Genetic Variation & Inheritance

Genetic Variation in Meiosis

• Crossing over (synapsis) in prophase I involves homologous chromosomes exchanging segments at chiasmata, creating recombinant chromatids and new gene combinations.
• Independent assortment in metaphase I is the random orientation of bivalents, leading to varied maternal/paternal chromosome combinations in daughter cells after anaphase I.
• Fertilization is the random fusion of sperm and egg, resulting in diverse offspring genotypes and phenotypes, further increased by allele interactions like complete/incomplete/co-dominance.
• Cross-fertilization produces more variation than self-fertilization due to a greater number of possible alleles for each gene in offspring

Inheritance

Mendel's Model of Autosomal Recessive Inheritance

• Mendel worked with monogenic and diallelic traits, concluding that each trait is controlled by a pair of inherited alleles (paternal and maternal).
• Law of dominance and segregation: heterozygous individuals express the dominant allele, masking the recessive allele (dominance)
• Gametes have only one allele for each gene (segregation), offspring inherit one from each parent, resulting in a 3:1 dominant-to-recessive ratio in hybrid crosses.
• Law of independent assortment: alleles for different traits are inherited independently if genes are on different chromosomes.

Mendel's Experiments

• Pea plants were used due to monogenic traits and short lifecycles, self-pollination of homozygous plants produces identical offspring.
• F1 generation (cross of AA and aa) expressed the dominant trait, indicating dominance.
• F2 generation from F1 heterozygotes (Aa) showed a 3:1 dominant:recessive phenotypic ratio
• Each F1 individual inherited one allele from each parent (Aa), resulting in a genotypic ratio of 1 AA: 2 Aa : 1 aa in the F2 generation (law of segregation).
• Homologous chromosomes are maternal and paternal pairs carrying the same genes, except for male XY sex chromosomes.
• Homozygous (AA/aa) means identical alleles, heterozygous (Aa) means different alleles for a gene.
• A gene codes for a trait, an allele is a gene version with specific base sequences at the same loci on homologous chromosomes.

Test Cross

• Dominant trait expression can be either homozygous dominant or heterozygous, requires test cross with homozygous recessive.
• Producing only dominant offspring indicates homozygous dominant, recessive offspring indicates heterozygous.

Exceptions to Mendelian Genetics

• Complete dominance is when a dominant allele is fully expressed over a recessive allele.
• Incomplete dominance is partial expression of both alleles (e.g., pink (RW) Japanese 4-o-clock flowers from red (RR) and white (WW) parents).
• Codominance is full expression of both alleles (e.g., BNBS blood cells with some normal & some sickle-celled proteins, roan cow coats).
• Blood type is determined by multiallelic genes with more than 2 alleles (A, B, and O).
  • AA/AO = blood type A, BB/BO = blood type B.
  • AB = blood type AB (codominant A and B antigens).
  • OO = blood type O.
• Rhesus factor (positive or negative) is dominant and independently inherited.
• Monogenic inheritance is a phenotype controlled by a single gene, polygenic inheritance controlled by multiple genes (continuous variation).
• Human height is controlled by ~50 genes, eye colour by ~16 genes (e.g., EYCL3 for brown/blue, EYCL1 for green/blue).
• Environmental factors can affect phenotype despite genotype (e.g., nutrition affecting height).
• Phenylketonuria (PKU) is a disorder where a mutation in an enzyme causes buildup of phenylalanine, leading to abnormal nervous system development, dietary changes can lessen phenotypic expression.
• Sex-linked genes are located on sex chromosomes.
• Males are more likely to inherit recessive X-linked diseases (hemizygous XnY) as they only need one maternal allele.
• Females need two recessive alleles (XnXn) to express recessive X-linked traits, one allele makes them a carrier (XnXN).
• Examples of sex-linked traits include haemophilia and red-green colour blindness.

Population Genetics

• Population genetics studies genetic variation in populations and changing gene pools, which informs a population's adaptability.
• For diallelic genes: p2 + 2pq + q2 = 1 (where p and q are allele frequencies).
• Blood type O+ is most common in Australia (40%), AB- least common (1%), A+ and B-/AB+ are second highest and lowest at 31% and 2%.
• A types prevalent in Aboriginal populations, B was absent until European settlement.

SNPs

• Individuals have varied genetic markers (DNA sequences at known chromosomal loci).
• Polymorphisms are variable regions inherited from parents, the vast genomes of humans are identical.
• A single nucleotide polymorphism (SNP) is an inherited single base pair variant at a specific locus in at least 1% of the population.
• SNPs usually occur in non-coding regions, rarely causing phenotypic change.
• Genome-wide association studies link genetic markers (haplotypes - groups of SNPs in particular regions of chromosomes) to diseases (not necessarily causation).
• Digital databases (HapMap, HGMD, COSMIC) store SNP-disease links, enabling quick disease screening.
• NSW newborn screening program tests for disease-associated SNPs for early detection and treatment.
• SNP data measures inherited genetic variation to determine evolutionary relatedness within/across populations.
• SNPs used must be closely located to accurately trace generations due to crossing over.
• Genotyping identifies DNA variations quicker than full DNA sequencing.

