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Principles of Science > Population Genetics > Flashcards

Population Genetics Flashcards

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1
Q

What are genetic principles applied to?

A

Entire populations

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2
Q

Where do genetic forces act?

A

At the population level

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3
Q

What is the phenotype of an animal?

A

What we can see and measure

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4
Q

What are the four genetic forces that act upon populations?

A

Genetic drift (inbreeding)SelectionMigration (out-crossing)Mutation

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5
Q

How can small population sizes have an adverse effect on genetic diversity?

A

Bigger fluctuations in allele frequency causing a loss in genetic diversityBottlenecks can form causing a contraction in the number of breeding populations (death or limited progenitors) leading to loss of diversity

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6
Q

What is the inbreeding coefficient?

A

The probability that the two copies of a gene are identical by descent

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7
Q

What is the inbreeding coefficient assessing?

A

Risk of inheriting genes not actually looking at a specific gene

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8
Q

What are some examples of inherited recessive disease in companion animals?

A

Primary lens luxationProgressive retinal atrophyFucosidosisLeukocyte adhesion deficiency

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9
Q

Describe foal immunodeficiency syndrome

A

Fell and Dales poniesWeight lossFailure to suckleIncreased salivationDull demeanourOpportunistic infectionsAnaemiaB-lymphocyte deficiency

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10
Q

What can inbreeding result in?

A

Very sick individuals as well as compromising the fitness of the whole inbred line

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11
Q

What is the rate of inbreeding?

A

Change in average inbreeding coefficient over time or generations

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12
Q

What does the rate of inbreeding apply to?

A

Populations

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13
Q

What does a steepr rate of inbreeding indicate?

A

Alleles are fluctuating to a greater degree and diversity lost more quickly

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14
Q

What is rate of inbreeding proportional to?

A

Effective population size

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15
Q

What is the formula for the effective population size?

A

Ne= 1/(2*rate of inbreeding)

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16
Q

What is the effective population size?

A

The number of breeding individuals in a random mating population that would have the same rate of inbreeding seen in the real population

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17
Q

Why does population substructure affect the effective population size?

A

Different subgroups used for breeding - either geographically or by use e.g. working, show etc.

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18
Q

How can the long-term health of a population be managed?

A

Manage loss of diversity by controlling the rate of increase in inbreeding

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19
Q

What is the first question we must ask when controlling inbreeding?

A

What is the end goal?

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20
Q

WHat should the rate of inbreeding be constrained to? What should the effective population size be at least?

A

Rate of inbreeding should be no more than 0.5% per generationEffective population should be 100 at least (<50 population at risk)

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21
Q

What are some possible solutions to controlling inbreeding in companion animals?

A

Minimise coancestry of matings - distantly related as possibleIncrease number of animals used for breedingEqualise use of males and femalesOptimise genetic contributionsOut-crossing

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22
Q

What should be set out when beginning a breeding programme?

A

Breeding goals

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23
Q

What test should be used when setting up a breeding programme to control a single gene disease?

A

Single locus DNA test

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24
Q

What needs to be used to evaluate the genetics within a breeding programme for complex diseases?

A

Estimated breeding valuesGenomic breeding values

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25
Q

Why is estimating the genetic variation using EBVs and GBVs not that reliable for making breeding selections?

A

Phenotype usually differs from genotype due to a number of different factorsSome examples of factors include in utero environment, neo-natal environment, feed intake, diet and exercise

26
Q

How do we analyse complex disease when using a breeding programme?

A

Use residual estimate maximum likelihood and best linear unbiased predictionInvolve phenotypic data and pedigree as well as genetic variation, heritability, genetic correlations and EBVs

27
Q

What is heritability?

A

The proportion of phenotypic variation made up of variation in the genes

28
Q

What is disease heritability specific to?

A

Populations

29
Q

What is the difference between EBVs and heritability?

A

EBV is the estimated genetic liabilities of diseaseHeritability is the proportion of observable variation made up of genetic variation

30
Q

What does the accuracy of EBVs rely on?

