Population Genetics SA

Question 1

How does genetic drift due to inbreeding impact allele frequency?

Answer 1

^ fluctuation in levels due to effective smaller sample size -> loss of genetic diversity

Question 2

what is another name for alleles?

Answer 2

variants

Question 3

What is migration or outcrossing?

Answer 3

INtroduction of new genetic material

Question 4

What is a bottleneck?

Answer 4

Dramatic v in population size (eg. due to mass cull) exacerbates genetic drift

Question 5

What is IBD and when does it occour?

Answer 5

Identical by descent genes

- occurs due to inbreeding -> some shared alleles in siblings being rematched when mated

Question 6

What is the inbreeding coefficient? Give some standard valus

Answer 6

> probability that 2 copies of a gene are IBD
- 0.25 for full sibling or parent offspring mating
- 0.125 for offspring half sibling mating
- 0.0625 for offspring of 1st cousins
- inbred strains of mice in labs may be 0.8/0.9
does NOT refer to a specific gene so must calculate for both alleles then add together

Question 7

Why may IBD genes cause problems?

Answer 7

• random mutations in DNA mean errors and disease cuasing alleles present in every genome, but usually masked by normal alleles
• IBD ^ risk of shared mutation

Question 8

Give 5 examples of inherited recessive disease

Answer 8

PLL - primary lens luxation
PRA - progressive retinal atrophy 
Fucosidosis
CLAD - leukocyte adhesion deficiency 
FIS - foal immunodeficiency syndrome

Question 9

What does inbreeding depression cause?

Answer 9

• sick individuals

- v fitness of whole line /less robust population

Question 10

What is the rate of inbreeding referred to as? How is it defined?

Answer 10

Delta F = change of average inbreeding coefficient over time or generations

Question 11

what is the expected inbreeding rate?

Answer 11

natural rate of inbreeding -> v genetic diversity
usually a lot lower than popular breeds inbreeding rates, may be higher than some rare breeds Id negative assortative mating is carried out [breeding least related individuals] (cf. random matings)

Question 12

What is the effective population size referred to as? How is it defined?

Answer 12

Ne = 1/2*DeltaF
- the number of breeding individuals in a hypothetical RANDOM mating population that would have the same rate of inbreeding as seen in the real population.
- ie. HIGH Ne =
LOW Ne =

Question 13

How does Ne differ to expected in popular breed populations?

Answer 13

Still relatively low - probably due to population substructure eg. working v pet breeds, geographical lociation etc.

Question 14

What Ne should be aimed for in a breeding population?

Answer 14

100 at least

Question 15

What is the aim for Delta F values per generation?

Answer 15

< 0.5%

Question 16

What will happen if Ne < 100 and Delta F >0.5%?

Answer 16

Population fitness will steadily decrease and become unviable in long term due to v fertility

Question 17

Give 5 possible solutions to breeding populations with high rate of inbreeding

Answer 17

• minimise kinship./copancestry of matings
• ^ no breeding animals
• === males and females number of breeding individuals
• optimise genetic contribution (negative assortative mating, evolutionary algorithsm -> breed least related individuals)
• Outcrossing -> hybrid vigour (only in first cross, not perpetuated in subsequent crossing)

Question 18

Why is optimising genetic contribution easier in some industries than others?

Answer 18

dairy = highly data driven, AI
dogs = breed local individuals, less data

Question 19

Why is affected/clear/carrier status not a helpful trichotomous distinction of individuals in some cases?

Answer 19

• multiple genes involved in most complex diseases

- allostatic, environmental interactions of genes mean genetic variation CURVE more useful

Question 20

Why may phenotypic judgement of individuals not be useful for genetic decsions? breeding etc/

Answer 20

Environmental factors likely to impact phenotype eg. hip score more than purely genetics

Question 21

What does heritability refer to?

Answer 21

Proportion of phenotype occouring due to genetics alone when environmental fators are removed

• ^ heritability means trait will respond well to selective breeding
• population specific
• relies on large database representative of the population, looking at phenotype and pedigree and taking into account relatives of each individual

Question 22

Give a disease with high heritability

Answer 22

Osteosarcoma in Scottish deerhounds

Question 23

Give a disease with low heritability

Answer 23

Elbow dysplasia (GSDs)

Question 24

What are EBVs?

Answer 24

Estimated breeding value based on relatives of an individual to try and minimise impact of environment - much more reliable than phenotype alone

Question 25

How have EBVs been mad more accurate?

Answer 25

Use of genomic information as well as dam/sire, sibling, offspring and own measurements

Question 26

Which population uses GBVs and which will likely begin to use them in the future?

Answer 26

Dairy currently uses

Dogs - next few years

Question 27

Why are EBVs useful for discrete disease? eg. bloat, epilepsy etc. (have it or don’t)

Answer 27

Distinguish between clear animals with high and low risk of disease (phenotype is imprecise as if animal doesn’t have disease, no further analysis can be carried out)

Question 28

How does selection intensity affect success of phenotype improvement in a population?

Answer 28

Due to normal (ish) distribution of hip scores, exluding above a certain threshold may only eliminate 20% of population, meaning seletion pressure is not very strong
- if selection intensity is increased (eg. by selecting from only best 20% animals (excluding 80% of population) same results can be achieved in a much shorter space of time)