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  • Pedigree Analysis using SNPs, though costly is becoming and invaluable tool in medical diagnosis and counselling.This presentation is very important for instructors in medical training
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  •   What we are looking at is a microsatellite fingerprint for 12 loci.   Each locus acts as a marker.   In contrast to SNPs - which only have 2 alleles - microsatellites can have multiple allele and average about 5 alleles per locus.   Microsatellites consist of short runs of a repeat of a simple sequence eg CA (a dinucleotide repeat), or CAT (a trinucleotide repeat). Each allele of the microsatellite locus contains a different number of repeats eg alleles of a dinucleatide microsatellite can be 10, 11, 12, 13, 14 etc repeats. Alleles are scored by amplifying the genome region carrying the microsatellite by PCR and measuring the size of the PCR products on an automated DNA sequencer - you need this kind of resolution as alleles can differ by only 2 bases.   Using automated DNA sequencers also allows us to look at several (12 in the example shown) microsatellite loci per animal at the same time. We can do this by using microsatellites with a different allele size range (so we do not confuse alleles of one marker with alleles of another) as well as different color dyes to label the PCR products which allows us to distinguish alleles of microsatellite markers of the same size range. Typically we use 4 colors and three size ranges and so can type animals for 12 markers at the same time. That is what we are seeing in the slide - on animal genotyped for 12 microsatellite markers.   Microsatellites are usually in non-coding regions of the genome and so there is usually no selection bias on alleles.   So if we consider that an average microsatellite has 5 alleles each with a frequency of 0.2, then roughly the chances for a given genotype at that locus is 0.04. So 1/25 chance of 2 animals having the same genotype for 1 marker. So chances of two unrelated animals having the same genotype over 5 markers is almost 1/10million. this is the basis of identity fingerprinting.   For parentage (paternity) we fingerprint the offspring, dam and potential sires. Knowing the offspring and dam, we can deduce the genotype (or at least one of the alleles) for each marker and so find the correct sire by elimination.  
  • The Wild Boar test (which is used in the UK in a similar way to the Japanese Kuro Buta test) is used by both Trading Standards and the British Wild Boar Association to verify the origin of premium pork. How to ensure that all animals meet the Wild Boar requirements? Test all breeding males and females Test new breeding animals entering the herd Only breed from animals with 2 wild boar alleles Re-test random individuals periodically Advantages Immediate and robust Quality Assurance scheme Further large scale testing not needed Disadvantages Initial Cost, but the extra value of the meat, (which increases in price when this scheme goes into action since “falsely labeled pork” quickly exits the market), pays for the increased costs very quickly. Wild boar meat is a lean, nutritious and good tasting product. Japan imports 2,000 tones per year, and they want a specific fat covering and a dark red meat color.
  • Only one difference between genotypes of LoAp and HiAp: HiAp has an A where LoAp has a G
  • Also talk about the difference between using gene markers and transgenics
  • Breeding bit handles many different technical areas. Easy extension to use of seedstock at commercial level. Extend to Gross Margin as criterion to maximise - Breeding objective is somewhat static and inflexible to the prevailing situation. Extent to tactical optimisation along the whole chain. Hutton Oddy, John Thompson, Scott Newman onside … Integrate with the Education program. “Total Resource Management”
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    1. 1. Using DNA Technology as a Complimentary Tool in the Value Chain for Source & Content Verification Stephen Pearce Director of Biotech Research Business Development International plc
    2. 2. Mission Leadership in creating value through the innovative application of quantitative genetics & biotechnology to animal breeding
    3. 3. Business Model Global Meat/Protein Supply Chain DNA link throughout the value chain SYGEN genetic, health and biotechnology improvements add value across the entire Global Supply Chain
    4. 4. Companies Around the World España Denmark France Germany UK Italia Polska Czeska Romania Portugal Japan China Korea Canada México Peru Brazil Chile USA Philippines Thailand New Zealand Australia South Africa Argentina Benelux Meat trade is becoming increasingly international Colombia
