1. 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 Genomics Laboratories, Agricultural Research Service, USDA, Beltsville, MD 3 Gene Seek, Lincoln, NE george.wiggans@ars.usda.gov 2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (1)Wiggans Characteristics and use of the Illumina BovineLD BeadChip (abstr. 450) Courtesy of Illumina, Inc.

2. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (2) Low-density array background l Illumina BovineLD BeadChip (6,909 SNP) replaced Bovine3K BeadChip l BovineLD chip includes add-on capability to allow array customization up to 80,000 SNP l GeneSeek Genomic Profiler (GGP) with 8,654 SNP and single-gene tests developed from BovineLD chip

3. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (3) Low-density array design goals l Higher SNP density at chromosome ends to aid imputation l High minor allele frequency l Adequate overlap with Bovine3K chip l Focus on dairy, but useful for beef l Use Infinium chemistry for improved reliability

4. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (4) Additional SNP on GGP l Single-gene tests l Increased overlap with Bovine3K chip l Imputation of microsatellite alleles l Elimination of large gaps between SNP

5. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (5) Distribution of SNP by chromosome SNP groupBovineLDGGP Autosome6,6518,291 X pseudoautosomal region17 X-specific219268 Y919 Mitochondrial13 New—46 Duplicates—108 All SNP6,9098,762

6. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (6) SNP overlap with other Illumina arrays BeadChipBovineLDGGP BovineSNP50 v26,8548,029 Bovine3K2,1592,677 BovineHD unique17486 All Illumina arrays6,9098,608 Used in genetic evaluation 6,8368,031

7. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (7) Low-density genotypes received

8. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (8) Breakdown by genotyping chip

9. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (9) Minor allele frequencies (MAF)

10. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (10) SNP call rates

11. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (11) Call rates for Y SNP in common – /

12. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (12) SNP parent-progeny conflicts

13. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (13) Imputation accuracy (%) BreedBovine3KBovineLDGGP Holstein 95.9 98.999.2 Jersey 94.6 98.398.9 Brown Swiss 93.9 97.9—

14. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (14) Reliability (%) for Holsteins <2 yr old MaleBovine3K1,77233.168.2 BovineLD74030.272.4 GGP1,73626.071.6 BovineSNP5021,00930.174.3 Animal sex Genotype Animals (no.)Parent AvgGenomic FemaleBovine3K23,95230.268.3 BovineLD32,93926.070.6 GGP10,66227.871.7 BovineSNP5013,98730.374.4

15. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (15) GGP-80K l Full 80K SNP added to 6,909 BovineLD SNP l SNP with largest magnitude of effect picked from BovineSNP50 and BovineHD chips l Includes single-gene tests l Expected to be available in September 2012 and to be licensed to other genotyping laboratories l Gives same 0.4 percentage-point increase in reliability as using 300K SNP from BovineHD Chip

16. Wiggans2012 ADSA-AMPA-ASAS-CSAS-WSASAS joint annual meeting (16) Conclusions l Illumina BovineLD BeadChip provides high- quality genotypes l GGP demonstrates the value of the add-on capability of the BovineLD chip l GGP-80K with gene tests and more informative SNP could replace BovineSNP50 BeadChip