Population Genetics Flashcards
What are genetic principles applied to?
Entire populations
Where do genetic forces act?
At the population level
What is the phenotype of an animal?
What we can see and measure
What are the four genetic forces that act upon populations?
Genetic drift (inbreeding)SelectionMigration (out-crossing)Mutation
How can small population sizes have an adverse effect on genetic diversity?
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
What is the inbreeding coefficient?
The probability that the two copies of a gene are identical by descent
What is the inbreeding coefficient assessing?
Risk of inheriting genes not actually looking at a specific gene
What are some examples of inherited recessive disease in companion animals?
Primary lens luxationProgressive retinal atrophyFucosidosisLeukocyte adhesion deficiency
Describe foal immunodeficiency syndrome
Fell and Dales poniesWeight lossFailure to suckleIncreased salivationDull demeanourOpportunistic infectionsAnaemiaB-lymphocyte deficiency
What can inbreeding result in?
Very sick individuals as well as compromising the fitness of the whole inbred line
What is the rate of inbreeding?
Change in average inbreeding coefficient over time or generations
What does the rate of inbreeding apply to?
Populations
What does a steepr rate of inbreeding indicate?
Alleles are fluctuating to a greater degree and diversity lost more quickly
What is rate of inbreeding proportional to?
Effective population size
What is the formula for the effective population size?
Ne= 1/(2*rate of inbreeding)
What is the effective population size?
The number of breeding individuals in a random mating population that would have the same rate of inbreeding seen in the real population
Why does population substructure affect the effective population size?
Different subgroups used for breeding - either geographically or by use e.g. working, show etc.
How can the long-term health of a population be managed?
Manage loss of diversity by controlling the rate of increase in inbreeding
What is the first question we must ask when controlling inbreeding?
What is the end goal?
WHat should the rate of inbreeding be constrained to? What should the effective population size be at least?
Rate of inbreeding should be no more than 0.5% per generationEffective population should be 100 at least (<50 population at risk)
What are some possible solutions to controlling inbreeding in companion animals?
Minimise coancestry of matings - distantly related as possibleIncrease number of animals used for breedingEqualise use of males and femalesOptimise genetic contributionsOut-crossing
What should be set out when beginning a breeding programme?
Breeding goals
What test should be used when setting up a breeding programme to control a single gene disease?
Single locus DNA test
What needs to be used to evaluate the genetics within a breeding programme for complex diseases?
Estimated breeding valuesGenomic breeding values
Why is estimating the genetic variation using EBVs and GBVs not that reliable for making breeding selections?
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
How do we analyse complex disease when using a breeding programme?
Use residual estimate maximum likelihood and best linear unbiased predictionInvolve phenotypic data and pedigree as well as genetic variation, heritability, genetic correlations and EBVs
What is heritability?
The proportion of phenotypic variation made up of variation in the genes
What is disease heritability specific to?
Populations
What is the difference between EBVs and heritability?
EBV is the estimated genetic liabilities of diseaseHeritability is the proportion of observable variation made up of genetic variation
What does the accuracy of EBVs rely on?
Information from relatives
How can DNA be used to improve the accuracy of breeding values?
Can tell you regions on the genome that have an influence on the trait in question and improve selection
What is the benefit of estimated breeding values with non-continuous diseases?
Allow us to distinguish between clear dogs with a high and low risk of the disease
How can we determine the response to selection?
Plot EBVs over time and look whether trend has gone down
What is the selection intensity?
The difference from the average of selected individuals to the population mean
How does excluding the very worst animals genetically affect rate of decrease in undesired trait?
Response occurs over a very long period of time
How can a much quicker response in selection be achieved?
Selecting only top percentage of dogs genetically to breed from - increase selection intensity
What must a high selection intensity be balanced with?
Only using small number of breeding animals so need to balance with inbreeding
What are the steps to breeding success in companion animals?
Have good population-wide breeding goalsGood data collection proceduresAppropriate evaluation of geneticsSufficient selection pressures
What is the main measure of fertility in the dairy industry?
Calving intervals - time between calvings
What has been made better and worse in the modern dairy cow?
Increased genetic potential for yieldComes at the cost of lower fertility, poorer health and the lower utility of the cow
What are high input/output systems?
Cows are managed for optimum milk yield by feeding high quailty diets and lowering energy output in other areas
What are the three likely systems used for dairy farming?
High input/output systemsPasture based productionNiche markets (organic production)
What is the main tool that a breeder has to improve his animals?
Genetic selection
What is the information used by farmers to select breeding animals?
Breeding values - genetic merit of the animalPredicted transmitting ability
What are selection indexes?
Combinations of desirable traits
What two things need to be decided when selecting for more than one trait?
Which traits to use?How to weight different traits optimally?
What do selection indexes allow us to do?
Independently rank animalsCombine PTAs using relative values
What are the two parts of the selection index?
Goal and index
What were selection indexes traditionally used for in dairy cows?
Production and profit
What is the recent transition in use of selection indexes in dairy cows?
Incorporating wider variety of traits (fertility, health, welfare etc.) into the production indexes
What six things were included in the profitable lifetime index?
MilkFatProteinLifespanSomatic cell countLocomotion
How can weighting the financial gains of certain traits in dairy cows affect herd health?
Farmer can select to improve profitable lifetime index of cow while improving herd health and making more money
What is the genetic correlation between SCC and mastitis?
0.65 - fairly well correlated
What is the heritability of SCC?
0.11 - not that heritable but more heritable than mastitis
What is SCC expressed as? What is a good SCC?
Expressed as % of PTAMinus PTA percentage as reduciton in transmission or heritability
Why do we need to look for bulls that break the average correlation values of traits with mastitis?
Will reduce the risk of mastitis by reducing the chance of the two values correlating and separating them if one is selected for
How can we improve traits within breeding programmes on farms?
Include them within the profitable breeding indexes
How can genetic improvement deliver results?
Higher outputLower costsGreater efficiency of productionHealthier cows
What needs to be done for genetic improvement to deliver?
Record our animals and manage them appropriately
What are the two ways that the breeding goals have been broadened in the dairy industry?
Enhance fertility by revising economic valuesInclude body energy loss (condition score) and environmental sensitivity to make more robust cows
What are the three things that the future dairy cow needs to be?
Higher yieldingHealthierMore efficient at turning inputs into outputs
What is driving the changes in breeding programmes in dairy cows?
The industry mainlyAlso government and society by addressing welfare issues within breeding programmes