    5. 5. Multi-Species Strategy & Application Biotechnology/Genomics Quantitative Genetics <ul><li>Acquisition </li></ul><ul><li>JV </li></ul><ul><li>License </li></ul>
    6. 6. Research & Development <ul><li>Improved Methods of Selection </li></ul><ul><li>Genomics </li></ul><ul><li>Animal Health </li></ul><ul><li>Applied to Food Animals </li></ul>
    7. 7. Leading R&D Team <ul><li>25 Molecular Biologists </li></ul><ul><li>25 Quantitative Geneticists </li></ul><ul><li>20 Veterinarians/Nutritionists </li></ul><ul><li>15 Reproduction/Meat Scientists </li></ul><ul><li>50+ PhDs </li></ul><ul><li>Laboratories in US and UK </li></ul>
    8. 8. R&D How we select <ul><li>Biotechnology </li></ul><ul><li>- Leverage 15 years of biotechnology experience </li></ul><ul><li>- Utilize biotechnology and genetic research </li></ul><ul><li>- Identify individual genes responsible for trait of interest </li></ul><ul><li>Utilize technology transfer vehicles (e.g. Animals) to transfer/sell our technology products to our customers </li></ul><ul><li>Quantitative Genetics </li></ul><ul><li>- Leverage 40 years of quantitative genetics experience </li></ul><ul><li>- “ Statistical sampling” of groups/herds of animals </li></ul><ul><li>- Identify individual animals with trait of interest </li></ul>
    9. 9. Earth Cell Continent Cell Nucleus State Chromosomal DNA City Chromosomal DNA Fragment Street Address Nucleotides Genome Research in Perspective
    10. 10. <ul><li>A Tool to Verify Traceability Systems </li></ul><ul><li>A DNA based identity preservation program (patent applied for) capable of linking a DNA sample from an animal, carcass or cut of meat back to its genetic origin </li></ul><ul><li>Assigns individual animals as parents to a resulting DNA sample and/or links a DNA sample collected at the packer or retail level back to the individual from whom the tissue was originally derived </li></ul>Verispec ™
    11. 11. Value Chain Questions <ul><li>Are you who you say you are? </li></ul><ul><li>Are you where you say you are from? </li></ul><ul><li>How do I substantiate the claims you make? </li></ul><ul><li>Are you safe? </li></ul>Verispec ™
    12. 12. Complex Networks with Many Touch Points <ul><li>Supply chain verification at first glance seems like a big bowl spaghetti. </li></ul><ul><li>It has many expectations that are varied in content and requirement, some random some constant </li></ul>Meat (live or fabricated) comes in different flavors (Species, breeds, programs) All contains a wealth of information in the form of DNA Verispec ™
    13. 13. Increasing amount of history and data (information & knowledge) Many Inputs Local & International Many Out puts Local & International Live animal Only ONE source of ID material stays the same throughout and that is DNA “ Bow Tie” Supply Chain Questions & Answers Consumable product Verispec ™
    14. 14. Using Genetic Markers in Traceability & Content Verification <ul><li>Regulatory Traceability </li></ul><ul><ul><li>Disease (Control , Diagnosis & Prevention) </li></ul></ul><ul><ul><li>Product Recall (Non-compliance, Not “in the spec”) </li></ul></ul><ul><ul><li>Supply Chain Security </li></ul></ul><ul><ul><li>(Fraud, Bioterrorism, other acts of Malice) </li></ul></ul><ul><li>Commercial Traceability </li></ul><ul><ul><li>Value Attributes </li></ul></ul><ul><ul><li>(Brand Differentiation & Genetic line customization) </li></ul></ul><ul><ul><li>Source / Process Verification </li></ul></ul>Verispec ™
    15. 15. Farm Packer/Processor (Brand Owner) Retail/Consumer Iris/ Retina/ EID/Tag/ Tattoo Shackle/ Barcode Product Claims/Added Value Product Concerns/Risk Mgt. Process Verification Identity Preservation: Tracking vs. Tracing DNA is a link through different parts of the chain Verispec ™ Tracking (I.P.) Tracing
    16. 16. DNA Markers and Traceability in the Pig Industry Verispec ™
    17. 17. <ul><li>What claims are being made or what do you want to trace? </li></ul><ul><ul><li>Animals, carcasses, primals, retail packs, organic, natural, “ours and not theirs” or “not ours” </li></ul></ul><ul><li>What level of traceaback is required? </li></ul><ul><ul><li>System, farm, finishing site, individual </li></ul></ul><ul><li>Are you planning to implement process verification? </li></ul><ul><ul><li>At what level? Who will audit? How often? </li></ul></ul><ul><li>Do you have individual animal or lot I.D. systems in place? </li></ul><ul><li>What will the average lot size be? (kill day, shift, hour, truck) </li></ul><ul><li>Turn-around time required on data? </li></ul><ul><li>Level of accuracy desired? (i.e. 95% confident of < 5% non-compliant, or 100% confident of 0 non-compliant) </li></ul>Implementing Traceability: What needs to be considered?
