Genetics and Genomics

Phenotype

The observable traits of an organism

Genotype

The genetic constitution of an organism

Wild Type

The most common variant in the wild.

Alleles

Alternative forms of a gene

Homozygote

Contains two copies of the same allele

Heterozygote

Contains two different alleles

Gregor Mendel

• Considered as the ‘father’ of modern genetics

• Discovered the basic principles of inheritance

What are Mendel’s 2 laws?

Law of segrations and law of independent assortment

Law of Segregation

• Diploid organisms have two alleles for each trait

• Alleles segregate during meiosis so that one allele is present in each gamet

Law of Independent Assortment

Different traits assort independently of each other. (this doesn’t always occur due to linkage)

What are the ratios of 1 and 2 gene crosses?

1 = 3:1

2 = 9:3:3:1

Two ways that phenotypes are generated

• Variation in amino acid sequences can result in related proteins with differences in function.

• Variation in gene regulation can change the amounts of gene product being made and/or change when and where the gene is expressed.

Round vs Wrinkled Peas

• Wrinkled peas have more sugar and less starch

• The starch-branching enzyme (sbe I) is not produced in wrinkled peas, leading to reduced concentrations of amylopectin, the branched form of starch.

Purple vs White Flowers in Peas

• Basic helix-loop-helix transcription factor

• Switches on the expression of genes involved in making anthocyanin (purple) pigments

• In white flowers there is a mutation that prevents the transcription factor from being made

Why are dominant and recessive simplistic definitions?

• Genes can have multiple alleles, not just two

• Dominance relationships between multiple alleles are relative, can be context-dependent, and depend on what you measure

Co-dominance

• A heterozygote expresses the phenotype of both alleles simultaneously

• Ex. ABO blood antigens where IA and IB alleles produce A and B antigens which can be expressed as the AB blood type

Incomplete Dominance

• A heterozygote is intermediate between the two homozygous phenotypes

• Ex. Pink flowers which are the product of a red and white flower

Loss of Function Mutations

• Decrease or complete loss of functional gene product

• These mutations are usually recessive

  • Partial loss of gene function: leaky or hypomorphic mutation

  • Complete loss of gene function: null mutation

Haplo-Sufficient

One wild-type allele provides enough normal gene product to produce a wild-type phenotype → mutation is recessive

Haplo-Insufficient

A single wild-type allele in a heterozygote cannot provide the amount of gene product needed → mutation is dominant

Gain of Function Mutations

• Increase in functional gene product or new cellular function

• These mutations are usually dominant

  • Increase in gene activity: hypermorphic mutation

  • New function: neomorphic mutation

Example of Gain of Function Mutation - Drosophila melanogaster

• The Antp gene is a developmental regulator that promotes leg growth

• Antennapedia mutants arise from mis-expression of Antp gene causing legs to grow where antennae should be

• Mutation is Dominant because the gain-of-function cannot be compensated by the wild-type allele à heterozygotes show the phenotype

Allelic Series

An order of dominance of alleles for the same trait according to phenotypes expressed in the heterozygotes. Ex. A^Y > A^w-J > a

Loss of Function Mutation

A genetic alteration that reduces or abolishes the activity of a gene or its corresponding protein.

Loss of Function Mutation Types

Hypomorphic or leaky mutation where there is a partial loss of gene function.

Null mutation where there is a complete loss of gene function.

Conditional mutation where the mutant phenotype changes depending on certain conditions. Ex. himalayan rabbits only produce pigment

Conditional Mutations

Mutation causes a phenotype only under certain environmental conditions; eg. temperature, chemical exposure, resource availability. Restrictive condition = mutant phenotype and permissive condition = wild-type phenotype.

Penetrance 

The proportion of individuals of a specific genotype that exhibit the corresponding phenotype. If the penetrance is 100% then everyone with the mutant gene will have the phenotype

Incomplete Penetrance

Not every individual with the mutant genotype displays a mutant phenotype

Lethal Alleles

A lethal allele is a gene variation that causes death in an organism carrying it, often due to a mutation in an essential gene. Because lethality requires both alleles to be present, the ‘lethal’ phenotype is considered to be recessive.

