1. Curt Van Tassell Bovine Functional Genomics Laboratory Agricultural Research Service, USDA Beltsville, MD curtvt@ars.usda.gov Applied Genomics for Sustainable Livestock Breeding (1) The use of SNP chips for selection of dairy cattle

2. Applied Genomics for Sustainable Livestock Breeding (2) A Little History… 1908 1936 1989 1997 2009 USDA organizes a national milk-recording program based on success in Michigan The first national sire evaluations are calculated from daughter-dam comparisons Animal model evaluations use the relationships among all cows and bulls InterBULL evaluations introduced to incorporate foreign daughter information First official genetic evaluations incorporating genomic data

3. Applied Genomics for Sustainable Livestock Breeding (3) History of genomic evaluations Oct. 2007BovineSNP50 BeadChip available Apr. 2008First unofficial evaluation released Jan. 2009Genomic evaluations official for Holstein and Jersey Aug. 2009Official for Brown Swiss Sept. 2010Unofficial evaluations from 3K chip released Dec. 20103K genomic evaluations official

4. Applied Genomics for Sustainable Livestock Breeding (4) Genome Selection l “Train” system using phenotypic and genotypic data w Large regression system l Predict genetic merit at birth by combining pedigree merit and merit predicted from SNP l Final genetic predictions are transparent to technology

5. Applied Genomics for Sustainable Livestock Breeding (5) Genomic Prediction

6. Applied Genomics for Sustainable Livestock Breeding (6) What’s a SNP genotype worth? l Pedigree information ~7 daughters l SNP information ~34 daughters for protein yield (h2 = 0,30) l SNP information ~ 31 daugthers for fertility (h2 = 0,04)

7. Applied Genomics for Sustainable Livestock Breeding (7) Reliability Gain1 by Breed TraitHOJEBS Net merit2393 Milk23110 Fat33155 Protein2241 Fat %434110 Protein %34295 1 Gain above parent average reliability ~35% Yield traits and NM$ of young bulls

8. Applied Genomics for Sustainable Livestock Breeding (8) Genotyped Holsteins Date All animals BullsCows Bulls Heifers 04-10 9,770 7,415 16,007 8,63041,822 08-1010,430 9,37218,65211,02149,475 09-1010,611 9,45319,38913,33352,786 10-1010,616 9,78720,18415,28855,877 11-1010,61910,17520,83617,09558,727 12-1011,29312,82521,16118,33663,615 01-1111,19413,58222,56722,99970,342 02-1111,19613,93523,33026,27074,731 03-1111,71314,38224,50529,92980,529 04-1112,15211,22425,20236,54585,123 Traditional evaluation No traditional evaluation

9. Applied Genomics for Sustainable Livestock Breeding (9) Training Bulls

10. Applied Genomics for Sustainable Livestock Breeding (10) 50K Genotypes

11. Applied Genomics for Sustainable Livestock Breeding (11) 3K Genotypes

12. Applied Genomics for Sustainable Livestock Breeding (12) April Genotypes – Holstein 0 500 1000 1500 2000 1998-200620072008200920102011 Birth year Number of Genotypes 3K Females3K Males50K Females50K Males

13. Applied Genomics for Sustainable Livestock Breeding (13) Holstein Bulls 0 1000 2000 3000 4000 5000 6000 7000 8000 9000 10000 200020012002200320042005200620072008200920102011 Birth Year Number of Bulls Total10 HerdsGenotypedBoth

14. Applied Genomics for Sustainable Livestock Breeding (14) Reliabilities for young animals* *Animals with no traditional PTA in March 2011

15. Applied Genomics for Sustainable Livestock Breeding (15) Determination of Reliability l Sum of genomic relationships with the predictor animals weighted by reliability l Call rate l Expected imputation error rate l Reliability of parent average w Larger impact if dam not genotyped

16. Applied Genomics for Sustainable Livestock Breeding (16) Use of genomic evaluations l Determine which young bulls to bring into AI service l Use to select mating sires l Pick bull dams l Market semen from 2-year-old bulls

17. Applied Genomics for Sustainable Livestock Breeding (17) Use of 3K genomic evaluations l Sort heifers for breeding w Flush w Sexed semen w Beef bull l Confirm parentage to avoid inbreeding l Predict inbreeding depression better l Precision mating considering genomics (future)

18. Applied Genomics for Sustainable Livestock Breeding (18) Results

19. Applied Genomics for Sustainable Livestock Breeding (19) 2009 Genomic Milk

20. Applied Genomics for Sustainable Livestock Breeding (20) 2009 Traditional Milk

21. Applied Genomics for Sustainable Livestock Breeding (21) Response to Selection - Milk

22. Applied Genomics for Sustainable Livestock Breeding (22) Response to Selection - Milk

23. Applied Genomics for Sustainable Livestock Breeding (23) Response to Selection – SCS

24. Applied Genomics for Sustainable Livestock Breeding (24) Response to Selection – SCS

25. Applied Genomics for Sustainable Livestock Breeding (25) Future

26. Applied Genomics for Sustainable Livestock Breeding (26) Increase in accuracy l Genotyped bulls get traditional evaluation when 5 years old l Possible genotyping of 10,000 bulls with semen in CDDR l Collaboration with more countries l Use of more SNP from HD chips l Full sequencing

27. Applied Genomics for Sustainable Livestock Breeding (27) Application to more traits l Animal’s genotype is good for all traits l Traditional evaluations required for accurate estimates of SNP effects l Traditional evaluations not currently available for heat tolerance or feed efficiency l Research populations could provide data for traits that are expensive to measure l Will resulting evaluations work in target population?

28. Applied Genomics for Sustainable Livestock Breeding (28) High density (HD) genotypes l Illumina Bovine HD BeadChip available w 777,962 SNP w Collaborations with GBR, ITA, & CAN to provide genotypes w Over 400 genotypes from research projects in database l Affymetrics HD w 648,855 SNP w Optimized for genetic coverage w NAAB negotiating plan for use

29. Applied Genomics for Sustainable Livestock Breeding (29) Use of HD l Some increase in accuracy from better tracking of QTL l Potential for across breed evaluations l Requires few new HD genotypes once adequate base for imputation developed l Imputation improvements were particularly beneficial in imputing HD

30. Applied Genomics for Sustainable Livestock Breeding (30) Low-Plex Genotyping l Need cost-effective genotyping platform for application to commercial cows w <$5 / animal l Applications: w Parentage, traceability w Relatedness w Targetted panels

31. Applied Genomics for Sustainable Livestock Breeding (31) Genome Sequencing? l Whole-genome sequences on individuals will be available in the next few years w How will we store and use those data? l Not feasible to calculate effects for 3,000,000,000 nucleotides or even 3,000,000 SNP l May be best to fine map then target genotype…

32. Applied Genomics for Sustainable Livestock Breeding (32) Exome Sequencing? l Capture and sequence coding part of genome and regulatory regions ~50-60 Mb l Higher likelihood of functional SNPs l Less data than complete sequence l Soon price difference irrelevant?

33. Applied Genomics for Sustainable Livestock Breeding (33) Summary l Extraordinarily rapid implementation of genomic evaluations l Young-bull acquisition and marketing now based on genomic evaluations l Genotyping of many females because of 3K chip

34. Applied Genomics for Sustainable Livestock Breeding (34)