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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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Animal biotechnology l.jpg

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 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)


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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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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

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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. 2007BovineSNP50 BeadChip available

  • Apr. 2008First unofficial evaluation released

  • Jan. 2009Genomic evaluations official for

    Holstein and Jersey

  • Aug. 2009Official for Brown Swiss

  • Sept. 2010Unofficial evaluations from 3K chip

    released

  • Dec. 20103K 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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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


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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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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


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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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