NEW GENETICS EXAM 4

Quantitative trait

Trait influenced by many genes of small effect and environment

Mendelian trait

Discontinuous trait controlled by discrete alleles

Polygenic trait

Trait controlled by many loci with additive effects

Continuous variation

Trait values that can take any value between extremes

Meristic trait

Trait that varies in whole numbers

Threshold trait

Trait expressed only above a quantitative cutoff

Mid-parent value

Average phenotype of the two parents

Additive genetic variation (VA)

Genetic variance due to summed effects of alleles

Dominance variance (VD)

Genetic variance due to dominance interactions

Gene interaction variance (VI)

Genetic variance due to epistasis

Genetic variance (VG)

Total genetic contribution to phenotypic variance

Environmental variance (VE)

Variation caused by environmental differences

Gene-by-environment interaction (VGE)

Variation caused by genotype responding differently across environments

Phenotypic variance (VP)

Total variance; VP = VG + VE + VGE

Broad-sense heritability (H²)

Proportion of phenotypic variance due to total genetic variance (VG/VP)

Narrow-sense heritability (h²)

Proportion of phenotypic variance due to additive variance (VA/VP)

Why narrow-sense heritability matters

Predicts response to selection

Heritability equation

h² = VA / VP

Response to selection (R)

Change in trait mean after one generation of selection

Selection differential (S)

Difference between selected parents' mean and population mean

Breeder's equation

R = h²S

Correlated response to selection

Change in one trait due to selection on another trait

Genetic correlation

Correlation between traits due to pleiotropy

Frequency distribution

Graph showing variation of a trait in a population

Mean

Average value of a population

Variance

Measure of spread in a distribution

Standard deviation

Standardized measure of variation

Normal distribution

Symmetric distribution (≈66% ±1 SD; 95% ±2 SD)

Correlation coefficient (r)

Strength of association between two variables

Regression

Method to predict one variable from another

Quantitative trait locus (QTL)

Genomic region associated with variation in a quantitative trait

QTL mapping

Identifying genomic regions linked to trait variation using genetic markers

GWAS

Genome-wide association study using SNPs across populations

Allele frequency (pq)

Proportion of each allele in a population

Genotype frequency

Proportion of individuals with a genotype

f(A)

2AA + Aa / 2N

f(a)

2aa + Aa / 2N

Hardy-Weinberg equilibrium

Condition where allele and genotype frequencies remain constant

Hardy-Weinberg assumptions

Random mating, no selection, no mutation, no migration, large population

Hardy-Weinberg equation

p² + 2pq + q² = 1

Chi-square test

Statistical test comparing observed vs expected genotype frequencies

Degrees of freedom (H-W test)

Number of genotypic classes minus number of alleles

Non-random mating

Mating that alters genotype frequencies

Assortative mating

Preference for similar phenotypes

Disassortative mating

Preference for different phenotypes

Inbreeding

Mating between relatives

Coefficient of inbreeding (F)

Probability alleles are identical by descent

Effect of inbreeding

Decreases heterozygotes; increases homozygotes

Inbreeding does NOT change

Allele frequencies

Inbreeding depression

Reduced fitness due to increased expression of deleterious recessives

Natural selection

Differential reproductive success changing allele frequencies

Fitness (W)

Relative reproductive success of a genotype

Selection coefficient (s)

s = 1 − W

Directional selection

Selection favoring one extreme phenotype

Stabilizing selection

Selection favoring heterozygotes/intermediate phenotype

Disruptive selection

Selection against heterozygotes

Overdominance

Heterozygote has highest fitness (stable equilibrium)

Underdominance

Heterozygote has lowest fitness (unstable equilibrium)

Genetic drift

Random change in allele frequencies due to small population size

Founder effect

Drift due to small group starting new population

Bottleneck effect

Drift due to sharp reduction in population size

Migration (gene flow)

Movement of alleles between populations

Effect of migration

Reduces population differences; increases within-population variation

Mutation (μ)

Introduction of new alleles at low rate

Mutation direction

Random

Mutation equation

Dq = μp

Role of mutation

Source of new variation; weak force on allele frequencies

Cancer

Disease caused by failure of cell cycle regulation

G1 phase

Cell growth phase before DNA replication

S phase

DNA synthesis phase

G2 phase

Preparation for mitosis

Cell cycle checkpoints

Regulatory control points in cell division

Cyclins

Regulatory proteins controlling cell cycle timing

CDKs

Enzymes activated by cyclins to advance cell cycle

Proto-oncogene

Normal gene promoting cell division

Oncogene

Mutated gain-of-function proto-oncogene

Tumor suppressor gene

Gene that inhibits cell division

Loss-of-function mutation in tumor suppressor

Removes cell cycle inhibition

Metastasis

Spread of cancer cells to other tissues

Benign tumor

Non-invasive tumor

Malignant tumor

Invasive cancer

Apoptosis

Programmed cell death

Hardy-Weinberg equilibrium application

If p and q are known, expected genotype frequencies are p², 2pq, and q²

How to find allele frequencies from genotype counts

p = (2AA + Aa) / 2N and q = (2aa + Aa) / 2N

How to find genotype frequencies from allele frequencies

Use p² + 2pq + q²

If a population has q = 0.6 under H-W

frequency of AA, p = 0.4 so AA = p² = 0.16

If a population has q = 0.6

frequency of carriers, 2pq = 2(0.4)(0.6) = 0.48

Interpreting excess heterozygotes in H-W test

Suggests balancing selection or heterozygote advantage

Interpreting excess homozygotes in H-W test

Suggests inbreeding, assortative mating, or population structure

Steps in a chi-square H-W test

Calculate p and q, compute expected p²/2pq/q², calculate χ², compare to critical value

If χ² > critical value

Reject null hypothesis of Hardy-Weinberg equilibrium

Degrees of freedom in H-W test

Number of genotypic classes − number of alleles

Breeder's equation application

Predict response to selection using R = h²S

If h² = 0

response to selection, No evolutionary response

If h² is high

response to selection, Strong evolutionary change possible

If selection differential is large

Evolutionary response increases proportionally

Inbreeding effect on genotype frequencies

Increases AA and aa; decreases Aa

Effect of inbreeding on allele frequencies

No change

If F increases

heterozygosity, Decreases

If F = 0

mating system, Random mating