Module 5

Question 1

What is a discontinuous (or qualitative) trait?

Answer 1

Discontinuous (or qualitative) trait: a trait having only a few, distinct, phenotypes; often with a simple relationship to genotype (but not always).

Question 2

What is a polygenic trait?

Answer 2

Polygenic trait: a trait determined by the affects of alleles at many different loci.

Question 3

What are quantitative traits?

Answer 3

Quantitative traits are continuous

Question 4

What are threshold traits?

Answer 4

Threshold traits are either present or absent

Question 5

What are meristic traits?

Answer 5

Meristic traits are countable traits.

Question 6

What makes up continuous variation?

Answer 6

Continuous variation is the result of genetic factors and environmental factors.

Question 7

What is the effect of the environment on genotype?

Answer 7

One genotype will have a range of phenotypes.
- therefore, we are no longer confident that we can always use phenotypes to distinguish among genotypes.

Question 8

Phenotypic range?

Answer 8

Phenotypic ranges can overlap

Question 9

How come we cannot determine genotype from phenotype anymore?

Answer 9

For many complex traits it can be impossible to assign a genotype to an individual on the basis of phenotype

Question 10

Definition of threshold traits and examples?

Answer 10

Threshold trait: phenotype is binary (1,0); but susceptibility varies continuously

examples:
* disease susceptibility (clinical)
* drug sensitivity (adverse side affects)

Question 11

Definition and examples of meristatic traits?

Answer 11

Meristic trait: countable phenotype vary continuously (“quasi” quantitative trait)

example: abdominal bristle number in fruit flies

Question 12

Definition and examples of continuous traits?

Answer 12

Continuous traits: have the potential to assume any value within a given range.

examples:
* height
* weight
* growth rate
* yield
* fertility
* milk production
* enzyme activity
* metabolic rate

Question 13

How many alleles do we have if we have 2 loci with 2 alleles? 3 loci with 2 alleles?

Answer 13

2 loci x 2 alleles = 4 alleles
3 loci x 2 alleles = 6 alleles

Question 14

What is incomplete/partial dominance?

Answer 14

Incomplete (partial) dominance: The phenotype of the heterozygote is intermediate between phenotypes of the two homozygotes. The heterozygote phenotype may fall at any point within the
range of the homozygotes

Question 15

What does the distribution of individuals with a phenotype arise from?

Answer 15

This arises from the distribution of contributing alleles. Let’s see how it works using a Punnet square.

Question 16

What are the 6 assumptions we make in out “toy model of polygenic traits”

Answer 16

assumptions:

1. only two types of alleles
   * contributing alleles (c)
   * non-contributing alleles (nc)
2. incomplete dominance
3. additive effects of alleles
4. each gene has small effect
5. no environmental effects
6. no linkage

Question 17

What are the several compounding factors in determining the phenotype in populations?

Answer 17

genetic level

➔ Large number of loci (each with very small effect)
➔ large number of genotypes (possible linkage effects)
➔ dominance and epistasis effects
➔ environmental influences (non genetic)
➔ continuous range of phenotypes

phenotype in populations

Question 18

What do we use when studying phenotypes in population?

Answer 18

use statistical methods to study groups of individuals
(not individual crosses).

Question 19

What is an assumption we use when observing phenotypes in population?

Answer 19

NO “DISCONTINUITIES”

(no single gene with a major effect)

Question 20

Where do mendelian traits arise from?

Answer 20

Arise from genes that have an effect large enough for a recognizable discontinuity in
the presence of segregation at other loci and non-genetic variation.

Question 21

Mendelian traits: segregation, ratios, progeny, single cross?

Answer 21

Mendelian inheritance: yes
Segregation: identifiable
Mendelian ratios: yes
Single sets of progenies: informative
Single crosses: predictable outcomes

Question 22

Quantitative traits: segregation, ratios, progeny, crosses?

