Wiggans, 2014CDCB meeting – August 5 (1) G.R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350.

Slides:

Advertisements

Similar presentations

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.

Advertisements

Genomic imputation and evaluation using 1074 high density Holstein genotypes P. M. VanRaden 1, D. J. Null 1 *, G.R. Wiggans 1, T.S. Sonstegard 2, E.E.

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

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD 2008 Genetic trends.

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Select Sires’

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD G.R. WiggansAlta Genetics.

G.R. Wiggans 1, T.S. Sonstegard 1, P.M. VanRaden 1, L.K. Matukumalli 1,2, R.D. Schnabel 3, J.F. Taylor 3, J.P. Chesnais 4, F.S. Schenkel 5, and C.P. Van.

2007 Jana L. Hutchison Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA

India Emerging Markets Conference, May 2009 (1) Leigh Walton Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

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

WiggansGenetics in the Age of Genomics, Scottsdale, AZ, March 4, 2015 (1) Dr. George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural.

Impacts of inclusion of foreign data in genomic evaluation of dairy cattle K. M. Olson 1, P. M. VanRaden 2, D. J. Null 2, and M. E. Tooker 2 1 National.

Wiggans, 2013Japanese Genomics Tour (1) Dr. George R. WiggansDr. H. Duane Norman Acting Research LeaderInterim Administrator Animal Improvement Programs.

G. R. Wiggans, Animal Improvement Programs Laboratory, Agricultural Research Service, USDA, Beltsville, MD M. A. Faust ABS Global,

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD National Association.

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

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

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

WiggansBritish Cattle Conference 2015 (1) Dr. George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville,

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.

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

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

Cooper, 2014CDCB Meeting Aug. 5(1) T.A. Cooper, G.R. Wiggans and P.M. VanRaden Animal Genomics and Improvement Laboratory, Agricultural Research Service,

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2008 G.R. WiggansDHI-Provo.

John B. Cole, Ph.D. Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD, USA The U.S. genetic.

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2009 G.R. WiggansGenomics:

T. A. Cooper and G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Council.

Adjustment of selection index coefficients and polygenic variance to improve regressions and reliability of genomic evaluations P. M. VanRaden, J. R. Wright*,

2007 Melvin Tooker Animal Improvement Programs Laboratory USDA Agricultural Research Service, Beltsville, MD, USA

G.R. Wiggans 1, T.S. Sonstegard 1, P.M. VanRaden 1, L.K. Matukumalli 1,2, R.D. Schnabel 3, J.F. Taylor 3, F.S. Schenkel 4, and C.P. Van Tassell 1 1 Agricultural.

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2009 G.R. WiggansCouncil.

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

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

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

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.

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2008 AIPL Centennial.

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

WiggansARS Big Data Computing Workshop (1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville,

George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Select Sires’

April 2010 (1) Prediction of Breed Composition & Multibreed Genomic Evaluations K. M. Olson and P. M. VanRaden.

Council on Dairy Cattle Breeding April 27, 2010 Interpretation of genomic breeding values from a unified, one-step national evaluation Research project.

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,

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.

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

Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD NDHIA Board – 2009 (1)

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.

Multibreed Genomic Evaluation Using Purebred Dairy Cattle K. M. Olson* 1 and P. M. VanRaden 2 1 Department of Dairy Science Virginia Polytechnic and State.

2002 George R. Wiggans and Curt P. Van Tassell Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

G.R. Wiggans* 1, P.M. VanRaden 1, L.R. Bacheller 1, F.A. Ross, Jr. 1, M.E. Tooker 1, J.L. Hutchison 1, T.S. Sonstegard 2, and C.P. Van Tassell 1,2 1 Animal.

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,* 1 P.M. VanRaden, 1 T.A. Cooper, 1 C.P. Van Tassell, 2 T. Sonstegard, 2 and B. Simpson 3 1 Animal Improvement Programs and 2 Bovine Functional.

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

2006 GEORGE R. WIGGANS Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, Maryland ,

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,

C.P. Van Tassell 1, * G.R. Wiggans 1, J.C. Philpot 1, and I. Misztal Animal Improvement Programs Laboratory Agricultural Research Service, USDA,

Multibreed Genomic Evaluations in Purebred Dairy Cattle K. M. Olson 1 and P. M. VanRaden 2 1 National Association of Animal Breeders 2 AIPL, ARS, USDA.