    18. 18. Identification Programs DNA Markers and Traceability in the Pig Industry- Lessons Learned Verispec ™
    19. 19. Establish the presence of genes associated with breed determination Analysis of DNA Sequencing DNA e.g. CATCATCATCATCATCAT Verispec ™
    20. 20. Breed Identity Preservation Test Verispec ™
    21. 21. Sygen Breed Identity Preservation Programs Verispec ™ ? ? ? ? bb
    22. 22. Genetic Methodology Understanding Microsatellites and SNPs <ul><li>Microsatellites </li></ul><ul><li>SNPs (Single Nucleotide Polymorphisms) </li></ul><ul><ul><li>Informative & Non-informative </li></ul></ul>Verispec ™
    23. 23. offspring 3 BACKGROUND -Parentage Microsatellite Markers Verispec ™ M F offspring 1 M F x Mother Father offspring 2 M F offspring 4 M F
    24. 24. PICmarq™ Technology A Single Nucleotide Polymorphism (SNP) C N S I I D P L I Y C N S I I N P L I Y NH 2 COOH Transmembrane dmains I II III IV V VI VII Allele 1 homozygote sequence Allele 2 homozygote sequence 293 295 297 299 300 G instead of A MC4R gene A marker that affects appetite and therefore leanness Verispec ™
    25. 25. Different Species / Common Genes Verispec ™
    26. 26. Genetic Markers in Beef Cattle Improvement Programs & Customized Line Development <ul><li>Growth & appetite </li></ul><ul><li>Ultimate pH </li></ul><ul><li>Japanese meat quality </li></ul><ul><li>Data base of >40K markers </li></ul><ul><li>Unique sample selection & association analysis tools </li></ul><ul><li>Continuous discovery </li></ul><ul><li>Traceability </li></ul><ul><li>Food safety </li></ul>Verispec ™
    27. 27. Verispec ™ $$ Profit
    28. 28. Genetic Methodology Understanding Microsatellites and SNPs <ul><li>Microsatellites </li></ul><ul><ul><li>Highly polymorphic (ave. 5 alleles) </li></ul></ul><ul><ul><li>Available now in large numbers </li></ul></ul><ul><ul><li>Relatively expensive </li></ul></ul><ul><ul><li>Technologically more difficult </li></ul></ul><ul><li>SNPs (Single Nucleotide Polymorphism) </li></ul><ul><ul><li>Biallelic </li></ul></ul><ul><ul><li>Unlimited numbers, but few publicly available now </li></ul></ul><ul><ul><li>Relatively cheap </li></ul></ul><ul><ul><li>Simple technology </li></ul></ul>Verispec ™
    29. 29. <ul><li>Ancestry or Pedigree </li></ul><ul><ul><li>Pros </li></ul></ul><ul><ul><ul><li>Traceability to the system or farm of origin </li></ul></ul></ul><ul><ul><ul><li>Less expensive than identity testing as requires far fewer samples </li></ul></ul></ul><ul><ul><li>Cons </li></ul></ul><ul><ul><ul><li>Requires more markers – so costs per sample tested are higher </li></ul></ul></ul>Genetic Methodology: Identity Preservation Verispec ™
    30. 30. <ul><li>Parentage testing </li></ul><ul><ul><li>Pros </li></ul></ul><ul><ul><ul><li>Traceability to the system or farm of origin </li></ul></ul></ul><ul><ul><ul><li>Less expensive than identity testing as requires far fewer samples </li></ul></ul></ul><ul><ul><li>Cons </li></ul></ul><ul><ul><ul><li>Requires more markers – so costs per sample tested are higher </li></ul></ul></ul>Genetic Methodology: Parentage Testing Verispec ™
    31. 31. Traceability to the farm of origin Dams vs. Sires <ul><li>Dams </li></ul><ul><li>Need for testing ALL dams in the system to form a reference database, so high number of reference tests required </li></ul><ul><li>Sires </li></ul><ul><li>If sires are dedicated to a system, traceability to the system is the least-cost option. All sires need to be tested to form a reference database </li></ul>Verispec ™
    32. 32. Verispec ™
    33. 33. Verispec ™
    34. 34. or preferably Genetic Evaluation Additive random QTL-BLUP Decision implementation All breeding issues Tactically Segregation Analysis Genotype Probabilities Genetic Evaluation Fixed interactive QTL within a BLUP model Strategic planning All issues Strategically [incl. breeding objectives] Decision implementation Whole Chain Tactically Data Recording Phenotypes, genotypes, pedigree Data collation and analysis delivery (can be Internet-hosted) Pedigree deduction From genetic markers Combines in to one program Genotyping strategies DNA testing Verispec ™
    35. 35. <ul><li>Lessons Learned </li></ul><ul><li>DNA-based traceability programs are in place now and working in Pork Supply Chain systems </li></ul><ul><li>Applications of DNA-based traceability programs depend on the intrinsic control of genetics within the system </li></ul><ul><li>Speed of implementation will depend on the Supply Chain’s ability to define value of ‘Farm-to-Consumer’ DNA-based traceability programs </li></ul><ul><li>DNA verification may assist with issues of animal health, zoonoses, security, as systems develop – timing is the issue </li></ul><ul><li>DNA technology will continue to improve in the future enabling its wide application in the Meat Industry </li></ul>DNA Markers and Traceability in the Pig Industry Verispec ™

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