Lab, Beltsville, MD 2013 Measuring genomic pre-selection in theory.

Paul VanRaden, 1 Katie Olson, 2 Dan Null, 1 Mehdi Sargolzaei, 3 Marco Winters, 4 and Jan-Thijs van Kaam 5 1 Animal Improvement Programs Laboratory, ARS,

Factors affecting heifer fertility in U.S. Holsteins M. T. Kuhn* and J. L. Hutchison Animal Improvement Programs Laboratory, Agricultural Research Service,

WiggansCDCB industry meeting – Sept. 29, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD AIPL Report.

John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD New tools for.

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (1) G.R. Wiggans* 1, T.A. Cooper 1, P.M. VanRaden 1, D.J. Null 1, J.L. Hutchison 1, O.M. Meland 2, M.E.

2007 Paul VanRaden Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA

Norman, 2014ICAR / Interbull annual meeting, Berlin, Germany, May 20, 2014 (1) Dr. H. Duane Norman Interim Administrator Council on Dairy Cattle Breeding.

University of Illinois at Urbana-Champaign Department of Animal Sciences Identification of a nonsense mutation in APAF1 that is causal for a decrease in.

Paul VanRaden and John Cole Animal Improvement Programs Laboratory Beltsville, MD, USA 2004 Planned Changes to Models and Trait Definitions.

Adjustment of breeding values for past and future inbreeding Paul VanRaden*, Lori Smith Animal Improvement Programs Laboratory Agricultural Research Service,

P. M. VanRaden and T. A. Cooper * Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA

2007 Paul VanRaden 1, Jeff O’Connell 2, George Wiggans 1, Kent Weigel 3 1 Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2 University of Maryland.

WiggansARPAS-DC meeting, Beltsville, MD – Dec. 9, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service,

Paul VanRaden and Chuanyu Sun Animal Genomics and Improvement Lab USDA-ARS, Beltsville, MD, USA National Association of Animal Breeders Columbia, MO, USA.

2007 Paul VanRaden 1, Jeff O’Connell 2, George Wiggans 1, Kent Weigel 3 1 Animal Improvement Programs Lab, USDA, Beltsville, MD, USA 2 University of Maryland.

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD What.

P.M. VanRaden and D.M. Bickhart Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, USA

Multi-trait, multi-breed conception rate evaluations P. M. VanRaden 1, J. R. Wright 1 *, C. Sun 2, J. L. Hutchison 1 and M. E. Tooker 1 1 Animal Genomics.

Fine Mapping and Discovery of Recessive Mutations that Cause Abortions in Dairy Cattle P. M. VanRaden 1, D. J. Null 1 *, T.S. Sonstegard 2, H.A. Adams.

H. D. Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD DRMS annual.

2007 John Cole, Paul VanRaden, George Wiggans, and Melvin Kuhn Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD,

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD G.R. WiggansADSA 18.

G.R. Wiggans 1, T. A. Cooper 1 *, K.M. Olson 2 and P.M. VanRaden 1 1 Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

H.D. Norman*, J.L. Hutchison, and J.R. Wright Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

2007 Paul VanRaden Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA 2008 New.

WiggansCornell University, ANSC 3310, March 10, 2015 (1) Dr. George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service,

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Select Sires‘ Holstein.

2007 Paul VanRaden 1, Curt Van Tassell 2, George Wiggans 1, Tad Sonstegard 2, Bob Schnabel 3, Jerry Taylor 3, and Flavio Schenkel 4, Paul VanRaden 1, Curt.

Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2014 Paul VanRaden Advancing.

US genomic evaluation system

My vision for dairy genomics

Druet T, Sartelet A, Hubin X, Tamma N, Georges M, Charlier C

Managing Genetic Defects--Bovine Genetic Disease and Trait Frequencies in Ireland: 96 causative alleles in >1.1M animals McClure, M.C., Flynn, P., Weld,

Gene editing algorithm

Methods to compute reliabilities for genomic predictions of feed intake Paul VanRaden, Jana Hutchison, Bingjie Li, Erin Connor, and John Cole USDA, Agricultural.

Contribution of inbreeding and recessive defects to early embryo loss

Percent of total breedings

Presentation transcript:

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

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

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

Interbull annual meeting, Norway, August 2011 (4) Paul VanRaden 2011 Haplotypes Affecting Fertility Name Chrom- osome Loca- tion Carrier FreqEarliest Known Ancestors BTAMbase% HH Pawnee Farm Arlinda Chief HH Willowholme Mark Anthony HH Glendell Arlinda Chief, Gray View Skyliner JH Observer Chocolate Soldier BH West Lawn Stretch Improver

Interbull annual meeting, Norway, August 2011 (5) Paul VanRaden 2011 Hapl- Additive EffectSire x MGS Interaction otypeCRNR60NR100NR140CR280 CVM BY HH HH HH JH BH Additive and Nonadditive Effects on nonreturn rates or full gestation conception

Interbull annual meeting, Norway, August 2011 (6) Paul VanRaden 2011 Haplo-Conception Rates typeBullService SireHeiferCow BYRamosN / A HH1Lucius HH2Colby HH3O-Man JH1Country BH1Payoff Carrier Bulls with High Fertility

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

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 BY HH HH HH JH BH Crossovers used in Fine Mapping

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

Interbull annual meeting, Norway, August 2011 (10) Paul VanRaden 2011 Haplotype False positive (%) False negative (%) Error rate (%) BY HH HH HH JH Detection with 3K Genotypes 500 carriers, 500 noncarriers, with imputation

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