G.R. Wiggans Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD Georgetown Ag Systems (1) G.R. Wiggans, 2010 Animal Biotechnology

G.R. Wiggans, 2010 Georgetown Ag Systems (2) Application of biotechnology l Identify superior animals early l Increase rate of genetic improvement l Detect abnormalities l Improve understanding of mechanisms of genetic control l Determine parentage

G.R. Wiggans, 2010 Georgetown Ag Systems (3) Applications in genetic improvement l Find easily detected genetic differences among animals l Develop SNP (single nucleotide polymorphism) panels to detect those differences l Relate SNP differences to productivity differences l Rank animals on their economic merit l Use best animals as parents of the next generation

G.R. Wiggans, 2010 Georgetown Ag Systems (4) 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 an organism’s genome as a whole rather than 1 gene at a time l Livestock and poultry genomes sequenced to understand how various genes function (functional genomics)

G.R. Wiggans, 2010 Georgetown Ag Systems (5) Bovine genome sequence

G.R. Wiggans, 2010 Georgetown Ag Systems (6) Federal support for genomics l Cattle l Sheep l Swine l Poultry l Horses l Aquaculture (fish and other water animals)

G.R. Wiggans, 2010 Georgetown Ag Systems (7) 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 obtained (even before birth) l Best animals to be parents can be determined earlier and more accurately

G.R. Wiggans, 2010 Georgetown Ag Systems (8) Dairy cattle selection before genomics l Slow! w Progeny testing for production traits takes 3 – 4 years from insemination w Bull will be at least 5 years old before first evaluation is available l Expensive! w Progeny testing costs $25,000 – 50,000/bull w Only 1 in 8 – 10 bulls graduate from progeny test w At least $200,000 invested in each active bull

G.R. Wiggans, 2010 Georgetown Ag Systems (9) Background: Genetic markers l 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 Markers not required to be part of a gene

G.R. Wiggans, 2010 Georgetown Ag Systems (10) Genetic markers l Allow inheritance to be followed in a region across generations l SNPs are the markers of choice l Need lots – 3 million in the genome!

G.R. Wiggans, 2010 Georgetown Ag Systems (11) Cattle SNP collaboration – iBMAC l Develop 60,000-bead Illumina iSelect assay w Agricultural Research Service, USDA − Beltsville Agricultural Research Center Bovine Functional Genomics Lab. Animal Improvement Programs Lab. − Meat Animal Research Center w University of Missouri w University of Alberta l Starting 60,800 beads – 54,000 usable SNPs

G.R. Wiggans, 2010 Georgetown Ag Systems (12)

G.R. Wiggans, 2010 Georgetown Ag Systems (13) Illumina  Marylinn Munson  Cindy Lawley  Christian Haudenschild BARC w Curt Van Tassell w Lakshmi Matukumalli w Tad Sonstegard Missouri w Jerry Taylor w Bob Schnabel  Stephanie McKay Alberta w Steve Moore USMARC – Clay Center w Tim Smith w Mark Allan 13 l USDA/NRI/CSREES w w w l USDA/ARS w D w D w D l Merial w Stewart Bauck l NAAB w Gordon Doak w ABS Global w Accelerated Genetics w Alta Genetics w CRI/Genex w Select Sires w Semex Alliance w Taurus Service iBMAC ConsortiumFunding agencies Participants

G.R. Wiggans, 2010 Georgetown Ag Systems (14) Genomic evaluation – US dairy cattle l Cooperating organizations w Breed associations (Holstein, Jersey, Brown Swiss) w Artificial-insemination organizations − Own bulls − Collect and market semen l Full sharing of genotypes and research with Canada l Trading of genotypes with Switzerland, Germany and Austria – expect to share with more countries l Over 60,000 animals genotyped starting in 2008

G.R. Wiggans, 2010 Georgetown Ag Systems (15) Getting DNA samples l Animals selected w Artificial-insemination organizations identify male and female calves to genotype w Farmers request breed association to arrange for genotyping l Animal nominated at Animal Improvement Programs Laboratory – insures pedigree information is in database l Sample sent to genotyping laboratory w Hair follicles (most common) w Blood  Nasal swab w Semen  Ear punch

G.R. Wiggans, 2010 Georgetown Ag Systems (16) History of application for US dairy cattle l Dec. 2007BovineSNP50 BeadChip available l Apr. 2008First unofficial evaluation released l Jan. 2009Genomic evaluations official for Holstein and Jersey l Aug. 2009Official for Brown Swiss l Sept. 2010Unofficial evaluations from 3K chip released l Dec K genomic evaluations become official

G.R. Wiggans, 2010 Georgetown Ag Systems (17) International implications l All major dairy countries investigating genomic selection l International Bull Evaluation Service (Interbull) working on how genomic evaluations should be integrated l EuroGenomics – European collaboration to share genotypes l Large number of predictor animals increases prediction accuracy l Importing countries changed rules to allow for genomically evaluated young bulls

G.R. Wiggans, 2010 Georgetown Ag Systems (18) Developed countries l 100 years of records w Phenotypes w Pedigree l Progeny testing for 50 years l Plentiful crop systems l Animals developed for temperate climate Developing countries l No records l No pedigree l Marginal production systems – tropical l No national testing systems to evaluate germplasm l No cash for investing in value-added animals Challenges of technology transfer

G.R. Wiggans, 2010 Georgetown Ag Systems (19) Priorities from Gates Foundation l Develop tools and reagents that are applicable to underdeveloped areas l Collect DNA for breeds to understand current genetic distances and admixture l Identify critical populations for preservation and selection – high density chip l Enhance local adapted breeds using combinations of crossbreeding and selection – low density chip

G.R. Wiggans, 2010 Georgetown Ag Systems (20) l Identified a set of parentage markers for testing at University of Lahore l Sequenced a native breed animal for SNP discovery in water buffalo l Lead role in Water Buffalo Genome Project (Italy) l Great training opportunity PAKUS – Water buffalo genomics

G.R. Wiggans, 2010 Georgetown Ag Systems (21) Summary l Genomics is revolutionizing animal breeding l Genomic selection used extensively in dairy cattle breeding l High quality genotypes support detection of parentage and other errors l International collaboration has been important for the success

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