Population Genetics

Question 1

What are genetic principles applied to?

Answer 1

Entire populations

Question 2

Where do genetic forces act?

Answer 2

At the population level

Question 3

What is the phenotype of an animal?

Answer 3

What we can see and measure

Question 4

What are the four genetic forces that act upon populations?

Answer 4

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

Question 5

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

Answer 5

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

Question 6

What is the inbreeding coefficient?

Answer 6

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

Question 7

What is the inbreeding coefficient assessing?

Answer 7

Risk of inheriting genes not actually looking at a specific gene

Question 8

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

Answer 8

Primary lens luxationProgressive retinal atrophyFucosidosisLeukocyte adhesion deficiency

Question 9

Describe foal immunodeficiency syndrome

Answer 9

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

Question 10

What can inbreeding result in?

Answer 10

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

Question 11

What is the rate of inbreeding?

Answer 11

Change in average inbreeding coefficient over time or generations

Question 12

What does the rate of inbreeding apply to?

Answer 12

Populations

Question 13

What does a steepr rate of inbreeding indicate?

Answer 13

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

Question 14

What is rate of inbreeding proportional to?

Answer 14

Effective population size

Question 15

What is the formula for the effective population size?

Answer 15

Ne= 1/(2*rate of inbreeding)

Question 16

What is the effective population size?

Answer 16

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

Question 17

Why does population substructure affect the effective population size?

Answer 17

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

Question 18

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

Answer 18

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

Question 19

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

Answer 19

What is the end goal?

Question 20

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

Answer 20

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

Question 21

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

Answer 21

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

Question 22

What should be set out when beginning a breeding programme?

Answer 22

Breeding goals

Question 23

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

Answer 23

Single locus DNA test

Question 24

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

Answer 24

Estimated breeding valuesGenomic breeding values

Question 25

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

Answer 25

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

Question 26

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

Answer 26

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

Question 27

What is heritability?

Answer 27

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

Question 28

What is disease heritability specific to?

Answer 28

Populations

Question 29

What is the difference between EBVs and heritability?

Answer 29

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

Question 30

What does the accuracy of EBVs rely on?

Answer 30

Information from relatives

Question 31

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

Answer 31

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

Question 32

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

Answer 32

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

Question 33

How can we determine the response to selection?

Answer 33

Plot EBVs over time and look whether trend has gone down

Question 34

What is the selection intensity?

Answer 34

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

Question 35

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

Answer 35

Response occurs over a very long period of time

Question 36

How can a much quicker response in selection be achieved?

Answer 36

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

Question 37

What must a high selection intensity be balanced with?

Answer 37

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

Question 38

What are the steps to breeding success in companion animals?

Answer 38

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

Question 39

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

Answer 39

Calving intervals - time between calvings

Question 40

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

Answer 40

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

Question 41

What are high input/output systems?

Answer 41

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

Question 42

What are the three likely systems used for dairy farming?

Answer 42

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

Question 43

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

Answer 43

Genetic selection

Question 44

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

Answer 44

Breeding values - genetic merit of the animalPredicted transmitting ability

Question 45

What are selection indexes?

Answer 45

Combinations of desirable traits

Question 46

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

Answer 46

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

Question 47

What do selection indexes allow us to do?

Answer 47

Independently rank animalsCombine PTAs using relative values

Question 48

What are the two parts of the selection index?

Answer 48

Goal and index

Question 49

What were selection indexes traditionally used for in dairy cows?

Answer 49

Production and profit

Question 50

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

Answer 50

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

Question 51

What six things were included in the profitable lifetime index?

Answer 51

MilkFatProteinLifespanSomatic cell countLocomotion

Question 52

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

Answer 52

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

Question 53

What is the genetic correlation between SCC and mastitis?

Answer 53

0.65 - fairly well correlated

Question 54

What is the heritability of SCC?

Answer 54

0.11 - not that heritable but more heritable than mastitis

Question 55

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

Answer 55

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

Question 56

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

Answer 56

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

Question 57

How can we improve traits within breeding programmes on farms?

Answer 57

Include them within the profitable breeding indexes

Question 58

How can genetic improvement deliver results?

Answer 58

Higher outputLower costsGreater efficiency of productionHealthier cows

Question 59

What needs to be done for genetic improvement to deliver?

Answer 59

Record our animals and manage them appropriately

Question 60

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

Answer 60

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

Question 61

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

Answer 61

Higher yieldingHealthierMore efficient at turning inputs into outputs

Question 62

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

Answer 62

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