Genetics Exam 2

What are systematic and/or natural forces for change in gene frequency/HWE?

• migration

• mutation

• selection

What are non-systematic forces for change in gene frequency/HWE?

• random drift or chance

Migration or gene flow

movement of individuals from one place or population to another resulting in the introduction of new genes into the mixed population

Outbreeding

The mating of unrelated individuals leading to increase in heterozygosity

Mutation

a heritable change in genetic material arising from processes such as deletion, addition, substitution, or duplication of a base or bases or from structural changes in chromosome. May be spontaneous or induced by radiation or chemicals.

Point mutation

Arise from changes in the base sequence of DNA

Selection

• natural selection: survival of the fittest, is often directed against the extreme phenotypes while the average phenotypes are naturally the fittest (heterozygote advantage)

• artificial selection is based on the choice by the breeder of individuals that become parents of the next generation

Fitness

An individuals ability to contribute offspring to the next generation. It is a function of the individuals viability (survival to reproductive age) and fertility (a measure of a number of offspring produced by a surviving individual)

Selection coefficient (s)

A measure of strength of selection, that is, the proportionate reduction in the contribution of a particular genotype, relative to the most favoured genotype

Hoe can we understand the strength of selection for a genotype?

By comparing it to the genotype with the strongest selection probability

Selection against dominant genotypes

selection against all dominant genotypes results in a frequency of zero for the dominant gene. This includes all heterozygotes, leaving behind only homozygous recessive.

Selection against recessive genotype

Reduction in frequency of recessive gene will occur but cannot be eliminated from the population. Leaves behind homozygous dominant and heterozygous.

Selection favouring heterozygotes

Selection that is favours heterozygotes is often due to heterozygotes advantage which drives the heterozygotes frequency to a maximum of 0.5

Random Genetic Drift or Chance

The change in allele frequency in a small population due to random fluctuation of genes or random sampling error rather than natural selection. Genetic drift can lead to loss or fixation of gene. Useful genes at low frequencies may be permanently lost while lethal or deleterious genes may be permanently fixed in small populations. The amount of change in allele frequency is described in terms of sampling variance, effective population, and amount of inbreeding.

True or false: Phenotypes are not affected by the environment. If you know the phenotype you can assume the genotype

True

Qualitative trait inheritance

• Traits that are controlled or affected by a single (monogenic) or a few gene pairs

• Largely inherited in a mendelian fashion

• Individuals showing the characters can be placed into discrete phenotypic classes (phenotypes for this trait exist in categories)

• Expression of phenotype is not typically affected by the environment

• Mathematically modeled as P = G

Penetrance

the percentage of animals carrying a specific gene who express the expected phenotype

Expressivity

refers to the degree, intensity or severity to which a particular penetrant genotype is expressed as a phenotype within individuals

What causes penetrance and expressivity in qualitative traits?

Caused by either gene modifiers, epistasis or the environment (polydactyly). The genes and alleles affecting qualitative traits are largely known.

Exceptions to penetrance and expressivity in qualitative traits?

• height in cattle is polygenic, but there are still single genes that have very large effects

• muscle mass in animals is likely polygenic but variation in myostatin can have a large effect

• breeding can address the simply-inherited form, the polygenic form, or both at the same time

How to infer genotypes

1. Phenotyping

2. Genotyping

3. Test mating

Simply inherited trait

physical or biological characteristic controlled by 1 or more genes, has clear phenotypic groups and consistent pattern of inheritance

Polygenic

controlled by many genes with small effects

How dominance level determines the effectiveness of using phenotype for selection

• no dominance or partial dominance we can use phenotype to infer genotype and select alleles we want

• complete dominance if desirable allele is b we can impose strong selection using phenotype alone, like by selecting red animals as parents

• If desirable is allele is B we can only impose moderate selection if we use phenotype since b alleles can hide in heterozygous genotypes

Selection based on phenotype: HYPP

Hyperkalemic periodic paralysis in horses is partially dominant. From phenotype alone its possible to infer the presence of the allele that causes muscle spasms and twitching. To reduce the frequency of this issue chose parents that don’t exhibit the twitching phenotype.

What three things influence effectiveness of selection?

1. Duration of selection

2. Intensity of selection

3. Current allele frequency

true or false: the more generations we apply selection the greater our progress.

True, duration influences effectiveness

When selecting against an unfavorable recessive using phenotype, how easy is it to eradicate the allele from the population?

Very difficult

Why do we not genotype all selection candidates so that carriers can be identified?

• cost may be prohibitive especially for large populations

• breeders may be concerned that an otherwise outstanding/valuable animal will be identified as a carrier and will lose value

• in dispersed populations different levels of adoption of genomics technologies can mean that many carriers are not identified

• for some simply-inherited traits that genes involved are still not known

How are the genes behind simply-inherited traits identified?

the general approach is to genotype many individuals from each phenotypic group at numerous loci in the genome. The genotypes are then compared to look for loci that show a difference between groups. Causation can be verified through additional experiments to show effects of DNA difference on gene products

VGL

Veterinary Genetics Laboratory is located at the UC Davis vet school

Are qualitative or quantitative traits affected by the environment?

quantitative

Quantitative trait inheritance

• expression of phenotype modeled as P = G + E

• show a continuous distribution

• in a large population, assume a bell-shaped normal frequency distribution

• many are of economic importance to animal breeders and are polygenic

• metric characters

Fisher’s infinitesimal (polygenic) model assumptions