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.

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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. Tooker 1, and H.D. Norman 2 1 Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD Council on Dairy Cattle Breeding, Reynoldsburg, OH Calculation and delivery of US genomic evaluations for dairy cattle Abstr. 152

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (2) New laboratory l Animal Improvement Programs Laboratory (AIPL) and Bovine Functional Genomics Laboratory (BFGL) were merged to form Animal Genomics and Improvement Laboratory (AGIL) l Animal Improvement Program (AIP) is one of 4 AGIL projects and continues in the same location with the same staff and some increase in funding l Dr. Erin Connor is AGIL Research Leader

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (3) AGIL sequencing collaborators l George Liu l Steve Schroeder l Tad Sonstegard l Curt Van Tassell

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (4) Collaboration with industry l Council on Dairy Cattle Breeding (CDCB) responsible for receiving data and for computing and delivering US genetic evaluations for dairy cattle l AIP responsible for research and development to improve the evaluation system l CDCB and AIP employees co-located in Beltsville Dr. João Dürr is CDCB CEO

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (5) Council on Dairy Cattle Breeding l 3 board members from each organization l Total of 12 voting members l 2 nonvoting industry members CDCB PDCANAABDRPCDHI Purebred Dairy Cattle Association National Association of Animal Breeders Dairy Records Processing Centers Dairy Herd Information

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (6) Funding l CDCB evaluation calculation and dissemination funded by fee system w Based on animals genotyped w 87% of revenue from bulls w Higher fees for herds that contribute less information l AIP research and development funded by U.S. Federal Government $

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (7) Accomplishments (last 12 mo) l Introduction of imputed indicators for inherited defects of dairy cattle l Introduction of genomic evaluations for Ayrshires l Discovery of additional haplotypes that affect fertility l Improved accuracy of genomic evaluations by an increase to 60,671 DNA markers l Improved weighting of cow evaluations l Multitrait traditional evaluations for heifer and cow conception rates

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (8) Gene tests (imputed and actual) l Bovine leucocyte adhesion deficiency (BLAD) l Complex vertebral malformation (CVM) l Deficiency of uridine monophosphate synthase (DUMPS) l Syndactyly (mulefoot) l Weaver Syndrome, spinal dismyelination (SDM), spinal muscular atrophy (SMA) l Red coat color l Polledness

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (9) New fertility haplotype for Jerseys (JH2) l Chromosome 26 at 8.8–9.4 Mbp l Carrier frequency w 14–28% in decades before 1990 w Only 2.6% now l Estimated effect on conception rate of –4.0% ± 1.5% l Additional sequencing needed to find causative genetic variant

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (10) Research projects l Discovery of causative genetic variants l Accounting for genomic pre-selection l Net merit update l Grazing index l Genomic mating program l Contribution of predictor population subsets l Preliminary evaluations when genotypes loaded

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (11) Genotypes received since July 2013 BreedFemaleMale All animals % female Ayrshire 1, ,58886 Brown Swiss*8926,2537,14512 Holstein172,95631,657204,61385 Jersey**26,4344,80431,23885 All201,64142,943244,58482 *Includes >5,000 bulls added from Interbull in June 2014 **Includes 1,068 Danish bulls added in November 2013

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (12) Growth in bull predictor population BreedMay mo gain Ayrshire Brown Swiss5, Holstein25,2762,361 Jersey4,2621,391

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (13) Reliability gains Reliability (%)Ayrshire Brown SwissJerseyHolstein Genomic Parent average2830 Gain Reference bulls 6805,767 4,207 24,547 Animals genotyped1,7889,01659,923469,960 Exchange partnersCanadaCanada, Interbull Canada, Denmark Canada, Italy, UK SOURCE: VanRaden, Advancing Dairy Cattle Genetics: Genomics and Beyond presentation, Feb. 2014

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (14) Parent ages for marketed Holstein bulls

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (15) Genetic merit of marketed Holstein bulls Average gain: $19.77/year Average gain: $52.00/year Average gain: $85.60/year

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (16) Conclusions l Genomic evaluation has dramatically changed dairy cattle breeding l Rate of gain has increased primarily because of large reduction in generation interval l Genomic research is ongoing w Detect causative genetic variants w Find more haplotypes that affect fertility w Improve accuracy

Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (17) 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