Answer 22

Mendelian inheritance: Yes
Segregation: NOT identifiable
Mendelian ratios: NO
Single progeny: uninformative
Single cross: unpredictable outcomes

Question 23

What do quantitative traits arise from?

Answer 23

Arise from many genes with small effects relative to segregation at other loci and
non-genetic variation

Question 24

What is quantitative genetics?

Answer 24

Quantitative Genetics the branch of genetics that uses statistical and analytical
procedures to understand how genes and environment influence continuous traits in
groups of individuals, and study the inheritance of such traits.

Question 25

What is the unit of study for quantitative genetics?

Answer 25

the unit of study for quantitative genetics is populations

Question 26

What are the properties of populations that we observe?

Answer 26

Means, variances and covariances

Question 27

Techniques of quantitative genetics can be used where?

Answer 27

same techniques can be used on: * meristic traits * threshold traits * quantitative traits

Question 28

Typical questions in quantitative genetic analysis?

Answer 28

* What is the genetic and environmental contribution to phenotype? * How many genes influence the trait? * Are the contributions of the genes equal? * How do alleles at different loci interact: additively epistatically? * How rapid will the trait change under selection?

Question 29

What is Vp?

Answer 29

Vp is the phenotypic variance

Question 30

What is the equation for Vp?

Answer 30

VP = VG + VE + VGXE VG = genetic variance VE = environmental variance (individual-specific environmental effects) VGXE = genetic-environmental interaction variance

Question 31

Example of genetic-environmental interaction variance?

Answer 31

in a dry environment, AA might be more favourable yet in a wet environment, aa might be much more favourable and dominate.

Question 32

What three variances make up the genetic variance?

Answer 32

VG = VA+ VD + VI VA = additive genetic variance VD = dominance genetic variance (alleles at a locus) VI = interaction genetic variance (between loci)

Question 33

What is the equation of broad sense heritability?

Answer 33

H^2 = VG/VP = VG/VA + VI + VD + VE + VGxE range of 0-1

Question 34

What does H2 tell us?

Answer 34

The fraction of phenotypic variance due to genetic variance NOTE: * parents transmit half of their genes, not their genotypes * gamete formation + fertilization= considerable reshuffling of the genotypes * phenotypic variation due to dominance and epistasis are not transmitted

Question 35

What is the equation for narrow-sense heritability?

Answer 35

h^2 = VA/VP = VA/VA + VD + VI + VE + VGxE range of 0-1

Question 36

What does h2 tell us?

Answer 36

The fraction of the phenotypic variance due to additive genetic variance Additive genetic variance is responsible for the AVERAGE resemblance between relatives, for example parent and offspring!

Question 37

What are the 5 ways we might estimate heritability?

Answer 37

1. eliminating some of the variance components (H2) * estimate VE + VGXE and simply subtract from Vp 2. twin studies (H2). * r: correlation coefficient * MZ: monozygotic & DZ: dizygotic * H2 ~ 2(rMZ– rDZ) 3. parent-offspring regression (h2) 4. resemblance among full-sibs & half-sib (h2) 5. selection experiment (h2)

Question 38

b = 0

Answer 38

A change in ave parent phenotype has no affect on the offspring: * no additive affects of genes * b=0

Question 39

0

Answer 39

Nature is often some place in middle: * many affects, including some additive affects of genes * 0< b < 1

Question 40

b = 1

Answer 40

One unit change in ave parent yield exactly 1 unit change in offspring: * 100% additive affects of genes * b=1

Question 41

What is a quantitative trait loci?

Answer 41

Quantitative Trait Loci (QTL): a chromosome segment containing gene(s) (polygene) that control a polygenic trait

Question 42

What is QTL mapping?

Answer 42

QTL mapping: detect association between the inheritance of a trait and the inheritance of genetic markers

Question 43

linkage of QTL and marker?

Answer 43

Limited recombination between marker B and the QTL Q (linkage) * most offspring that inherit B1 will also inherit Q (contributing allele) * most offspring inheriting B2 will inherit q (noncontributing allele)