1. G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD *george.wiggans@ars.usda.gov G.R. WiggansAg Discovery 2010 (1) Animal Genomics

2. G.R. WiggansAg Discovery 2010 (2) Goals of animal scientists l Increase efficiency of food production l Learn how animals work l Improve resistance to disease l Improve adaptation of animal products to human needs

3. G.R. WiggansAg Discovery 2010 (3) What is genomics l Study of how the genome (DNA) of any species is organized and expressed as traits l New technologies allow examination of the genome of an organism as a whole, rather than one gene at a time l Livestock and poultry genomes sequenced to understand how various genes function (functional genomics)

4. G.R. WiggansAg Discovery 2010 (4) Federal support for genomics in l Cattle l Sheep l Swine l Poultry l Horses l Aquaculture (fish and other water animal)

5. G.R. WiggansAg Discovery 2010 (5) How do we use genomics l Identify DNA sequences associated with disease resistance and production traits. l Animals can be evaluated as soon as DNA can be taken (even before birth) l Best animals to be parents can be determined earlier and more accurately

6. G.R. WiggansAg Discovery 2010 (6) Dairy cattle selection before l Slow! w Progeny testing for production traits takes 3 to 4 years from insemination w A bull will be at least 5 years old before his first evaluation is available l Expensive! w Progeny testing costs $25,000 - $50,000 per bull w Only 1 in 8 to 10 bulls graduate from progeny test w At least $200,000 invested in each active bull!!

7. G.R. WiggansAg Discovery 2010 (7) Bovine Genome Sequence

8. G.R. WiggansAg Discovery 2010 (8) Background: Genetic Markers l A segment of DNA at a unique physical location in the genome that varies sufficiently between individuals that its inheritance can be tracked through families. l A marker is not required to be part of a gene.

9. G.R. WiggansAg Discovery 2010 (9) Genetic Markers l Allow inheritance to be followed in a region across generations l Single nucleotide polymorphisms (SNP) are the markers of choice l Need lots! w 3 million in the genome

10. G.R. WiggansAg Discovery 2010 (10) Cattle SNP Collaboration - iBMAC l Develop 60,000 Bead Illumina iSelect® assay w USDA-ARS Beltsville Agricultural Research Center: Bovine Functional Genomics Laboratory and Animal Improvement Programs Laboratory w University of Missouri w University of Alberta w USDA-ARS US Meat Animal Research Center l Starting 60,800 beads – 54,000 useable SNP

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12. G.R. WiggansAg Discovery 2010 (12) Participants  Illumina  Marylinn Munson  Cindy Lawley  Christian Haudenschild  BARC  Curt Van Tassell  Lakshmi Matukumalli  Tad Sonstegard  Missouri  Jerry Taylor  Bob Schnabel  Stephanie McKay  Alberta  Steve Moore  USMARC – Clay Center  Tim Smith  Mark Allan 12  USDA/NRI/CSREES  2006-35616-16697  2006-35205-16888  2006-35205-16701  USDA/ARS  1265-31000-081D  1265-31000-090D  5438-31000-073D  Merial  Stewart Bauck  NAAB  Godon Doak  ABS Global  Accelerated Genetics  Alta Genetics  CRI/Genex  Select Sires  Semex Alliance  Taurus Service iBMAC Consortium Funding Agencies

13. G.R. WiggansAg Discovery 2010 (13) Genomic evaluation - dairy cattle l Cooperating organizations w Breed associations Holstein Jersey Brown Swiss w Bull studs − Own bulls − Collect and market semen l Full sharing of genotypes and research with Canada l Trading of genotypes with Switzerland w Expect to share with more countries l Over 50,000 animals genotyped starting in 2008

14. G.R. WiggansAg Discovery 2010 (14) How is it done? l Animals selected w Studs identify male and female calves to genotype w Farmers request breed association to arrange for genotyping l Animal nominated at AIPL – insures that pedigree information is in database l Sample sent to lab w Hair follicles (most common) w Blood w Semen w Nasal swab

15. G.R. WiggansAg Discovery 2010 (15) Lab work l Extract DNA l Incorporate DNA into reagents on chip (3 days) l Laser scanner collects intensity data l GenomeStudio software assigns genotype after clustering intensities

16. G.R. WiggansAg Discovery 2010 (16) What is done at AIPL l Genotypes checked w Sex w Breed w Parents w Duplicate of another animal w ≥90% of SNP genotyped l Requesters notified of conflicts w For parent conflicts, alternative parents usually suggested l Parentage and sample ID Corrected l Genotypes extracted l Genotypes for >2000 dams figured out from their progeny (imputation)

17. G.R. WiggansAg Discovery 2010 (17) Traits evaluated Milk yield Fat in milk Protein in milk Resistance to udder infection Fertility Length of productive life Difficulty having a calf Likelihood of calf being alive 2 days after birth 18 traits describing the cows appearance such as stature

18. G.R. WiggansAg Discovery 2010 (18) Genotyped Holsteins Date Young animals** All animals Bulls*Cows* Bulls Heifers 04-097,600 2,711 9,690 1,94321,944 01-108,974 4,348 14,061 6,03133,414 02-109,378 5,086 15,328 7,62037,412 04-109,770 7,415 16,007 8,63041,822 05-109,958 7,940 16,594 9,77244,264 06-109,958 8,122 17,507 10,71346,300 07-109,963 8,186 18,187 11,30947,645 *Traditional evaluation **No traditional evaluation

19. G.R. WiggansAg Discovery 2010 (19) Summary l Genomics is revolutionizing animal breeding l Genomic selection is used extensively in dairy cattle breeding l High quality genotypes support detection of parentage and other errors l International collaboration has been important to the success

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