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

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2011 National Breeders.

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

G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 2011 G.R. Wiggans DNA.

US genomic evaluation system

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

T. A. Cooper Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD NAAB meeting April 2010.

My vision for dairy genomics

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

Genomic Selection in Dairy Cattle

Use of a threshold animal model to estimate calving ease and stillbirth (co)variance components for US Holsteins.

Increased reliability of genetic evaluations for dairy cattle in the United States from use of genomic information Abstr.

Presentation transcript:

Wiggans, 2014CDCB meeting – August 5 (1) G.R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD Immediate evaluations and new chips

Wiggans, 2014CDCB meeting – August 5 (2) Immediate evaluation proposal l Proposal to be presented to Board of Council on Dairy Cattle Breeding l Input solicited from Research Advisory Working Group and Nominators

Wiggans, 2014CDCB meeting – August 5 (3) Efforts in other countries l Weekly evaluations in the Netherlands l Daily evaluations in Germany of animals with 50K genotypes (No imputation required)

Wiggans, 2014CDCB meeting – August 5 (4) Immediate evaluation details l Released to nominator at 8 am on the Tuesday after genotype is loaded or becomes usable l Contains pedigree, genomic evaluation, parent average, and imputed recessive codes l Approximations for additional fields possible

Wiggans, 2014CDCB meeting – August 5 (5) Genotypes submitted (June 2014) SunMonTueWedThuFriSat

Wiggans, 2014CDCB meeting – August 5 (6) Characteristics l Quick access to evaluations for early decision on which calves to raise l Quick turnaround possible because no reliability calculated l Selection-index combination step approximated with fixed weights

Wiggans, 2014CDCB meeting – August 5 (7) Comparison with official evaluation l High correlation (.995) with following month’s official evaluation l Reasons for differences w Approximate selection index combination w New estimates of SNP effects w Changes in imputed genotypes w Pedigree changes (e.g., adding maternal grandsire)

Wiggans, 2014CDCB meeting – August 5 (8) Immediate-evaluation summary l Quick turnaround l Highly accurate prediction of official monthly evaluation l Distribution to nominator, DRPC, and Breed association l Enables early decisions on which calves to raise l Recommended by RAWG, Awaits board action

Wiggans, 2014CDCB meeting – August 5 (9) Genotype chips Chip NameNo. of SNPChip NameNo. of SNP 50K54,001GHD77,068 50K V254,609GP219,809 3K2,900ZLD11,410 HD777,962ZMD56,955 Affy648,875ELD9,072 LD6,909LD26,912 GGP8,762GP326,151

Wiggans, 2014CDCB meeting – August 5 (10) Revised low-density chip (July 2014) l GeneSeek Genomic Profiler, version 3 (GP3) w 26,151 SNPs (19,808 for GP2) w 13,218 SNPs used for evaluation (8,422 for GP2) l Improved imputation accuracy especially when: w Missing pedigree w Nongenotyped ancestors l Chip 14 in formats 38 and 105 (August 2014)

Wiggans, 2014CDCB meeting – August 5 (11) Low-cost chip (in development) l ~ 5,000 SNPs l Built-in validation l Single-gene tests l Lower imputation accuracy if neither parent genotyped l Imputation accuracy within 1% of LD chip if at least 1 parent genotyped

Wiggans, 2014CDCB meeting – August 5 (12) New GHD version (in development) l 120–150K SNPs l Include 16,248 among the 60,671 SNPs currently used that are not on the GHD l Research underway to determine if adding SNPs with a low to moderate minor allele frequency (MAF) improves accuracy of genomic evaluations

Wiggans, 2014CDCB meeting – August 5 (13) Chip summary l New versions of chips frequently released w Allows adding SNP for newly discovered causative genetic variants w Improved accuracy from better SNP l New chips Improve value w Lower cost, or w More SNP, same cost

Wiggans, 2014CDCB meeting – August 5 (14) Questions? Holstein and Jersey crossbreds graze on American Farm Land Trust’s Cove Mountain Farm in south-central Pennsylvania Source: ARS Image Gallery, image #K ; photo by Bob Nichols