Dairy Cattle Genetics

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Dairy Cattle Genetics

• AVS 346

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Breeding Dairy Cattle

• Easier than in most other types of livestock
• Milk is most important economic trait
• Large database of information
• USDA-AIPL, DHIA studs
• 4 million cow records annually in the US
• Accurate information on individual cows
• Controversial
• No two breeders can agree on how to breed 
• Complicated formulas
• Population genetics is entirely statistics

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Milk Production Is Primary Trait

• Every other trait is minor in comparison
• Quantitative trait
• Controlled by a large number of gene pairs
• Expression affected greatly by the environment of
  the individual
• Moderate heritability
• 0.25 - 0.30
• Large database of information aids in calculating
  BV
• USDA-AIPL, DHIA studs
• 4 million cow records annually in the US
• Accurate information on individual cows

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Phenotypic and Genotypic Trends in Holstein Cattle
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Dairy Cattle Breeder Tools

• Selection
• Picking the animals that will be parents of the
  next generation
• Mating
• Matching cows and bulls
• Culling
• Eliminating undesirable individuals from the
  population
• Actually influences selection
• If cows arent there they cant be selected

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Genetic Change/Year

• Accuracy x Intensity x Genetic Variation
• Generation Interval

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Genetic Variation

• Cannot practice genetic selection unless genetic
  differences exist between animals
• Breeding for white in the Angus breed

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Selection

• Picking the parents of the next generation
• Not much selection done on the maternal side
• Increase frequency of good genes in population
• Influenced by
• Genetic Variation
• Accuracy of Selection
• Intensity of selection
• Number of traits selecting for
• Generation Interval

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Accuracy of Selection

• Correlation between the phenotype and genotype
• Is what you see what you get? (Genetically
  speaking)
• Ability to accurately predict the breeding value
  of an individual
• Higher repeatability and heritability improves
  accuracy
• Power in numbers
• More information on more relatives means higher
  accuracy
• In the animal model the accuracy of the
  prediction in the reliability

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Phenotype

• Visible properties of an organism
• Measured or observed
• Three components G E permanent E temporary
• Genetic effects
• The variability due to genetics is heritability
• Permanent environmental effects
• Care a calf receives while growing up
• Illness that causes permanent effect
• Temporary environmental effects
• Age at calving 
• Illness with no permanent effect

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Repeatability

• Expression of the trait at different times in the
  animals lifetime.
• Range from 0 to 100
• Sum of genotypic and permanent environmental
  effects.
• A 0 means trait has no genetic and permanent
  environmental effects
• Important in estimating animals genotype
• Fraction of difference in a single record that
  will occur in a subsequent record(s).
• Repeatability of milk production is about 0.5
• First lactation animal produces 1000 over herd
  average, at 50 repeatability she should produce
  an average of 500 above average in future
  lactations

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Repeatability of Dairy Traits
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Heritability

• Heritability extent to which genetics influences
  a trait
• Determines the extent to which offspring resemble
  their parents
• Proportion of the phenotypic differences we see
  that are due to genetics.
• Range from 0 to 100
• Helps estimate animals genotype
• Even lowly heritable traits, such as fertility,
  can have a genetic component
• Estimate of the genetic progress that may be
  achieved with selection.
• Measure of how much of a trait will be passed on
  to next generation
• Faster genetic progress can be made for traits
  with high heritability

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Heritability of Dairy Traits
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Environment

• Animals opportunity to express a trait
• Conditions under which the animal is raised
• Some conditions have very short term effects,
  Others very long or permanent.
• Short term
• What she was fed today
• Long term
• Pneumonia as a calf

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Breeding Value

• Estimate of animals genotype
• Genetic superiority of inferiority
• Information is power
• More measurements on a individual increases
  accuracy of BV estimate
• More measurements on relatives increases accuracy
  of BV estimate
• Half of breeding value is transmitted to
  offspring
• Predicted Transmitting Ability

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Breeding Values of Dairy Cattle
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Estimating Genotype (Proofs)

