Genetics

What are the 2 main types of genetic disease?

hereditary and congenital

What is genetic disease?

a disease caused completely or partly by genetic variation

What is a hereditary disease?

a genetic disease that can be transmitted from parent to offspring

What is a congenital disease?

a disease that is present from/ before birth which can be due to genetic or environmental factors

How do vets use preventative medicine to reduce genetic disease?

By scoring at-risk breeds for certain diseases as they mature, and preventing individuals with the worst cases of the disease from breeding

What are the reasons for selective breeding?

to change the appearance of animals

to reduce hereditary disease

to improve productivity and fitness

to improve the resilience of populations to stresses/diseases

to adapt animals to their current environment/function

What are the different technologies used to control breeding?

artificial insemination

semen sexing

multiple ovulation and embryo transfer

in-vitro fertilisation

juvenile in-vitro embryo transfer

cloning

gene editing

What is a gene?

a DNA segment at a specific position on the genome that encodes a functional product

What is an allele?

a different form of the same gene which combines with another to code for a characteristic

What is genotype?

the genetic makeup of an animal at one or more loci (can be a single gene or multiple)

What does it mean to genotype an animal?

to measure the genetic variants across the genome of an animal, typically using SNPs

What is phenotype?

the physical representation of the genetic makeup of an animal combined with environmental factors

What are the features of qualitative genetic traits?

discrete categories

usually monogenic or oligogenic

What are the features of quantitative genetic traits?

vary on a continuous or ordered scale

usually polygenic

Oligogenic/ monogenic

A genetic trait that is influenced by a small number of genes

Polygenic

A genetic trait that is influenced by many genes and environmental factors

What is complete genetic dominance?

When one allele is always dominant over another, meaning that a heterozygous genotype will produce the dominant phenotype

What is incomplete genetic dominance?

When the dominant allele for a trait is not completely dominant and so the heterozygous phenotype is closer to the homozygous dominant but not completely the same, causing 3 different phenotypes to be possible as an intermediate is formed

What are the different patterns of inheritance?

sex-linked, sex-limited, sex-influenced, genomic imprinting

What is a sex-linked gene?

a gene found on a sex chromosome

What is a sex-limited gene?

a gene which is only expressed in the phenotype of one gender

What is a sex-influenced gene?

a gene which is expressed differently between the different genders

What is genomic imprinting?

when the expression of an allele depends on whether it was inherited from the sire or the dam

How does sex-linked inheritance work?

Certain genes are usually X-linked, because there are more genes on the X chromosome than the Y, which means that recessive X-linked diseases are more readily expressed in males

If the father is the X-linked gene carrier, he cannot pass this onto his sons because they must inherit his Y chromosome

What happens during X-inactivation?

one X chromosome is randomly inactivated in each cell in females, meaning that each allele on one X chromosome in each cell is turned off so one trait is represented e.g. tortoiseshell cats

Can X-inactivation happen in males?

yes, but it causes them to be sterile

What is epistasis?

When the allele at one locus masks or enhances the effect of an allele at another locus

What is pleiotropy?

When variation at one locus influences more than one phenotypic trait

What is incomplete penetrance?

only a proportion of animals with a particular genotype express the associated phenotype

What is variable expressivity?

animals with the same gene can differ in the severity or form of the phenotype caused by that gene

(e.g. polydactyl cats have a range of the number of extra digits)

What is genetic codominance?

When the effects of both alleles are visible in a heterozygous animal

How are mitochondrial genes inherited?

they are passed down from mother to offspring, but they are not sex-linked

What are Mendel’s 3 laws?

law of dominance, law of segregation, law of independent assortment

What does Mendel’s law of segregation say?

each parent passes one of their alleles onto their offspring at random

What does Mendel’s law of dominance say?

some alleles are dominant and others are recessive

What does Mendel’s law of independent assortment say?

genes for different traits are inherited independently

How does gene editing work?

an enzyme (e.g. Cas9) is used to cut open DNA and disrupt, delete or insert DNA at a target location

What phenomenon contradicts Mendel’s law of independent assortment?

genes that are close together on the same chromosome are more likely to be inherited together, meaning that they are not always assorted independently

What is linkage disequilibrium?

when alleles at different loci occur together more often than expected by chance

What is a haplotype?

a group of genetic variants on the same chromosome that tend to be inherited together

What does SNP stand for?

single nucleotide polymorphism

What is an SNP?

a single-base difference in DNA between animals

What do genome-wide association studies test?

the association between SNPs across the genome and a phenotype

What is allele frequency?

the proportion of all copies of a gene that are a particular allele

What is genotype frequency?

the proportion of animals in a population with a particular genotype

What can allele and genotype frequency be used to predict?

carrier frequency for recessive diseases and the genetic profile for the next generation

When must you use the Hardy-Weinberg equilibrium to identify genotype from phenotype?

when complete dominance is occuring so you cannot identify the genotype of individuals just form looking at them

What must occur for the allele frequency of a population to stay the same according to the Hardy-Weinberg equilibrium?

large population

random mating

no selection pressure

no mutations

no movement of genetics in or out of the population via migration

What is the Hardy-Weinberg equation for allele frequency?

p + q = 1

What does p represent in the Hardy-Weinberg equation?

the dominant allele

What does q represent in the Hardy-Weinberg equation?

the recessive allele

What does p² represent in the Hardy-Weinberg equation?

the frequency of homozygous dominant genotypes in a population

What does 2pq represent in the Hardy-Weinberg equation?

the frequency of heterozygous genotypes in a population

What does q² represent in the Hardy-Weinberg equation?