Pleiotropic

A gene that affects more than one phenotype or process.

What test is used to assess if a mutation is caused by the same or different gene?

Using the complementation test which is a functional test between recessive mutants with the same phenotype.

Normal/Standard Gene Interaction

Two heterozygotes Aa;Bb mated to each other produce an expected phenotypic ratio of 9:3:3:1.

Complementary Gene Interaction and Ratio

The activity of both genes is needed for the final phenotype. Results in a 9:7 ratio.

Duplicate Gene Interaction and Ratio

Either gene can carry out the biological process (redundancy). Result in 15:1 ratio.

Dominant Gene Interaction and Ratio

Two genes with the same phenotype interact additively. Results in a 9:6:1 ratio.

Epistasis

One gene stops/masks the phenotype of another.

Recessive Epistasis and Ratio

The recessive genotype of one gene blocks the phenotype controlled by another gene. Results in a 9:3:4 ratio.

Dominant Epistasis and Ratio (very rare)

The dominant genotype of one gene blocks the phenotype controlled by another gene. Results in a 12:3:1 ratio.

Dominant Suppression Epistasis (very rare)

Dominant allele of one gene suppresses the expression of the dominant allele of another gene. Results in a 13:3 ratio.

Karyotype for Humans

Complete set of chromosomes which is 23 homologous pairs (46 chromosomes)

Heterogametic Sex

The sex with different sex chromosomes (males for humans).

Homogametic Sex

The sex with homologous (same) sex chromosomes (females for humans).

Human Sex Chromosomes

Differ greatly in size and morphology. Y chromosomes are a lot smaller and contain about 200 genes whereas X chromosomes are a lot bigger and contain about 1000 genes.

Hemizygotes

Only one copy of an allele is present at a locus instead of two (XY for males for X-linked genes). 

Genetic Notation in Drosophila 

• A recessive trait with allele e has wild-type e⁺ and a dominant trait B has wild-type B⁺.

• A homozygote is written as: ex. e⁺/e⁺

• Genes on different chromosomes are separated by a semicolon: ex. bw/bw;st/st.

• Genes on the same chromosome are written in sequence: ex. bw cn /bw cn

Drosophila Life Cycle

Generation time in a lab is 10-14 days.

How to distinguish between male and female Drosophila?

• Abdominal markings: males have lower stripes that are fused to form a black area.

• Sex comb: present on the forelegs of males

• Shape of genitalia: females have a pale bloated abdomen with pointed tip and males have a brown circular plate, and the abdomen curves inwards.

Reciprocal Crosses

• Used to determine sex-linkage where two crosses are performed, where the genotypes of the male and female parents are swapped

• If offspring ratios differ, indicates the trait is sex-linked

Criss-Cross Inheritance

The transmission of sex-linked genes from a father to his daughter, and from a mother to her son. This pattern occurs because the genes are located on the X chromosome.

Why are pedigrees used?

They are useful to understand the mode of inheritance of a trait when offspring numbers are low, but family records are available- like humans and animals used in breeding.

GO OVER PEDIGREES!

Mendelian Traits in Humans

• Autosomal dominant: one mutant allele is sufficient for trait or disease

• Autosomal recessive: two mutant alleles result in trait or disease

• X-linked: hemizygous males express the trait, regardless of dominance

Gamete Size in Determining Sex (Gender)

• In sexually reproducing organisms, gamete size usually defines which individual of a reproducing pair is ‘male’ or ‘female’

• ‘male’ gametes are small and numerous (sperm, pollen)

• ‘female’ gametes are large and few (ovum, ovule)

Anisogamy

Fusion of gametes that differ in size or form

Isogamy

Fusion of gametes of similar morphology.

