DSCI 422 Midterm 2

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kderaad
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302819
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DSCI 422 Midterm 2
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2015-05-18 00:22:18
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DSCI 422
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Dairy Science 422 Dairy Cattle Genetics Midterm 2
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  1. Inbreeding
    mating closer than the average of the population
  2. Linebreeding
    planned inbreeding often breeding to the "line"
  3. Linecrossing
    Crossing two inbred line
  4. Outbreeding
    • Mating father away than the average of the population
    • mating animals less closely related than the average of the population
    • increases heterosis
    • combines desired traits from different breeds, especially when maternal breeds combine with terminal
  5. Crossbreeding
    Crossing one or more breeds
  6. Outcrossing
    Mating unrelated animals within the same breed
  7. Homozygosity
    • Goes from AaBb, etc. to AABB and aabb
    • inbreeding increases homozygosity
  8. Heterzygosity
    • Goes from AABB and aabb to AaBb
    • Outbreeding increases heterzygosity
  9. Coefficient of Inbreeding
    • the percent of common genes due to ancestry
    • Fx=Sume of (1/2n+1)
    • n=number of generations from the sire + the number from the dam for a common animal
  10. Pedigree calculations
  11. Inbreeding Losses Holstein Averages
    • 1995 - 2.6%
    • 2002 - 4.5%
    • 2010 - 5.6%
    • Loose:
    • -65 pounds of milk
    • -2.1 pounds of fat
    • -2.1 protein
    • For each percent above 4.5
  12. Inbreeding losses example
    • 12.5% inbreeding coefficient 
    • -4.5%
    • 8% x 65 = 520 lbs. milk
    • 8% x 2.1 = 16.8 lbs. Fat and protein
  13. Inbreeding Trends in Holsteins
    Inbreeding coefficient of cows in less than the expected future inbreeding
  14. Inbreeding losses in Jersey
    • Inbreeding has increased from 1% in 1980 to nearly 7% today
    • (Its a real challenge to optimize genetic gain while maintaining genetic diversity)
    • Inbreeding coefficient of cows is less than expected future inbreeding
  15. Expected Future Inbreeding (EFI)
    • USDA calculated inbreeding coefficient for cows and bulls
    • Mated to a random sample of 600 mates
  16. Percent Heterosis Calculation
    (progeny average - parent average) x 100
  17. Heterosis Definition
    The tendency of a crossbred individual to show qualities superior to those of both parents
  18. 4 Breeds good for crossbreeding
    • Jersey
    • Holstein
    • Montbeliard
    • Scandinavian Red
  19. Breed numbers
    Holstein
    Jersey
    Montbeliare
    Scandinavian Red
    • Holstein: 25 million; 23,000 avg. milk; 3.6% ave fat; 3.0% avg. protein; 4,00 bull/yr sampled
    • Jersey: 1.2 million; 17,600 avg. milk; 4.6% avg. fat; 3.6% avg. protein, 630 bull/yr sampled
    • Montbel.: 330,000; 18,000 avg. milk; 3.8% avg. fat; 3.4% avg. protein, 170 bull/yr sampled
    • Scandiv: 284,000-205,000; 20,000 avg. milk; 4.2% avg. fat; 3.5% avg. protein; 125-100 bull/yr sampled
  20. Rotational cross hybrid vigor sustained (%s)
    • Two-breed rotation: 67%
    • Three-breed rotation: 85%
    • Four-breed rotation: 94%
  21. Advantages of crossbreeding
    • To take the best traits from each breed and combine to one
    • Try to achieve and maintain heterosis
  22. Disadvantages of Crossbreeding
    • Difficult to manage
    • -depends of the complexity of the breeding program
    • -multiple sets of herd sires
    • Decreased consistency of calf crop
    • Accuracy of genetic prediction
  23. Composite Breeds
    • originated as crossbreds
    • continued the same breeding line to develop new "breed"
    • Brangus = brahman + angus
  24. Why crossbreeding now
    • economy has changed
    • Eliminate inbreeding (in first generation)
    • Combine milk yield of Holsteins with fertility, calving ease and component percentages of Jerseys
    • Get hybrid vigor for fertility, survivability, health and production
  25. Heterosis for traits percentages
    • Production is about 6%
    • Reproduction is about 10%
    • Percentages will likely be less over time

    • Production 5%
    • Health 10%
  26. Best crosses in CA field study.
    Procross and other
    • Holstein
    • Normandie x Holstein: 305 Fat + Protein, days to open, culling
    • Mont x Holstein:milk, 305 Fat + Protein, days to open, culling
    • Scand. Red x Holstein:milk, Calving diff of calf, calving diff of cow, stillbirths, days to open, culling
  27. # of base pairs, SNPS, DNA Markers
    • 3 billion base pairs
    • 50,000 SNPs
    • DNA reacts to chemicals (DNA markers) in the chip's 50,000 tiny beads to document SNPs each animal possesses
  28. Van Tassel & Sonstegard  research project
    • 15,197 older
    • 5,987 younger 
    • 40,000 SNPs and 10,000 QTLs
    • 80% vs 34% expected for young bulls
    • 72% vs 30% observed in simulation
    • August 2003 PTAs for 3,576 older bulls to predict January 2008 daughter deviations for 1,759 younger bulls (total = 5,335)
    • Results computed 27 traits: 5 yield, 5 health, 16 conformation, and Net Merit
  29. Basis of Genomics
    • Basis of genomics is to increase Reliability (REL) Accuracy
    • Parent Averages 42%
    • 3K 60%
    • 3K SNP test 65%
    • 50K SNP test 72%
    • 800K (HD) SNP test 74%
  30. Direct Genomic evaluation
    Combined genomic evaluation
    • Direct genomic evaluation
    • -young bull
    • Combined genomic evaluation
    • -traditional PA and PTA, and direct genomic combined
  31. Bovine Genome Sequence
    • 1st sequence, a hereford cow
    • 30 base pairs of chromosomes
    • 3 billion base pairs
  32. Marker Effects
    • For milk and net merit
    • Chromosome of x axis
    • Beta SNP on y axis
  33. Prices for genomic testing
    • U.S. Prices International
    • 3K SNP Test $45
    • 50K SNP Test $150
    • 800K (HD) SNP Test $365
  34. Genetic Evaluations and parent average
    • Parent average 42%
    • 3K (if sire and MGS have 50K results, but dam does not) 60%
    • 3K SNP Test 65%
    • 50K SNP Test 72%
    • 800K (HD) SNP Test 74%
  35. Heritability
    • In general: a calculation of the part that comes form environment genetics. percent from genetics. genetics + environment
    • Narrow Sense: mathematic calculation adding squared
    • Broad Sense: add interaction
  36. h2 estimates
    • Milk- 2nd highest 30%
    • Fat and Protein-highest heteribilty (50-60%0
    • Services/Conception- low 5-10%
    • Calving ease-low 5-10%
  37. Repeatablility
    Tendency of successive records to repeat
  38. Reliability
    • How sure you are of numbers
    • affected by: 
    • -number of records
    • -number of herds
    • -location
    • -relatives
    • -heritability and repeatability
    • (KNOW 5)
  39. Mean
    average
  40. Variance
    • S2
    • tells you how the numbers vary from the mean
  41. Standard Deviation
    • S
    • the square root of variance
  42. Correlation
    • have two sets of numbers vary together
    • r
    • r=a number from -1 to +1
  43. Why calculate variance?
    so you know how what normal is. Outliers do not have much standard deviation
  44. Variability
    Variation due to chromosome numbers and different gametes.

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