lecture 16- quantitative genetics Flashcards
polygenic inheritance
Polygenic inheritance refers to the inheritance of a trait governed by more than one genes. Generally, three or more genes govern the inheritance of polygenic traits. Multiple independent genes have an additive or similar effect on a single quantitative trait.
continuous traits
influenced by
1) alleles at many loci (polygenic) and/or
2) environmental effects
many genes contribute to single phenotype
quantitative trait loci
heritability
the proportion of phenotypic variance that can be attributed to genetics
*if same genetics but different environment, lower heritability (increase in environmental variance)
***specific to particular population in particular environment
backcross
Backcrossing is a crossing of a hybrid with one of its parents or an individual genetically similar to its parent, to achieve offspring with a genetic identity closer to that of the parent. It is used in horticulture, animal breeding, and production of gene knockout organisms
intercross
A mating between two members of the F1 generation or between two animals that are heterozygous at the same locus
A cross between two identically hybrid individuals (A/a X A/a).
heritability
the proportion of total phenotypic variation that is due to genetic differences
mean (x with bar on top)
average measure which provides information about the center of the distribution
variance (s^2)
indicates the variability of a group of measurements, or how spread out the distribution is
(the great the variance, the wider the spread in the distribution)
phenotypic variance (v with subscript p)
can be measured in a population and then partitioned into two components: genetic and environmental
phenotypic variance (v with subscript p)
can be measured in a population and then partitioned into two components: genetic and environmental
broad sense heritability (h^2)
proportion of phenotypic variance that is due to genetic variance
(i.e.) how much of the variation is genetic vs how much is environmental?
broad sense heritability
Broad-sense heritability, defined as H2 = VG/VP, captures the proportion of phenotypic variation due to genetic values that may include effects due to dominance and epistasis.
narrow sense heritability
Narrow-sense heritability is defined as the fraction of phenotypic variance that can be attributed to variation in the additive effects of genes ( V A ) : h 2 = V A / V P ⋅ . Narrow-sense heritability is always less than or equal to broad-sense heritability.
monozygotic twins
single egg breaks in two
100% same genes, so same phenotype
dizygotic twins
two eggs fertilized at same times
50% same genes
correlation coefficient (r)
measures the strength of association between two variables, as in the degree of scatter in the points from the line (NOT slope)
higher r, stronger correlation
how do we calculate heritability in twin studies
broad sense heritability can be estimated by taking twice the difference of the correlation coefficients for a quantitative traits in monozygotic vs dizygotic twins
H^2= 2(r for monozygotic- r for dizygotic)
interaction variance
arises when the effect of a genotype depends on the specific environment it was found
(such as man and woman having same genotype for height but man is taller because of testosterone and hormones affecting gene expression)
norm of reaction
the pattern of phenotypic expression of a single genotype across multiple environments
components of phenotypic variance
genetic variance (vg)
environmental variance (ve)
genetic environment interaction variance (vge)
**a GE interaction doesnt require the lines to cross, they just have to have different slopes
dominance effects
when interactions between alleles complicate things
another way to find little h^2 besides v additive/v phenotype?
R/S
Selection differential/response to selection
limitations of heritability
There are many aspects of experimental design that can help to
increase power (i.e., chances to find QTL).
what are the steps?
1) Ideally, when you set up a cross between two “parental” lines, you would like those parents to be as different as possible in the trait of interest to increase power
2) one should consider the genetic makeup of the parents of
the cross. If the parents of the cross are inbred strains (i.e., they are
homozygous at all sites), then any differences between the strains will be a maximally informative marker locus, and useful for QTL mapping
3) Another factor to consider (once you have decided on the parents
of the cross) is the cross design itself; that is, if you choose to perform an
F2-intercross or a backcross
4) the final step is to ask which marker loci
show an association with the phenotype of interest in the second
generation hybrids. The closer the marker is to the causal genetic variant, the stronger the association
how do you determine if you should perform an intercross vs a backcross?
This decision can be based on
the phenotype of the first generation (F1) hybrid phenotype. If the F1 (let’s call it “Aa” genotype) phenotype strongly resembles parent 1 (AA), this suggests that the alleles in parent 1 (A alleles) are dominant. Thus, it makes sense to “backcross” the F1 hybrids to parent 2 with the recessive aa alleles; this way, the F2 offspring will be either Aa or aa in equal frequency. (Note: if you did an intercross Aa x Aa, then you would have 1:AA, 2:Aa 1:aa, but since AA and Aa are indistinguishable, the phenotypic ratio is 3:1, which is less diverse than 1:1 of the backcross). If the F1 hybrid resembles parent 2 in phenotype, then you should backcross it to parent 1, for the same reasons stated above. In either case, we want the individuals in the next generation to be as genotypically and phenotypically diverse as possible. Finally, if the F1 phenotype is intermediate in phenotype between the two parents, then the F2- intercross design provides maximal power and will likely produce a range of phenotypes and genotypes between the two extreme phenotypes of the parents.
total phenotypic variance can be apportioned into three components
VP = VG + VE + VGxE
Additive genetic variance
(VA)
comprises the additive effects of genes on phenotype, which can
then be summed to determine the overall effect on phenotype. This can
also be thought of as incomplete dominance, whereby the heterozygote
has an intermediate phenotype to the two homozygotes
dominance genetic variance (VD)
In the case of VD, the heterozygote has the same phenotype as the dominant homozygote, which means that one cannot predict the offspring’s phenotypes based solely on the parent’s phenotypes. VD is therefore a complicating factor that can make investigating the genetic basis of traits harder. Importantly, it’s the additive variance that determines the resemblance between parents and offspring. For these reasons, scientists are often more interested in the proportion of VP that is due to VA, which is referred to as the narrow sense heritability: h2 = VA/VP
response to selection (R)
is dependent on the narrow sense heritability. R is defined as the differences in means between the trait in the new generation and the original population. When h2 is high, offspring resemble their parents, making the selection process more efficient. Conversely, when h2 is low, offspring will bear less resemblance to their parents, impeding selection efforts. The response to selection is therefore dependent on h2