Hermaphrodites

• Contain both male and female reproductive organs

• Plants: 94% produce both pollen and ovules within the same flower

• Also in animals: (~5%)- some worms, snails and fish

Monoecious and Dioecious Plants

Monoecious: male and female flowers in separate structures on the same plant.

Dioecious: male and female flowers on different plants

Two Mechanisms of Sex Determination

Genetic and Environmental

Genetic Sex Determination

Genetic elements specify whether individuals are biologically female or male.

3 Mechanisms of Genetic Sex Determination

Heteromorphic sex chromosomes (ex. XY and ZW systems), sex-determining genes on homomorphic chromosomes, and chromosome ploidy.

Y Chromosome Sex Determination

• Testes development depends on a master sex-determining locus, the SRY (sex determining region Y) gene

• SRY encodes a protein, the testis-determining factor (TDF), which leads to testis differentiation.

XO Chromosome System

The number of X chromosomes determines sex in Drosophila and many other invertebrates. 2X chromosomes = female (XX orXXY); 1X chromosome = male (XO or XY).

The Y Chromosome of Drosophila

The Drosophila Y chromosome is not involved in sex determination but contains genes required for fertility. An XO is biologically male but sterile.

Sex-Lethal Locus in Drosophila

Sex-lethal (Sxl) is the master sex-determining locus in Drosophila

• XX embryo: high Sxl expression → Triggers production of the female isoform of the gene doublesex (dsx) via alternate splicing, leading to female development

• XY or XO embryo: low Sxl expression → production of the male isoform of dsx

Sex Chromosomes in Platypus

• Monotremes have 10 sex chromosomes:

• Females: X1X1X2X2X3X3X4X4X5X5; Males: X1Y1X2Y2X3Y3X4Y4X5Y5

ZW Sex Determination

All birds, some reptiles, some insects (eg. moths & butterflies). Males are the homogametic sex (ZZ) while females are the heterogametic sex (ZW). The Z chromosome is large and gene rich whereas the W chromosome is small and has few genes.

Sex Determination Without Sex Chromosomes

• Sex-determining/mating-type genes are located on autosomes

• Species do not have sex chromosomes. Most amphibians, some fish and inverts.

• Often have a mating type gene where AA alleles make female and Aa alleles make male.

Haplo-Diploidy

• Males develop from unfertilized eggs and are haploid (n)

• Females develop from fertilized eggs and are diploid (2n)

• All Hymenopteran insects (ants, bees, wasps), some mites and ticks

Sex Determination in Honey Bees

• Sex is determined by the complementary sex determiner (csd) gene

• Males are haploid and hemizygous for csd

• Females must be heterozygous at the csd locus to develop normally

• Homozygous diploid eggs develop into inviable males

Gynadromorphs

Embryos develop as mosaics of two sexes, often leading to spectacular phenotypes. Occur in species where sex is cell autonomous: each cell decides its own sexual fate based on its sex chromosome constitution. 

Causes of Gynadromorphs

• Chimeras: fusing of two embryos in early development

• Polyspermy: multiple sperm fertilise egg; different lineages develop

• Errors in mitotic division early in development (sex chromosome loss)

Cell Nonautonomous Sex Determination in Mammals

• Sex determining gene controls the fate of the gonads- ovaries or testes

• Gonads direct establishment of phenotypic sex through the production of hormones.

• Hormones direct development of sex-specific characteristics throughout the body

Environmental Sex Determination

External stimuli control sex determination. Favoured when specific environments are more beneficial to one sex.

What are the 3 ways that sex chromosome imbalance is fixed?

1. Up-regulation of expression of X-linked genes in XY individuals

2. Down-regulation of X-linked genes in XX individuals

3. Complete inactivation of one of the two X chromosomes in XX individuals

Inactivation of an X Chromosome in Placental Mammals

• Xist is transcribed from the ‘X-inactivation centre’ of the future inactive X (Xi) to produce a 17kb long non-coding RNA

• Xist RNA coats the inactive X chromosome and recruits proteins that silence gene expression and result in chromosome condensation

• Once an X chromosome has been inactivated, it remains inactive through subsequent cell divisions and is called a Barr body.

