1. 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 20705-2350 2 Council on Dairy Cattle Breeding, Reynoldsburg, OH 43068 *george.wiggans@ars.usda.govgeorge.wiggans@ars.usda.gov Calculation and delivery of US genomic evaluations for dairy cattle Abstr. 152

2. 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

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

4. 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

5. 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

6. 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 $

7. 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

8. 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

9. 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

10. 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

11. Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (11) Genotypes received since July 2013 BreedFemaleMale All animals % female Ayrshire 1,3592291,58886 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

12. Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (12) Growth in bull predictor population BreedMay 201412-mo gain Ayrshire 67830 Brown Swiss5,862366 Holstein25,2762,361 Jersey4,2621,391

13. Wiggans, 2014ASAS-ADSA-CSAS Joint Annual Meeting (13) Reliability gains Reliability (%)Ayrshire Brown SwissJerseyHolstein Genomic37546170 Parent average2830 Gain 9243140 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

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

15. 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

16. 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

17. 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 #K8587-14; photo by Bob Nichols