Population Genetics Flashcards
Companion Animals and Farm
1
Q
Genetics
(3 aspects)
A
2
Q
Cellular Genetics
(4)
A
- Genome is the entire genetic makeup of each animal
- variation in numbers accross species, but accross all species, we have generally the same number of genes
- Meiosis is the important one in terms of breeding and selection –> this is where you get changes accross populations
3
Q
Population Genetics
(3)
A
- looking at wider population rather than the individual
- May be looking between 2 breeds or within one
- If a breed moves from Europe to US and then you get a change in genetic makeup of one breed
- bottleneck: world war I and then breed form there
- lose variation in genetics!
- Phenotype is partially driven by genotype but also env’tal effects
4
Q
Inheritance
(3)
A
- can be simple or complex
- natural selection –> cruel world picks out best
- artificial: we are making it softer, helping animals that naturally wouldnt survive
5
Q
Single- gene vs. Complex
A
- complex: 2,3,4,5 or 6 genes are involved
- complex is more common
- you can have hundreds of genes involved - complexity is huge
- and then you get the env’tal factors involved
6
Q
Single Genes to Genetic Variation to Phenotypic Variation
A
- pheotypic variation: variation we can see externally
- Different ratios
- 9:9:9:3
- 9:6:6:3
7
Q
Multi-Gene Genetic Variation
A
- Even with 3 genes affecting a phenotype, there are lots of variations (echo)
8
Q
Selection
(natural or Artificial)
A
- we have a distribution onf disease
- you can allow breeding of an animal with less than a certain level of “disease” - selection
- should really be called man-driven or not man-driven
- We think diseases are binary: they have it or they don’t
- but really there are levels of disease
9
Q
Selection
A
- We can see this natural selection in the wild
- “cruel world” effect
- all look a little different because they have been driven in different directions
- breeds could be in effect be called species
10
Q
Genetic Forces Acting on Breeds/Populations
A
- What are the pushers driving things to happen?
- litter sizes are dropping bc there is likely larger death before birth
- genetic drift: if you have a small population there are more random things likely to happen in comparison to a large population (hardy-weinberg theory)
- Immigration (echo)
- Mutation are often single gene so you usually can breed them out
11
Q
Selection can lead to Disease
A
- pugs : big eyes and smashed mouth
- a lot of white dogs are associated with disease
12
Q
Selection can also lead to Improved Health
(2)
A
- simple ones are usually for recessive genes (sometime dominant)
- in complex: you often don’t know which genes are involved but that the genotype is involved
13
Q
Molecular Genotyping
A
- kennel club does most of this
- for simple mendelian genetics
- They decide if the breed has an issue with an inherited disorder and then may force for people to select out the phenotype
- DNA tests isnt always the best method but breeders love it for certainty
- Mate Select: holds the records for past tests
14
Q
Breeding Advice
(3)
A
- Need to get 3 main answers back from tests
- If an animal is a carrier then they will not be bred which is bad! you are then lowering the gentic diversity like crazy
- If you breed a carrier with clear then it should be fine
- Dominant dogs are more difficult
- Linkage: sometimes you don’t know the exact gene, but you know the area, but you can test for genomic areas nearby it
15
Q
Common Disorders in Dogs
(prevalence %)
A
- EBV testing is much better and relates to complex
- most common disease is Otitis Externa
- least common: laceration
- None are single gene diseases!