Why are XX individuals for X-linked recessive traits wild-type sometimes?

Half of their cells will have inactivated the mutant X, while half have inactivated wild-type. The products of both alleles are expressed and are often sufficient to prevent full manifestation of X-linked recessive traits in a heterozygote.

LUCA

Last Universal Common Ancestor

What is meant by the term “the selfish gene”?

Evolution occurs not for the survival of species, or individuals, but for the survival of genes.

Population Genetics

The study of the fundamental processes that cause allele frequency changes: selection, drift, mutation, migration.

Allele Frequency for 2 Alleles

p + q = 1

Genotype Frequency for 2 Alleles

p² + 2pq + q² = 1

Allele Frequency for 3 Alleles

p + q + r = 1

Genotype Frequency for 3 Alleles

p² + q² + r² + 2pq + 2pr + 2qr = 1

Calculating Sex-Linked Allele Population Frequency

Allele frequencies = genotype frequencies for males (because they only have one X)

Female is same as autosomal.

Hardy-Weinberg Equilibrium

When allele + genotype frequencies don’t change and so the population is at equilibrium.

Assumptions for Hardy-Weinberg

Mating occurs at random, no mutation occurs, no migration, extremely large population, and no differential reproduction.

Directional Selection

• An allele can provide a survival and/or reproductive advantage to its bearer (advantage can be very small)

• Individuals with that allele will leave more offspring and therefore copies of those same alleles.

• Ex. peppered moth

Heterozygote Advantage

A type of natural selection that maintains multiple alleles in a population's gene pool, preventing any single allele from becoming dominant and thereby preserving genetic diversity.

Balancing Selection

When two different alleles each provide a selection benefit. Ex. sickle cell anemia and malaria resistance (heterozygote is healthy but has defense against malaria)

Explanations for why genetic diversity exists even with favourable alleles

• The favorable allele is slowly becoming fixed but there has not yet been enough time for that to occur

• Genetic drift + migration are also shaping allele frequencies

• Fitness of an individual depends on the genotype at many loci

• The environment is not constant, so a favorable allele in one environment at one time may not always be the favorable allele

• Other forms of selection may be at work...

Frequency Dependent Selection

The favorable allele or genotype in the host depends on which allele is more common. Often seen in host pathogen interactions where mutations that prevent infection arise and become more frequent but the pathogen then mutates and so the new allele is less favourable. 

Haplotype

• A specific combination of alleles for different genes along a chromosome. (each letter represents the haplotype for a different gene)

• These alleles will tend to be passed on together during meiosis, unless separated by recombination

• Haplotypes become shorter each generation due to recombination

What does a long haplotype indicate?

• Recent origin

• Large selective advantage - i.e. recent, strong positive selection

Synonymous and Nonsynonymous Mutations

Synonymous mutations do not change the encoded amino acid, while non-synonymous mutations change it to a different one. 

Lactase Persistance

Controlled by the LCT gene which normally shuts off transcription at 2 years but some people continue to produce it due to a mutation. Lactase persistence mutations are found in the upstream regulatory region of the LCT gene (MCM6). 

EDAR Variant

EDAR affects many processes including sweat gland production. A variant in the EDAR gene (V370A) is nearly fixed (90%) in Han Chinese but absent elsewhere and results in increased sweat gland production. 

What does non-random mating change?

Genotype frequencies not allele frequencies but can accelerate changes in allele frequencies. 

Positive Assortative Mating

A type of non-random mating where individuals with similar traits choose each other as mates more frequently than they would by random chance.

Negative Assortative Mating

A type of non random amting where individuals with dissimilar phenotypes choose each other as mates more often than would be expected by chance.

Coefficient of Inbreeding (F)

Probability that two alleles in an individual are identical by descent, because they descend from the same copy in an ancestor.