Animal Genomics

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Animal Genomics
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Goals of animal scientists

• Increase efficiency of food production
• Learn how animals work
• Improve resistance to disease
• Improve adaptation of animal products to human
  needs

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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 the genome
  of an organism as a whole, rather than one gene
  at a time
• Livestock and poultry genomes sequenced to
  understand how various genes function (functional
  genomics)

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Federal support for genomics in

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

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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
  taken (even before birth)
• Best animals to be parents can be determined
  earlier and more accurately

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Dairy cattle selection before

• Slow!
• Progeny testing for production traits takes 3 to
  4 years from insemination
• A bull will be at least 5 years old before his
  first evaluation is available
• Expensive!
• Progeny testing costs 25,000 - 50,000 per bull
• Only 1 in 8 to 10 bulls graduate from progeny
  test
• At least 200,000 invested in each active bull!!

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Bovine Genome Sequence
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Background Genetic Markers

• 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.
• A marker is not required to be part of a gene.

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Genetic Markers

• Allow inheritance to be followed in a region
  across generations
• Single nucleotide polymorphisms (SNP) 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
• USDA-ARS Beltsville Agricultural Research Center
  Bovine Functional Genomics Laboratory and Animal
  Improvement Programs Laboratory
• University of Missouri
• University of Alberta
• USDA-ARS US Meat Animal Research Center
• Starting 60,800 beads 54,000 useable SNP

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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
• Godon Doak
• ABS Global
• Accelerated Genetics
• Alta Genetics
• CRI/Genex

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Genomic evaluation - dairy cattle

• Cooperating organizations
• Breed associations
• Holstein
• Jersey
• Brown Swiss
• Bull studs
• Own bulls
• Collect and market semen
• Full sharing of genotypes and research with
  Canada
• Trading of genotypes with Switzerland
• Expect to share with more countries
• Over 50,000 animals genotyped starting in 2008

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How is it done?

• Animals selected
• Studs identify male and female calves to genotype
• Farmers request breed association to arrange for
  genotyping
• Animal nominated at AIPL insures that pedigree
  information is in database
• Sample sent to lab
• Hair follicles (most common)
• Blood
• Semen
• Nasal swab

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Lab work

• Extract DNA
• Incorporate DNA into reagents on chip (3 days)
• Laser scanner collects intensity data
• GenomeStudio software assigns genotype after
  clustering intensities

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What is done at AIPL

• Genotypes checked
• Sex
• Breed
• Parents
• Duplicate of another animal
• 90 of SNP genotyped
• Requesters notified of conflicts
• For parent conflicts, alternative parents usually
  suggested
• Parentage and sample ID Corrected
• Genotypes extracted
• Genotypes for gt2000 dams figured out from their
  progeny (imputation)

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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

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Genotyped Holsteins
Date Young animals Young animals All animals
Date Bulls Cows  Bulls     Heifers  All animals
04-09 7,600  2,711     9,690       1,943 21,944
01-10 8,974  4,348   14,061      6,031 33,414
02-10 9,378  5,086   15,328      7,620 37,412
04-10 9,770  7,415   16,007      8,630 41,822
05-10 9,958  7,940   16,594      9,772 44,264
06-10 9,958  8,122   17,507    10,713 46,300
07-10 9,963  8,186   18,187    11,309 47,645
  Traditional evaluation No traditional
evaluation
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Summary

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

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