the frequency of homozygous recessive genotypes in a population

Which 2 factors affect the phenotype of an animal?

genetics and environment

What is the aim of selective breeding?

to change the average genetic merit of a population over multiple generations via increasing the frequency of desirable alleles and reducing disease-causing recessive alleles

What does selective breeding rely on?

genetic variation in a population

What are the 5 main mechanisms that create genetic variation?

mutation

meiosis

migration

genetic drift

selection

How does genetic mutation create genetic variation?

it is a source of new alleles in a population

How does meiosis create genetic variation?

random alignment and recombination creates new combinations of alleles

How does migration create genetic variation?

it allows alleles to move between populations

How does genetic drift create genetic variation?

it causes random changes in allele frequencies

How does selection create genetic variation?

certain alleles increase the survival of animals and become more common (either naturally or artificially)

In what circumstance can a genetic mutation be inherited by offspring?

when a mutation occurs in the germline

How does the distribution of phenotypic variation of a population appear as a graph?

bell-shaped curve

What is the study of quantitative genetics?

splitting up the phenotypic variation in a population into genetic and non-genetic variation

What are the features of additive genetic effects?

the effects of alleles can be added together and each allele contributes a predictable amount

What are the features of non-additive genetic effects?

the overall effect depends on the combination of alleles which interact differently with each other, making it harder to predict the presentation of offspring

What is narrow-sense heritability?

the additive genetic variation as a proportion of the total phenotypic variation in a population, which shows how much of a population’s characteristics are due to additive genetic variation

How do you calculate heritability?

additive genetic variation (±non-additive genetic variation)/ phenotypic variation

How do you interpret the results for the calculated heritability of a population?

the value calculated shows the percentage amount that the variation in a specific characteristic is attributable to genetic variation in the population

What are the common reasons for low heritability estimates?

errors in pedigree recording

misclassification of phenotype

large environmental variation

low additive genetic variation

What is a correlation?

an association between two variables

What is the correlation coefficient?

a mathematical measure of the strength and direction of the association between 2 quantities (-1 to +1)

What is phenotypic correlation?

when animals with one phenotype tend to also have another phenotype

What is genetic correlation?

when the genetic merit for one trait is associated with genetic merit for another trait, meaning that selection for one trait can also change another trait

What are the 2 main causes of genetic correlation?

one gene affects 2 traits

variants affecting the two traits are inherited together because of linkage disequilibrium

What does indentical by descent mean?

when a randomly selected allele from two individuals are inherited from the same ancestral copy and so are identical

What is the inbreeding coefficient?

the probability that a randomly selected allele from two individuals are inherited from the same ancestral copy and so are identical, therefore giving a measure of how genetically related two individuals are

How do you calculate the inbreeding coefficient of an individual?

1. identify the common ancestors between the individual’s parents

2. find all loops from the individual’s parents to the common ancestor(s) and back to the other parents

3. count the number of individuals in each loop

4. the number(s) you have calculated is n, subsitute this into the inbreeding coefficient equation

What are some problems caused by inbreeding?

decline in performance

increased homozygous individuals expose harmful recessive alleles

reduced genetic variation in a population

genetic selection increases relatedness and inbreeding

What is the current advice to manage inbreeding?

aim to limit the increase in inbreeding between generations to less than 1%

What is the difference between broad-sense and narrow-sense heritability?

broad-sense includes both additive an non-additive genetic variation, whereas narrow-sense only includes additive genetic variation

would typically always use narrow-sense

What is the estimated breeding value of an animal?

an estimate of the genetic merit of that animal calculated using the animal’s performance, relations’ performance, genomic information and systematic environmental effects

How is the predicted transmitting ability of an individual calculated?

the expected deviation of the offspring’s performance from the population mean is doubled, because each parent passes on half of their genetics

What is the predicted transmitting ability of an animal?

the expected deviation of the offspring’s performance from the population mean

How is the estimated breeding value of an animal calculated?

heritability x (

How do you calculate the estimated breeding value of an animal at birth?

(0.5 x EBV of sire) + (0.5 x EBV of dam)

What is the reliability of EBV?

how confident you are that the EBV measures the true genetic merit of an animal, sometimes given as accuracy

What is the average reliability of parental-average EBV?

30-35%

How much weight is progeny performance given when calculating EBV?

when there are many progeny, it provides much stronger evidence but when few progeny or low heritability the estimate is pulled more towards the population average

Which factors affect reliability?

number of records

genomic information

pedigree

number of offspring

What is phenotypic selection?

assessing an animal’s characteristics to decide whether it has good genetics for breeding or not

Why is phenotypic selection not always very accurate?

does not account for heritability of a trait

doesn’t actually measure the genetics of an animal

only tests for traits that have already been presented (doesn’t include genes for degenerative disease that might develop later in life)

How should you implement genetic selection?

set breeding goals

aim to improve the average genetic merit of a population to improve the average phenotype

have a breeding strategy

maximise genetic gain

control inbreeding

What is a selection index?

a measure of a variety of different important traits in a population which contribute to herd productivity, this promotes balanced selection when breeding

What are the advantages of crossbreeding?

combines the strengths of different breeds

introduces genetic variation

reduces inbreeding/ relatedness

heterosis

What is heterosis/hybrid vigor?

an extra boost in performance above the mid-parent mean due to increased heterozygosity which leads to more non-additive genetic effects in the offspring

What is genetic gain?

the increase in genetic merit over time for a given trait or a group of traits in a breeding objective

What causes faster genetic gain?

better animals selected

increased accuracy of selection

maintaining genetic variation

reducing intervals between generations