1. WiggansCDCB industry meeting – Sept. 29, 2015 (1) George R. Wiggans Animal Genomics and Improvement Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 george.wiggans@ars.usda.gov http://aipl.arsusda.gov/ AGIL Technical Report Animal Improvement Program (AIP) Project

2. 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

3. 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

4. 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

5. 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

6. 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)

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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)

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