echo for full list
16
Q
Mendelian Traits and Dog Phenes
A
- only 3.3% were single gene disroders - and were quite rare
- Dog phenes–> physical characteristics htat are associated with disease
17
Q
Genetic x Environmental Variation
A
- things happen along the way
- phenotype is what we see in practice
- we wont really ever know the genotype of this complexes
18
Q
Heritability
A
- The higher the heratibility the more we can drive away by selective breeding
19
Q
Heratibilities of Notable Diseases
A
- these values have to be taken as population specific
20
Q
Survival of the Fittest vs. Reproductive Success
A
- Darwins message was about reproductive success
- leave behind copies after you succeed
- this breed was bred to be short to go into badger holes
- bred for design and the task they have: so this does not mean they arent the fittest breed for a certain purpose
21
Q
Analysis of Complex Disease
A
22
Q
Estimated Breeding Values
(EBV’s)
A
- % of that animal to pass on that disease
- EBV is for complex genetics where it is too complex to understand the true genetics behind the phenotype of a disease
- can use a timeline to generate and EBV
- current way for hip dysplasia: x-rays
- but hips may be bad/good from the way it was brought up
- need to look down the family line and see frequency of bad hips (traits)
23
Q
Use of EBV’s
A
24
Q
More accurate selection
(Hip Scores)
A
- red line can be considered actual hip score
- even in the best 5% there may be ones with a lower score than the lowest 5%
- (echo)
*
25
Q
Binary Diseases
A
- We think of animals having a disease or not
- but it isnt just yes or no!
- SM: a disease in King Charles Spaniels
26
Q
Advantages of EBV’s for a “binary” trait
A
27
Q
Selection Intensity (i)
A
- all those is red are out–> then that is a high selection
- echo
- Problem with too high of a selection intensity is that we are losing diversity
- selecting your breeding for one disease is not the smartest, may be inadvertently selecting for another disease and ridding of diversity
28
Q
Ensuring Successful Selection
A
29
Q
Selection and Health
A
30
Q
Mating of Relatives
A
- We have genes that are passed down that are the exact same copy of the gene
- you can work out probabilities
- If those red genes both appear at the bottom they are identical by decent
- meaning the probabiltiy of IBD is 2.0
31
Q
Coefficient of Inbreeding
(COI)
A
- level of recessivity goes really high
- how related are the parents
- used in pedigree analyses
*
32
Q
Inbreeding and Specific Inherited Disease
A
33
Q
Inbreeding
(gene frequency)
A
- Even with not that high of a level of inbreeding, there can still be a rather decent effect
34
Q
Inbreeding Depression
A
- modern dog breeds have small litters: may be a big result of recessive genes being acquired
- echo
*
35
Q
Heterosis/Hybrid Vigour
A
- In reality you don’t get in the middle, you get the extra effect
- will decrease as generations continue
36
Q
Hybrid vigour deteriorates after the F1
A
- Blue and Brown: totally inbred
- want 1st generation?
37
Q
Effective Population Size
(Ne)
A
38
Q
Genetic Drift
A
- If we have a small breed and a big breed
- this is the probability for populations that are small or large
- small pops will see a larger effect
39
Q
Inbreeding/Genetic Drift Summary
(5)
A
40
Q
Control of Inbreeding
A
41
Q
Possible Solutions to Inbreeding
(5)
A
42
Q
Why Outcross?
A
43
Q
Conservation Genetics
(why does it matter?)
A
44
Q
Conservation Genetics
(genetic Diversity, Production Species, and Dogs)
A
- Things may change in the future, may be important to keep these genes in play
- ex: otter hounds smell like shit. breed may be on the way out
45
Q
National Trends in UK Dairy Herd
A
- milk production has gone up quite a lot while the number of cows has decreased
46
Q
Lifetime Performance of a Dairy Cow
A
- remember: farmers need to make money while tending to animal welfare
- ideally the cow doesnt start lactating until 2 years of age
- tend to not even meet the breakeven point (in terms of $$) until their second lactation (eve mid way through it)
- Cows that are survivng longer have to account for the loss of the ones culled younger than 2nd lactation
- may be lowering fertility this way too
47
Q
Key Performance Indicators for UK Dairy Herd
(2017)
A
- He selects 500 herds from a population (each bar is a herd)
- somatic cell count is an indicator of mastitis
*
48
Q
NMR Herds KPI
(2016-2017)
A
- aim for calving intervals is 365 days but hardly anyone actually reaches that
- part of the variation between herds is due to genetics and the farm (environment)
49
Q
Population Statistics of a Typical Dairy Herd
A
- losing 25% each time
- less than half of the cows make it through to the 4th lactation
- echo
- Dairy cows in the UK are not survivng a particularly long time - but why is this occurring?
