Module 4

• Breeding Pyramids


  Nucleus at the top, multiplier in the middle and commercial in the bottom represents a breeding scheme typically used in swine production
• Nucleus tier

  Consist of elite animals that were carefully selected for their traits. Those with the best performance of one or many traits is identified and are used to parent the next generation
• Multiplier tier

  The intermediate between nucleus and tier and still have well performing animals and purpose is to utilize the superior genetics and pass them down
• Commercial tier

  Bottom level that includes those going to production of some sort and could be bred from either multiplier or nucleus stock
• Types of breeding schemes

  • Open
  • Closed
• Open nucleus breeding


  There is regular exchange between the nucleus and commercial population. Helps with more breeding flexibility, less inbreeding and loss of genetic diversity in the nucleus population
• Closed nucleus breeding

  No exchange between the top and bottom tiers. Top tier becomes genetically isolated and are usually used in genetically exclusive populations. Superior genes are passed to the commercial level by AI, ET etc.
• Animal Pedigree Act is a Canadian federal law pertaining to purebred animals. Gives authority to Breed Associations and Canadian breed associations will send proof or purebred or pedigree within 6 months
• The Canadian Livestock Records Corp is a national pedigree and purebred service for livestock. They serve small beef breeds such as Belgian Blue, Galloway, most horses except Thoroughbreds and most other livestock except for poultry
• Requirements for animal registrations

  • Integrity
  • Identification
  • Accurate records
  • Participation of an "association"
• Cattle tattoos

  Herd letters + year letter + individual number. Owner ID of 3 letters, their number and birth year. RFID tags do not replace tattoos
• Breeding value


  The number that represents the value as a parent and the deviation of the animal's progeny compared to the average reference population
• Expected Progeny Difference (EPD)


  The expected difference in performance of a bull's progeny when compared to the average progeny of all bulls evaluated. Expressed relative to other animals in the same population or breed
• Calculating EPD

  1. Use the animal's own performance

  2. Use the animal's pedigree

  3. Use progeny records
• Maternal EPD

  Reflects the milking abilities of the sire's daughter. The sire's milk EPD can be expressed as additional pounds of calf weaned by high daughters due to milk
• Accuracy of EPD


  The closer the range in "true" EPD is to 1, the more accurate it'll be because it is more likely to represent the true genetic makeup for the animal
• Estimated Breeding Value (EBV)


  A predictor of the genetic worth of an animal. The bull transmits half of its own breeding value into the offspring, the dam gives the other half
• SNP (single nucleotide polymorphism)


  Markers in direct or indirect DNA tests that are used to select for traits
• Polymerase Chain Reaction (PCR)


  Used to detect the presence of specific genetic material. RNA or DNA is extracted, amplified using heat, and primers bind to complementary sequences on the single stranded DNA template
• DNA for PCR can be extracted from hair roots, semen, blood, embryo, milk, and tooth pulp
• Central dogma of molecular biology

  DNA is transcribed into RNA, and RNA is translated into proteins. This unidirectional flow serves as the fundamental process underlying gene expression and the functioning of living organisms
• Genomic vs. cDNA

  Genomic is the complete DNA sequence, cDNA is DNA synthesized from mRNA which lacks introns. cDNA is used to look for mutations as it contains only the coding regions of genes
• Types of mutations in coding sequences

  • Silent mutation
  • Missense mutation
  • Nonsense mutation
  • Frameshift mutation
  • In frame insertion or deletion
• Silent mutation


  Amino acid does not change, usually in the third position of the codon
• Missense mutation

  Whole amino acid change - impairs or abolishes the protein function
• Nonsense mutation


  Change in the nucleotide results in amino acid change to a STOP codon. Causes a truncated protein
• Frameshift mutation

  Insertion or deletion of nucleotides that is not divisible by 3. Shifts the reading frame
• In frame insertion or deletion

  Insertion or deletion that is divisible by 3. Just adds or takes away whole amino acids
• Double muscling

  Mutation in the myostatin gene that causes muscular hypertrophy and reduced body fat
• Potential effects of mutations in non-coding DNA

  • Affect regulatory regions
  • Affect splice sites
  • Affect enhancer/suppressor regions
• Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP)


  Used to look for a mutation that has already been identified. Restriction endonucleases cut DNA at specific sequences, and the presence/absence of a cut site indicates the mutation
• Genotyping by KASP

  Kompetative allele-specific PCR. Uses allele specific forward primers with fluorochromes to identify different alleles
• DNA tests used in the industry

  • A.I sires: Milk traits
  • Purebred sales: Color, polled, leptin, genetic abnormalities
  • Chicken: FMO3 for egg taint
  • Pigs: Coat color, litter size, pH, water holding capacity, Rendement Napole, Porcine stress syndrome
  • Holsteins: BLAD, mulefoot
  • Kappa Casein for cheese properties
• Changeling


  A calf born red, but their coat changes color to black, usually within 3-6 months. Caused by a mutation in the MC1R gene
• QTL mapping


  Graphs of traits on chromosomes. Qualitative traits are "this or that" and shown as a bar graph
• Chicken industries


  • FMO3 to remove egg taint
• Pig industry traits

  • Coat color
  • Litter size
  • pH
  • Water holding capacity
• Rendement Napole (RN)


  A dominant mutation in pigs that can cause the meat to become pale and soft "acid meat"
• Porcine stress syndrome

  Can be detected in a restriction enzyme
• Holsteins farms must test their sires for diseases such as BLAD and mulefoot