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Animal Biotechnology

Animal Biotechnology . Application of biotechnology. Identify superior animals early Increase rate of genetic improvement Detect abnormalities Improve understanding of mechanisms of genetic control Determine parentage. Applications in genetic improvement.

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Animal Biotechnology

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  1. Animal Biotechnology

  2. Application of biotechnology • Identify superior animals early • Increase rate of genetic improvement • Detect abnormalities • Improve understanding of mechanisms of genetic control • Determine parentage

  3. Applications in genetic improvement • Find easily detected genetic differences among animals • Develop SNP (single nucleotide polymorphism) panels to detect those differences • Relate SNP differences to productivity differences • Rank animals on their economic merit • Use best animals as parents of the next generation

  4. What is genomics? • Study of how the genome (DNA) of any species is organized and expressed as traits • New technologies allow examination of an organism’s genome as a whole rather than 1 gene at a time • Livestock and poultry genomes sequenced to understand how various genes function (functional genomics)

  5. Bovine genome sequence

  6. Federal support for genomics • Cattle • Sheep • Swine • Poultry • Horses • Aquaculture (fish and other water animals)

  7. How do we use genomics? • Identify DNA sequences associated with disease resistance and production traits • Animals can be evaluated as soon as DNA can be obtained (even before birth) • Best animals to be parents can be determined earlier and more accurately

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

  9. Background: Genetic markers • Segment of DNA at a unique physical location in the genome that varies sufficiently between individuals that its inheritance can be tracked through families • Markers not required to be part of a gene

  10. Genetic markers • Allow inheritance to be followed in a region across generations • SNPs are the markers of choice • Need lots – 3 million in the genome!

  11. Cattle SNP collaboration – iBMAC • Develop 60,000-bead Illumina iSelect assay • Agricultural Research Service, USDA • Beltsville Agricultural Research Center • Bovine Functional Genomics Lab. • Animal Improvement Programs Lab. • Meat Animal Research Center • University of Missouri • University of Alberta • Starting 60,800 beads – 54,000 usable SNPs

  12. Illumina Marylinn Munson Cindy Lawley Christian Haudenschild BARC Curt Van Tassell LakshmiMatukumalli Tad Sonstegard Missouri Jerry Taylor Bob Schnabel Stephanie McKay Alberta Steve Moore USMARC – Clay Center Tim Smith Mark Allan Participants iBMAC Consortium Funding agencies • 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 • Gordon Doak • ABS Global • Accelerated Genetics • Alta Genetics • CRI/Genex • Select Sires • Semex Alliance • Taurus Service 13

  13. Genomic evaluation – US dairy cattle • Cooperating organizations • Breed associations (Holstein, Jersey, Brown Swiss) • Artificial-insemination organizations • Own bulls • Collect and market semen • Full sharing of genotypes and research with Canada • Trading of genotypes with Switzerland, Germany and Austria – expect to share with more countries • Over 60,000 animals genotyped starting in 2008

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

  15. History of application for US dairy cattle • Dec. 2007 BovineSNP50 BeadChip available • Apr. 2008 First unofficial evaluation released • Jan. 2009 Genomic evaluations official for Holstein and Jersey • Aug. 2009 Official for Brown Swiss • Sept. 2010 Unofficial evaluations from 3K chip released • Dec. 2010 3K genomic evaluations become official

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

  17. Developed countries 100 years of records Phenotypes Pedigree Progeny testing for 50 years Plentiful crop systems Animals developed for temperate climate Developing countries No records No pedigree Marginal production systems – tropical No national testing systems to evaluate germplasm No cash for investing in value-added animals Challenges of technology transfer

  18. Priorities from Gates Foundation Develop tools and reagents that are applicable to underdeveloped areas Collect DNA for breeds to understand current genetic distances and admixture Identify critical populations for preservation and selection – high density chip Enhance local adapted breeds using combinations of crossbreeding and selection – low density chip

  19. Identified a set of parentage markers for testing at University of Lahore Sequenced a native breed animal for SNP discovery in water buffalo Lead role in Water Buffalo Genome Project (Italy) Great training opportunity PAKUS – Water buffalo genomics

  20. Summary • Genomics is revolutionizing animal breeding • Genomic selection used extensively in dairy cattle breeding • High quality genotypes support detection of parentage and other errors • International collaboration has been important for the success

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