Quantitative genetics

Question 1

discontinuous qualitative

Answer 1

traits can be categorised into few classesc

Question 2

continuous quantitative

Answer 2

characteristics vary along scale of measurement

Question 3

quantitative traits

Answer 3

complex- many genetic environmental influences

Question 4

qualitative traits

Answer 4

can be complex traits if categories reflect continuously variable underlying traits

Question 5

discontinuous characteristics

Answer 5

exhibits only a few easily distinguished phenotypes

Question 6

continuous characteristics

Answer 6

continuous quantitative characteristics exhibits a continuous range of phenotypes

Question 7

normal distribution

Answer 7

create bell shaped curve

Question 8

positively skewed distribution

Answer 8

to the right

Question 9

polyphenism (bimodal)

Answer 9

individuals in different conditions represent different traits

Question 10

meristic countable traits

Answer 10

determined by multiple genetic and environmental factors

Question 11

threshold traits

Answer 11

measured by presence or absence
how susceptible you are to a disease
takes into account a risk store

Question 12

complex traits are polygenic

Answer 12

controlled by many genes
phenotypic reflects the cumulative effects of alleles at many loci
influenced by environmental factors

Question 13

phenotypic variance

Answer 13

total amount of variation among individuals in some trait

Question 14

components of phenotypic variance

Answer 14

genetic variance
environmental variance

Vp=Vg+Ve (simple partitioning)

Question 15

heritable genetic variation

Answer 15

parent offspring variation
additive genetic variance

Question 16

non heritable genetic variation

Answer 16

genetic variation that does not contribute to parent-offspring resemblance

dominance genetic variance
epistatic variance Vi

Vg=Va+Vd+Vi +Ve

Question 17

heritable

Answer 17

phenotypic trait differences of individual reflect genetic differences

Question 18

inherited

Answer 18

property passed down from parent to offspring

Question 19

narrow sense heritability

Answer 19

the proportion of phenotypic variation that contributes to the resemblance between parents and offspring.

Va/Vp

Question 20

broad sense heritability

Answer 20

The proportion of phenotypic variation attributed to all types of genetic differences between individuals

Vg/Vp

Question 21

how can something be genetic but not heritable

Answer 21

for example, healthy parents and diseased child

diseased parents and healthy child

Question 22

how can narrow sense heritability be measured

Answer 22

by regression
linear relationship between phenotype of offspring and phenotype of their parents

Question 23

regression

Answer 23

predicting value of one variable if the other variable value is given

Question 24

regression coefficient

Answer 24

represents the slope of the regression line, indicating how much one value changes on.

Question 25

environmental impact on genotypes

Answer 25

variation due to different environments (eg more or less moist) Vp=Vg+Ve+Vge

Question 26

why are some traits correlated (eg taller and larger feet)

Answer 26

could be environmental (well fed) could be genetic due to pleiotropy or linkage disequilibrium

Question 27

correlations can reflect trade offs

Answer 27

trade off between seed size and number of Italian ryegrass folium multiform

Question 28

what is pleiotropy

Answer 28

single locus affects expression of multiple traits

Question 29

linkage disequilibrium

Answer 29

occurs when there is association between alleles at different loci not necessarily physical, but physical linkage can facilitate LD

Question 30

linkage disequilibrium

Answer 30

overrepresentation of alleles frequencies of coupling and repulsion gametes eg tall and big feet inherited together

Question 31

equation for deviation

Answer 31

F(AB)*F(ab)-F(Ab)*-F(ab)

Question 32

what does complete LD look like

Answer 32

pleiotropy

Question 33

recombination erodes LD

Answer 33

breaks up associated alleles effective at reducing linkage disequilibrium

Question 34

single heterozygote

Answer 34

only one chromosome is a heterozygote, no new haplotypes are created

Question 35

double heterozygotes

Answer 35

both homozygotes (AB, ab) so when recombination occurs new haplotypes are created

Question 36

genetic interactions

Answer 36

genetic effects we have discussed are assigned to a single locus ( so measured independent of other loci) effects on one loci will often depend on the alleles present at another locus

Question 37

epistasis

Answer 37

one gene controlling or modifying the expression of another gene masks or modifies (epistatic) gene whose effect is altered (hypostatic)

Question 38

genetic background dependence

Answer 38

another locus that has an affect on the locus we focus on or more generally multi locus genotype for example affects on mutations on mice depends on the strain of mice

Question 39

independence and interactions

Answer 39

genes have no effect on their own. genes contribute to regulatory networks, biochemical pathways, metabolic pathways so many opportunities for genes to interact

Question 40

how do loci interact

Answer 40

in complex networks constructed from pairwise interactions (between two loci)

Question 41

how do we identify genes causing continuous variation

Answer 41

locate loci that affect quantitative characteristics map quantitative trait loci (QLS) genome-wide association studies (GWAS)

Question 42

QTL analysis

Answer 42

location of genome that causes different values of the trait in question does not have to be caused by differences in the coding regions of the gene (instead maybe regulatory elements) not associated with differences I proteins but rather in gene expression

Question 43

how are QTL analysis identified

Answer 43

using statistical approaches testing either different genotypes have significantly different trait values (phenotypes) done using genetic markers (where alleles can be distinguished) identify causal variation linked to markers

Question 44

genome wide association studies

Answer 44

identifies locus associated with that variation testing whether groups of different phenotypes have different frequencies of alleles at a locus use genotyping array data, also be done using type of marker data

Question 45

linear model approach

Answer 45

can we predict a phenotype by taking into account allele frequency in an individual

Question 46

characteristics of gwas

Answer 46

can be done for any measurable trait large sample sizes can be controversial

Question 47

results of GWAS depend on what

Answer 47

depends on trait heritability and size effects

Question 48

missing heritability problem

Answer 48

GWAS often fail to explain most variation traits due to statistical power enormous number of loci with small effect too low effect to pick up on also overestimation of heritability- usually environment plays a key role in

Question 49

what do GWAS and QTL analysis aim to identify

Answer 49

specific loci associated with trait variation and characterise their effects simply want to use genomic data to predict the phenotype of an individual

Question 50

what info do we have from previous GWAS

Answer 50

500K id from UK biobanks whole genome sequences correlations of around 0.65 between what we are predicting and what we are observing in phenotypic variations