Population Genetics Flashcards by Leah Arth

Genetics

(3 aspects)

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Cellular Genetics

(4)

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

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Population Genetics

(3)

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

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Inheritance

(3)

can be simple or complex
natural selection –> cruel world picks out best
artificial: we are making it softer, helping animals that naturally wouldnt survive

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Single- gene vs. Complex

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

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Single Genes to Genetic Variation to Phenotypic Variation

pheotypic variation: variation we can see externally
Different ratios
9:9:9:3
9:6:6:3

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Multi-Gene Genetic Variation

Even with 3 genes affecting a phenotype, there are lots of variations (echo)

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Selection

(natural or Artificial)

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

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Selection

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

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Genetic Forces Acting on Breeds/Populations

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

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Selection can lead to Disease

pugs : big eyes and smashed mouth
a lot of white dogs are associated with disease

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Selection can also lead to Improved Health

(2)

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

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Molecular Genotyping

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

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Breeding Advice

(3)

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

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Common Disorders in Dogs

(prevalence %)

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

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Mendelian Traits and Dog Phenes

only 3.3% were single gene disroders - and were quite rare
Dog phenes–> physical characteristics htat are associated with disease

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Genetic x Environmental Variation

things happen along the way
phenotype is what we see in practice
we wont really ever know the genotype of this complexes

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Heritability

The higher the heratibility the more we can drive away by selective breeding

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Heratibilities of Notable Diseases

these values have to be taken as population specific

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Survival of the Fittest vs. Reproductive Success

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

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Analysis of Complex Disease

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Estimated Breeding Values

(EBV’s)

% 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)

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Use of EBV’s

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More accurate selection

(Hip Scores)

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)
*

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Binary Diseases

* We think of animals having a disease or not * but it isnt just yes or no! * SM: a disease in King Charles Spaniels

Advantages of EBV's for a "binary" trait

Selection Intensity (*i*)

* 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

Ensuring Successful Selection

Selection and Health

Mating of Relatives

* 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

Coefficient of Inbreeding ## Footnote **(COI)**

* level of recessivity goes really high * how related are the parents * used in pedigree analyses *

Inbreeding and Specific Inherited Disease

Inbreeding | (gene frequency)

* Even with not that high of a level of inbreeding, there can still be a rather decent effect

Inbreeding Depression

* modern dog breeds have small litters: may be a big result of recessive genes being acquired * echo *

Heterosis/Hybrid Vigour

* In reality you don't get in the middle, you get the extra effect * will decrease as generations continue

Hybrid vigour deteriorates after the F1

* Blue and Brown: totally inbred * want 1st generation?

Effective Population Size | (Ne)

Genetic Drift

* 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

Inbreeding/Genetic Drift Summary | (5)

Control of Inbreeding

Possible Solutions to Inbreeding | (5)

Why Outcross?

Conservation Genetics | (why does it matter?)

Conservation Genetics (genetic Diversity, Production Species, and Dogs)

* 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

National Trends in UK Dairy Herd

* milk production has gone up quite a lot while the number of cows has decreased

Lifetime Performance of a Dairy Cow

* 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

Key Performance Indicators for UK Dairy Herd (2017)

* He selects 500 herds from a population (each bar is a herd) * somatic cell count is an indicator of mastitis *

NMR Herds KPI | (2016-2017)

* 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)

Population Statistics of a Typical Dairy Herd

* 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?

Milk Production and Fertility | (phenotypic trends)

* 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

Milk Production and Fertility | (genetic correlations)

* 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

Main reasons for culling UK Cows?

* about 25% per each lactation * mastitis and lameness are very prevalent in the pop

Summary of Today's Dairy Cow | (4)

* 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

Goals for Future Dairy Cows

* 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

Population Genetic Tools

* each bull has its own individual genetic merit

Change in Emphasis

International Comparison

* proof done for bulls at an international level * different qualitites of the bulls in their pop * echo..ooops

Genetic Indices for Selection in UK

* 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

Genetic Links b/w Production, Health, and Fertility Rates (milk, fat, protein)

* 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

Selection against a Correlation

* echo

Somatic Cell Score | (1998)

* highly correlated with mastitis * PTA: predictable transmitable ability * trying to get somatic cell count to go down

Selection and Mastitis Susceptibility

* daughters of the bulls were doing worse in presence of SCC and Mastitis * luckily making a turn but still really high

Genetic Trends: Fertility Index

* Fertility is going downwards

Fertility Index | (FI)

* In rebuttal to a dropping Fertility--\> an index was created * Now is an aspect of picking a sire quality

Fertility Index - having an effect

until introduction of FI, the calving interval was increasing and then dropped after

Herd Health

* want to select for but harder to record

Health and Welfare Traits

* 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?

Lifespan Evaluation

* cows that have those traits on average have a longer life

Genomic Selection

Traditional v. Genomic | (bull traits)

* 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.

Inbreeding Index | (bulls)

Pedigree Analysis

* 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

Genetic Causes of Embryo Loss

* 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 *