50
Q
Milk Production and Fertility
(phenotypic trends)
A
- 50s onwards AI became available
- could use semen from selected bulls
- there was selection for only high milk yields and they didnt realize there was some negative effects
- as milk yields were going up, fertility was going down
51
Q
Milk Production and Fertility
(genetic correlations)
A
- calving interval is well recorded, but not super helpful as not many cows make it into 2nd lactation to have a calving interval
- conception rates can be calcualted from non-return
52
Q
Main reasons for culling UK Cows?
A
- about 25% per each lactation
- mastitis and lameness are very prevalent in the pop
53
Q
Summary of Today’s Dairy Cow
(4)
A
- increased milk prod, but associated with that fertility has decreased
- short productive life is a disadvantage to the farmer as they arent getting to the age to make a profit
54
Q
Goals for Future Dairy Cows
A
- want to breed for healthier cows, but you also need to consider the profit of the farm (high milk yield)
- don’t lose sight of healthier cows
55
Q
Population Genetic Tools
A
- each bull has its own individual genetic merit
56
Q
Change in Emphasis
A
57
Q
International Comparison
A
- proof done for bulls at an international level
- different qualitites of the bulls in their pop
- echo..ooops
58
Q
Genetic Indices for Selection in UK
A
- PIN originally just included milk production
- now only about 1/3 of the selection is on production rates
- hopefully this means we are on the way to breeding healthier cows
59
Q
Genetic Links b/w Production, Health, and Fertility Rates
(milk, fat, protein)
A
- get negative association between production and diseases
- amount of fat in the milk is highly correlated with lowered fertility
- If you tend to go for one then you tend to lose fertility
60
Q
Selection against a Correlation
A
- echo
61
Q
Somatic Cell Score
(1998)
A
- highly correlated with mastitis
- PTA: predictable transmitable ability
- trying to get somatic cell count to go down
62
Q
Selection and Mastitis Susceptibility
A
- daughters of the bulls were doing worse in presence of SCC and Mastitis
- luckily making a turn but still really high
63
Q
Genetic Trends: Fertility Index
A
- Fertility is going downwards
64
Q
Fertility Index
(FI)
A
- In rebuttal to a dropping Fertility–> an index was created
- Now is an aspect of picking a sire quality
65
Q
Fertility Index - having an effect
A
until introduction of FI, the calving interval was increasing and then dropped after
66
Q
Herd Health
A
- want to select for but harder to record
67
Q
Health and Welfare Traits
A
- people are trying to pull more health aspects into selection
- calving ease is a new thing to have been recorded
- how many of those daughters will last to their 6th lactation?
68
Q
Lifespan Evaluation
A
- cows that have those traits on average have a longer life
69
Q
Genomic Selection
A
70
Q
Traditional v. Genomic
(bull traits)
A
- If you wait until you have a fairly elderly bull with lots of daughters, can be assured there is a reliability for milk yield, etc.
71
Q
Inbreeding Index
(bulls)
A
72
Q
Pedigree Analysis
A
- A deleterious mutation (recessive) could have come from a common ancestor
- as there is more inbreeding, you are more likely to have offsroing that are homozygous zygotes for the recessive gene
73
Q
Genetic Causes of Embryo Loss
A
- the uterus could be a bad environment
- but equally there could be an inherit quality of the embryo itself
- 30% are due to the embryo itself and not the env’t or dam
*
74
Q
Haplotypes and Genes –> prenatal death cattle
A
- increasing # of mutations are becoming identified
75
Q
Breeding Goals
A
76
Q
KPI’s
A
- Can’t be better at everything
- need to pick specific qualities to focus on
77
Q
Choosing a Bull: 1
A
78
Q
Choosing a Bull:2
(PLI)
A
- is sexed semen availabe? (not all bulls have this available)
79
Q
Bull Evaluations
A
80
Q
Breeding Bull Semen
A
81
Q
How to Choose a Bull?
A
82
Q
A
