Animal Biotechnology

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Animal Biotechnology
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Application of biotechnology

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

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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

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What is genomics?

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

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Bovine genome sequence
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Federal support for genomics

• Cattle
• Sheep
• Swine
• Poultry
• Horses
• Aquaculture (fish and other water animals)

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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

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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

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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

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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!

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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

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Participants
iBMAC Consortium
Funding agencies

• 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

• 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

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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

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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

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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

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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

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Challenges of technology transfer

• Developed countries

• Developing countries

• 100 years of records
• Phenotypes
• Pedigree
• Progeny testing for 50 years
• Plentiful crop systems
• Animals developed for temperate climate

• No records
• No pedigree
• Marginal production systems tropical
• No national testing systems to evaluate germplasm
• No cash for investing in value-added animals

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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

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PAKUS Water buffalo genomics

• 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

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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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