Pedigrees and Punnett Squares

• Pedigree conventions: square is male, circle is female, shaded is affected, generations are in Roman numerals left, siblings are left to right.
• Determine autosomal or X-linked inheritance.
  • More affected males suggest X-linked recessive. More affected females suggests X-linked dominant. If affectedM:affectedF = 1:1, likely autosomal.
• Dominant traits never skip generations.

DNA Sequencing and Profiling

Polymerase Chain Reaction (PCR)

• PCR amplifies a specific DNA segment.
  • Denaturation: heat DNA to 95°C to separate strands.
  • Annealing: cool to 45-60°C for primers to bind target sequences.
  • Extension: heat to 72°C for DNA polymerase to add nucleotides complementary to the target sequence (5' to 3'), starting from a primer.
• Repeats n times to produce 2n copies of the sequence.

Genetic Sequencing

• Genetic sequencing identifies a DNA segment's base sequence.
• Use in disease allele screening, GMO production via insertion of desired base sequences, study of antibiotic resistance, and population genetic analysis.
• High-throughput analysis sequences many genomes at once, measuring genetic variations and changes in allele frequencies for inheritance pattern analysis.

Sanger Method

• Amplified target strand has a primer that binds to the start.
• DNA polymerase adds dNTP nucleotides (5' to 3') to form complementary fragments until a ddNTP (chain-terminating nucleotide) is incorporated and terminates the strand.
• Fragments are dye-labelled by their terminating nucleotide.
• Fragments separate by length via gel electrophoresis.
• A laser detects the dye colours, a chromatograph detects the colours of the terminating bases in order of their position in the final strand, identifying the complementary sequence.

DNA Profiling

• DNA profiling represents a section of a genome as bands to compare individuals.
• Short tandem repeats (STRs) are non-coding DNA repeats whose length is inherited.
• PCR amplifies STR sequences, fragments separate by length via gel electrophoresis, creating unique band patterns, comparisons determine genetic relatedness.
• Ethical concerns arise regarding data ownership and its use by life insurance companies.

Population Genetics

• Population genetics studies genetic variation, allele frequency changes, and factors influencing survival and adaptation of populations.
  • Including mutations, natural selection, genetic drift, gene flow, population size and environmental pressures
• Conservation genetics utilizes genetic data to promote diversity preventing extinction through improved adaptation. An example of conservation is introducing individuals with particular traits to the population or facilitating gene flow between populations

Examples

• Tasmanian devils: Dingoes introduction and climate decreased population size which reduces genetic diversity decreasing resilience to facial tumor disease. Combatted by captive breeding and promotion of gene flow.
• UNIFOA's "The State of the Worlds Animal Genetic Resource for Food and Agriculture" present findings and suggestions on the conservation of a species.

Isolated Populations and Genetic Disorders

• Investigation of the inheritance of genetic disorders is simplified in isolated populations due to minimal gene flow, resulting in a concentration of otherwise rare traits due to inbreeding.
• Pitcairn island demonstrates the founder effect, where low founder numbers and no gene flow concentrated alleles, such as those related to cardiovascular disease, making it a useful population to study heart disease.

Population Genetics and Human Evolution

• Anthropological genetics uses genetic data to determine human evolution and diversity.
• Multiregional hypothesis: Homo erectus evolved simultaneously into humans with gene flow, supported by fossil continuity but lacks evidence of scattered ancient alleles.
• Replacement hypothesis: modern humans evolved in Africa and replaced Homo erectus with minimal interbreeding, supported by mtDNA analysis and greater genetic diversity in Africa based on the molecular clock hypothesis.
• Neanderthals and Denisovans migrated with humans into Eurasia, Europeans and Asians have 2% Neanderthal DNA due to interbreeding.

Types of Mutations:

• Mutations alter DNA base sequences, potentially changing amino acid sequences and protein function.
• They can occur naturally or be caused by mutagens and may be neutral, beneficial, or harmful.
• Point mutations are changes to single nucleotides.
  • Substitution mutations:
    • Silent: no amino acid change.
    • Missense: different amino acid.
    • Nonsense: stop codon.
  • Frameshift mutations: deletions or insertions altering all downstream codons, leading to non-functional proteins.

