1. Wiggans, 2014CDCB meeting – August 5 (1) G.R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 george.wiggans@ars.usda.gov Immediate evaluations and new chips

2. 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

3. 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)

4. 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

5. Wiggans, 2014CDCB meeting – August 5 (5) Genotypes submitted (June 2014) SunMonTueWedThuFriSat 1234 85 5 756 67 89 973 10 361 11 1417 12 449 13 1091 14 524 1516 4212 17 1706 18 5419 19 1228 2021 92 2223242526 101 27 29 28 29 6 30 36

6. 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

7. 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)

8. 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

9. 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

10. 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)

11. 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

12. 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

13. 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

14. 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 #K8587-14; photo by Bob Nichols