• Show winners
• Dam - daughter comparisons
• Herdmate comparisons
• Nationwide comparisons
• Modified contemporary comparisons
•  Base year, cow index
• Animal model
• Considers all relatives
• PTA

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Animal ModelUsing All Available Information

• In an animal model, an animals own phenotypic
  data is combined with data from all of its
  maternal and paternal relatives (more weight is
  given to data from closer relatives)

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Reliability (REL)

• Measures the accuracy of a PTA
• Estimate of the squared correlation between a PTA
  and the animals true genetic merit
• Example Cow REL 50
• Means based on information from this cow and her
  relatives, the correlation between her PTA and
  her true transmitting ability is about 71

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Reliability of Predicting BV for Milk Production
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Reliability of Sire Proof for Milk Yield
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Intensity of Selection

• A measure of the degree by which performance of
  the selected group of parents exceeds the average
  of the population
• Intensity is a function of
• Population size
• Percentage of animals selected
• Few animals selected High intensity
• Large population High intensity
• The greater the intensity the greater the genetic
  progress
• Different for cows and bulls
• All cows need to carry calf to produce milk
• A very small number of bulls needed to breed all
  cows
• AI 0.0003
• ET 25
• Sexed Semen 50

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Factors That Influence Selection Intensity

• Selection Accuracy
• Litter Size
• Longevity
• Reproductive Performance
• Calf Mortality
• Cow Mortality
• Involuntary Culling
• Reproductive Technologies
• AI
• ET
• Cloning

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Selection Intensity in AI

• Two-Stage Selection
• Selection of elite sires and dams to be parents
  of young bulls (top 1 of population)
• Selection among young bulls based on progeny test
  results (top 10 are marketed)

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Relative Progress in Primary From selecting for
Other Independent Traits
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Selection Index

• One trait that is a function of several traits
• Can give each included trait a different weight
• Simplifies selection because your looking at one
  trait
• Maximizes genetic progress
• Can calculate your own
• Need to consider, mean, range and variation in
  each trait included

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Indexes

• Udder composite
• Fore udder attachment
• Rear udder height width
• Udder depth and cleft
• Front teat placement
• Feet and leg composite
• Rear legs side and rear view
• Foot angle
• Net merit
• PTAM, PTAF, PTAP, pl, SCS
• TPI
• Type production index
• Total performance index
• PTAP, PTAF, PTAT, UDC, FLC, SCS

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Generation Interval

• Average age of parents
• Quicker you turn over generations the more
  genetic progress youll make
• Heifers have the most modern genetics in herd
• Dairy cattle 4-5 years
• AI Increases GI 7-8 years
• ET Increase GI by 1 year
• MOET Select heifers - GI 2

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Genomic Selection

• Selection based the actual DNA
• As opposed to phenotypic traits
• Identify DNA markers for an single trait at a
  single locus
• Red in Holsteins, Polled, Genetic lethals
• DNA techniques now make it possible to scan large
  sections of the DNA for little substitutions
• Correlate what is seen phenotypically in the
  animal with the DNA sequences
• Not just on simple traits but on milk production
  and other quantitative traits.
• Revolutionize animal breeding!

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SNPs

• Single nucleotide polymorphisms
• (pronounced snips)
• Tiny changes in the sequence of nucleotides or
  mutations
• A new chip developed by USDA can scan cattle
  50,000 points on the DNA for SNPs
• Determine the breeding value by summing all the
  effects of the SNPs

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Genomic Selection

• Advantages
• Decision to keep or cull an animal could be made
  earlier in an animals life.
• Expensive progeny testing would not be required.
• Generation interval could be reduced resulting in
  more rapid genetic gain.

• Disadvantages
• Variability available for future genetic gain
  would be reduced.
• The rate of genetic gain would diminish over
  time.
• Incorrect associations between phenotypes and the
  SNPs could lead to unexpected results, some of
  which would be unfavorable.

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Other uses

• Avoiding inbreeding
• Identify related and diverse germplasm for
  conservation
• Animal identification DNA fingerprints
• Tracing of livestock products from farm to plate