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

Slides:

Advertisements

Similar presentations

2007 Paul VanRaden, Mel Tooker, and Nicolas Gengler Animal Improvement Programs Lab, Beltsville, MD, USA, and Gembloux Agricultural U., Belgium

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.

2002 Paul M. VanRaden and Ashley H. Sanders Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD

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

Wiggans, 2014CDCB meeting – August 5 (1) G.R. Wiggans 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’

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

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.

2005 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD AIPL Projects.

J. B. Cole 1, P. D. Miller 2, and H. D. Norman 1 1 Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD 2 Department.

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

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

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.

2007 J. B. Cole 1,*, P. M. VanRaden 1, J. R. O'Connell 3, C. P. Van Tassell 1,2, T. S. Sonstegard 2, R. D. Schnabel 4, J. F. Taylor 4, and G. R. Wiggans.

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

WiggansANSC UMD(1) 2013 George R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD , USA

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 ,

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.

Norway (1) 2005 Status of Dairy Cattle Breeding in the United States Dr. H. Duane Norman Animal Improvement Programs Laboratory Agricultural Research Service,

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

Bovine Genomics The Technology and its Applications Gerrit Kistemaker Chief Geneticist, Canadian Dairy Network (CDN) Many slides were created by.

2006 Paul VanRaden Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA Fertility Trait.

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

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

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

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

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

2007 J.B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Overview.

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

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

2003 Melvin Tooker, Paul VanRaden, Ashley Sanders, and George Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville,

Paul VanRaden and Melvin Tooker* Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD 2006.

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

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.

7 th World Congr. Genet. Appl. Livest. Prod Selection of dairy cattle for lifetime profit Paul M. VanRaden Animal Improvement Programs Laboratory.

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

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

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’

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

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

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.

2005 Paul VanRaden and Mel Tooker Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Genetic.

2006 Paul VanRaden Animal Improvement Programs Laboratory Agricultural Research Service, USDA, Beltsville, MD Predicting Genetic.

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

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

2001 ADSA Indianapolis 2001 (1) Heterosis and Breed Differences for Yield and Somatic Cell Scores of US Dairy Cattle in the 1990’s. PAUL VANRADEN Animal.

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

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.

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

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

CRI – Spanish update (1) 2010 Status of Dairy Cattle Breeding in the United States Dr. H. Duane Norman Animal Improvement Programs Laboratory Agricultural.

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

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.

John B. Cole Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 2016 AGIL Report.

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

My vision for dairy genomics

2017 AGIL-AIP Update John B. Cole

Y. Masuda1, I. Misztal1, P. M. VanRaden2, and T. J. Lawlor3

Where AIPL Fits In Agricultural Research Service (ARS) is the main research arm of USDA (8,000 employees with 2,000 scientists at >100 locations) Beltsville.

Presentation transcript:

WiggansCDCB industry meeting – Sept. 29, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD AGIL Technical Report Animal Improvement Program (AIP) Project

WiggansCDCB industry meeting – Sept. 29, 2015 (2) AIP objectives l Expand national and international collection of phenotypic and genotypic data l Develop a more accurate genomic evaluation system with advanced, efficient methods to combine pedigrees, genotypes, and phenotypes l Use economic analysis to maximize genetic progress and financial benefits from collected data

WiggansCDCB industry meeting – Sept. 29, 2015 (3) AIP scientists l Paul VanRaden (project leader) w Genomic evaluation methods, haplotypes l George Wiggans (CDCB liaison) w SNP selection, genotype exchange, goats l John Cole w Fertility, health, heat stress resistance, indexes l Derek Bickhart w Sequence data analysis, genome assembly correction and gene annotation l Kristen Parker Gaddis (UFL postdoctoral associate) w Fertility, health, use of sequence data, data-mining

WiggansCDCB industry meeting – Sept. 29, 2015 (4) Primary traits evaluated l Yield (milk, fat, and protein) l Longevity (productive life) l Fertility (conception and pregnancy rates) l Calving (calving ease and stillbirth) l Health (somatic cell score) l Conformation

WiggansCDCB industry meeting – Sept. 29, 2015 (5) Changes during past year l New software for traditional PTAs w Replaced programs used since 1989 w Multitrait evaluation w Changed input data for pregnancy rate l Base change for all traits l Net merit revision with more traits l Weekly instead of monthly genomic evaluation l Added 140K chip

WiggansCDCB industry meeting – Sept. 29, 2015 (6) In the pipeline or recently implemented l Genomic evaluations for Guernseys l Breed composition and GPTAs for crossbreds l Increase to 77,531 SNPs used for evaluations (includes 30 gene tests provided by GeneSeek) l New GeneSeek 7K chip l Goats (separate management groups for miniature and standard)

WiggansCDCB industry meeting – Sept. 29, 2015 (7) Research areas l Develop applications for sequence data l Develop evaluations for new traits l Acquire data for additional traits l Improve evaluations

WiggansCDCB industry meeting – Sept. 29, 2015 (8) Impute to sequence l Determine variants in sequence data of most interest l Impute genotypes of bulls in predictor population to sequence l Include HD genotypes to add imputation accuracy

WiggansCDCB industry meeting – Sept. 29, 2015 (9) Sequencing to aid imputation l Cooperative project with CDDR to build haplotype library l Bulls homozygous for haplotype give highest accuracy l Selected over 200 bulls to identify rare variants needed for high accuracy imputation

WiggansCDCB industry meeting – Sept. 29, 2015 (10) Further use of sequence data l Discovery of causative genetic variants l Refinement of SNPs used in genomic evaluation w Add discovered causative variants w Use some SNPs for imputation but not for estimation of SNP effects l Create genotypes for genomic evaluation from sequence data to enable immediate use through imputation of any new SNPs

WiggansCDCB industry meeting – Sept. 29, 2015 (11) Evaluation of new traits l Mortality l Days to first breeding l Gestation length l Resistance to heat stress (predicting genotype × environment interactions) l Persistency

WiggansCDCB industry meeting – Sept. 29, 2015 (12) Additional traits requiring data l Clinical mastitis l Displaced abomasum l Ketosis l Foot health l Immune response l Other health traits l Feed efficiency l Methane production l Milk fatty acid composition from mid-infrared

WiggansCDCB industry meeting – Sept. 29, 2015 (13) Improved evaluation techniques l Avoid bias due to genomic preselection l 1-step evaluation w Include genotypes along with trait observations in a single analysis w Developments by University of Georgia enable inversion of large genomic relationship matrix

WiggansCDCB industry meeting – Sept. 29, 2015 (14) Mating programs l Genomic relationships of genotyped females with available bulls provided l Determination of best mate possible l Dominance effects could be considered

WiggansCDCB industry meeting – Sept. 29, 2015 (15) Take-home message l Ongoing research to improve genetic evaluations l Sequence data provides great opportunity to make genomic evaluations more accurate l CDCB plans to acquire data necessary for evaluating new traits

WiggansCDCB industry meeting – Sept. 29, 2015 (16) Acknowledgments l CDCB l Binational Agricultural Research and Development (BARD) l National Institute of Food and Agriculture (NIFA), USDA l Washington State University (NIFA grant)

WiggansCDCB industry meeting – Sept. 29, 2015 (17) AIP research team