A

Information from relatives

31
Q

How can DNA be used to improve the accuracy of breeding values?

A

Can tell you regions on the genome that have an influence on the trait in question and improve selection

32
Q

What is the benefit of estimated breeding values with non-continuous diseases?

A

Allow us to distinguish between clear dogs with a high and low risk of the disease

33
Q

How can we determine the response to selection?

A

Plot EBVs over time and look whether trend has gone down

34
Q

What is the selection intensity?

A

The difference from the average of selected individuals to the population mean

35
Q

How does excluding the very worst animals genetically affect rate of decrease in undesired trait?

A

Response occurs over a very long period of time

36
Q

How can a much quicker response in selection be achieved?

A

Selecting only top percentage of dogs genetically to breed from - increase selection intensity

37
Q

What must a high selection intensity be balanced with?

A

Only using small number of breeding animals so need to balance with inbreeding

38
Q

What are the steps to breeding success in companion animals?

A

Have good population-wide breeding goalsGood data collection proceduresAppropriate evaluation of geneticsSufficient selection pressures

39
Q

What is the main measure of fertility in the dairy industry?

A

Calving intervals - time between calvings

40
Q

What has been made better and worse in the modern dairy cow?

A

Increased genetic potential for yieldComes at the cost of lower fertility, poorer health and the lower utility of the cow

41
Q

What are high input/output systems?

A

Cows are managed for optimum milk yield by feeding high quailty diets and lowering energy output in other areas

42
Q

What are the three likely systems used for dairy farming?

A

High input/output systemsPasture based productionNiche markets (organic production)

43
Q

What is the main tool that a breeder has to improve his animals?

A

Genetic selection

44
Q

What is the information used by farmers to select breeding animals?

A

Breeding values - genetic merit of the animalPredicted transmitting ability

45
Q

What are selection indexes?

A

Combinations of desirable traits

46
Q

What two things need to be decided when selecting for more than one trait?

A

Which traits to use?How to weight different traits optimally?

47
Q

What do selection indexes allow us to do?

A

Independently rank animalsCombine PTAs using relative values

48
Q

What are the two parts of the selection index?

A

Goal and index

49
Q

What were selection indexes traditionally used for in dairy cows?

A

Production and profit

50
Q

What is the recent transition in use of selection indexes in dairy cows?

A

Incorporating wider variety of traits (fertility, health, welfare etc.) into the production indexes

51
Q

What six things were included in the profitable lifetime index?

A

MilkFatProteinLifespanSomatic cell countLocomotion

52
Q

How can weighting the financial gains of certain traits in dairy cows affect herd health?

A

Farmer can select to improve profitable lifetime index of cow while improving herd health and making more money

53
Q

What is the genetic correlation between SCC and mastitis?

A

0.65 - fairly well correlated

54
Q

What is the heritability of SCC?

A

0.11 - not that heritable but more heritable than mastitis

55
Q

What is SCC expressed as? What is a good SCC?

A

Expressed as % of PTAMinus PTA percentage as reduciton in transmission or heritability

56
Q

Why do we need to look for bulls that break the average correlation values of traits with mastitis?

A

Will reduce the risk of mastitis by reducing the chance of the two values correlating and separating them if one is selected for

57
Q

How can we improve traits within breeding programmes on farms?

A

Include them within the profitable breeding indexes

58
Q

How can genetic improvement deliver results?

A

Higher outputLower costsGreater efficiency of productionHealthier cows

59
Q

What needs to be done for genetic improvement to deliver?

A

Record our animals and manage them appropriately

60
Q

What are the two ways that the breeding goals have been broadened in the dairy industry?

A

Enhance fertility by revising economic valuesInclude body energy loss (condition score) and environmental sensitivity to make more robust cows

61
Q

What are the three things that the future dairy cow needs to be?

A

Higher yieldingHealthierMore efficient at turning inputs into outputs

62
Q

What is driving the changes in breeding programmes in dairy cows?

A

The industry mainlyAlso government and society by addressing welfare issues within breeding programmes

Principles of Science (9 decks)

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