Chromosomal Mutations

• Chromosomal mutations affect multiple genes and can be serious or lethal.
  • Duplication amplifies gene expression, causing multiple copies.
  • Inversion reverses a chromosome section, disrupting gene expression.
  • Deletion removes a chromosome section, leading to gene loss and cell malfunction.
  • Insertion attaches a chromosome section to another.
  • Translocation swaps sections of non-homologous chromosomes, disrupting base sequences and gene function.
• Chromosomal abnormalities involve whole chromosomes.
  • Aneuploidy: abnormal chromosome number (e.g., Down syndrome/trisomy 21 due to chromosome 21 nondisjunction).
  • Polyploidy: additional sets of chromosomes, lethal in humans but common in plants because they can reproduce asexually.

Mutagens and Their Impact

• Mutagens can disrupt regulatory mechanisms of cell division, like oncogenes which turn from porto-oncogenes due to mutations, and tumor suppressants, causing uncontrolled growth/cancer.
• Carcinogens are mutagens that cause cancer.
• Chemical mutagens:
  • Intercalating agents: alter DNA shape, causing replication errors.
  • Base analogues: substitute for bases, preventing translation.
  • DNA reactive chemicals: damage DNA.
• Physical mutagens:
  • Ionizing radiation can breaks chemical bonds and damage DNA.
  • UV radiation causes thymine dimers.
• Biological mutagens:
  • Oncogenic viruses carry viral oncogenes or create inflammation that damages DNA.
  • Transposable elements insert into genes, causing mutations.

Mutations in Non-Coding Regions

• Intron mutations can affect splicing at binding sites, causing introns to be included in mRNA, resulting in missense and nonsense mutations.
• Promoter and terminator mutations can cause over/under-expression of genes.
• Mutations to rRNA and tRNA can disrupt protein synthesis.
• There are no known human genetic diseases based on functional mutations to non-coding RNA, however there is evidence of such diseases in the mitochondrial rather than nuclear genome

Mutations and Genetic Variation

• Somatic (postzygotic) mutations: occur in body cells(non-reproductive)
  • Natural somatic mutations are more frequent than germline mutations.
  • Aging increases cancer risk due to accumulated somatic mutations, counteracted by the action of DNA repair enzymes
  • Mosaicism occurs when mutated somatic cells survive and populate tissue.
• Germline mutations are source of new alleles in a population, enabling natural selection.
• Prevention of gene flow leads to genetic drift and differences between populations.
• A genetic bottleneck reduces genetic diversity and makes a population susceptible to disease and minimizes their capacity for adaptation.

Reproductive Technologies

Artificial Insemination

• Introduction of sperm into the female tract to fertilize an egg.
• Animal husbandry: produce offspring with specific traits, can be fresh or preserved via cryopreservation.
• Wildlife conservation: introduces beneficial alleles to boost resilience, used in captive breeding.
• Humans: intrauterine insemination to assist conception.

Genetic Screening

Artificial Pollination

• Human-facilitated pollination to produce plants with ideal traits.
  • Mass dusting via aircraft/blower or hand pollination with brush.
• Conservation efforts involves preserving plant species who lack natural mutualistic pollinators

Cloning

Whole Organism Cloning

• Research and agriculture: to produce genetically identical organisms for more reliable research outcomes
  • Artificial embryo twinning: mimics twin formation.
  • Somatic cell nuclear transfer (SCNT): replaces egg DNA with somatic cell nucleus.

Gene Cloning

• Gene cloning: In vivo: Use of viruses or bacterial plasmids
  • DNA and genome sequencing
  • Characterizing genes: Gene therapy: correcting defective genes.
• SCNT generates embryonic stem cells for therapeutic cloning to replace diseased cells, banned for reproductive purposes.

Recombinant DNA Technologies:

• Recombinant DNA: joining DNA from different sources.
• Plasmids: vectors for introducing foreign DNA into a cell.
  • Restriction enzymes excises target DNA
  • Inserted into plasmids; creating recombinant plasmids
  • Ligase joins the sugar-phosphate backbones of the DNA.
• Bacterial Transformation Techniques: new DNA incorporated into bacteria with are now said to be transformed. Two techniques exist
  • Heat Shock: Rapid increase in temp to introduce plasmids into the cell
  • Electroporation: Passing current over membranes to incorporate plasmids into cells and into DNA
• Selection of Transformed Bacteria:
  • Known plasmid traits (e.g., antibiotic resistance) identify transformed cells.

Genetically Modified Organisms (GMOs)

• Has a modified genome
• Transgenic species has a modified genome with genes from another organism.
• GMO crops: improved productivity, yield, pest resistance, and marketability.
  • Vector mediated: transferred genes by introducing genes into plant bacterial cells Salt-tolerant wheat: salt tolerance protein is introduced into wheat BT cotton: gene from soil bacterium which grants insect pest resistance
  • Transgenic animals