Mendelian Genetics and Gene Interactions

Mendel's Laws

• Law of segregation: alleles segregate during meiosis, one allele per gamete
• Law of independent assortment: different traits assort independently
• Chi-square (X²) test: used to determine if observed results differ significantly from expected results

Gene Interactions

• Co-dominance: heterozygote expresses both alleles
• Incomplete dominance: heterozygote expresses an intermediate phenotype
• Loss-of-function mutations: decrease or complete loss of functional gene product, usually recessive
• Hypomorphic mutations: partial loss of gene function
• Null mutations: complete loss of gene function
• Haplo-sufficient: one WT allele produces enough product for WT phenotype
• Haplo-insufficient: one WT allele does not produce enough product for WT phenotype
• Gain-of-function mutations: increase in functional gene product or new cellular function, usually dominant
• Hypermorphic: increase in gene activity
• Neomorphic: new function
• Conditional mutants: phenotype only under specific conditions

Mutants

• Conditional mutants: phenotype only under specific conditions
  • Restrictive condition: mutant phenotype occurs
  • Permissive condition: wild-type phenotype occurs
• Incomplete penetrance: not everyone with a mutant genotype shows the phenotype
• Penetrance: proportion of individuals with a genotype that show the corresponding phenotype
• Dominant lethal alleles: homozygous mutant is lethal
• Recessive lethal alleles: F1 intercross of heterozygotes; 1/4 offspring will die
• Complementation test: determines if mutations are in the same or different genes (if two same phenotype mutants create WT offspring, mutations are in different genes)

Sex-Linked Inheritance

• Mitosis: somatic cells, chromosome number maintained
• Meiosis: germline cells, chromosome number halved
• Chromosome theory of inheritance: each member of a homologous pair comes from each parent; homologous pairs sort independently
• Sex chromosomes: X and Y chromosomes differ greatly in size and morphology
• Heterogametic sex: sex with different sex chromosomes (XY in humans)
• Homogametic sex: sex with homologous sex chromosomes (XX in humans)
• Hemizygote: having only one allele of a gene
• Reciprocal crosses: determining sex linkage; switch genotypes of male and female parents in crosses

Population Genetics

• Haplotype: set of DNA variants on a chromosome inherited together
• Allele frequency: p+q = 1
• Genotype frequency: p² + 2pq + q² = 1
• Assumptions for Hardy-Weinberg equilibrium: large population, no genetic drift, random mating, no mutations, no natural selection

Quantitative Genetics

• Nilsson-Ehle experiment: inheritance of traits might not be due to one single gene pair but multiple genes
• Edward East experiment: crossing strains with opposing traits demonstrate phenotypic variance dependent on genetic and environment
• Phenotypic variance (VP): the variance in a trait among individuals in a population
• Genetic variance (VG): variance in trait due to genetic differences
• Environmental variance (VE): variance in trait due to environmental differences
• Broad-sense heritability (H²): proportion of the phenotypic variance due to total genetic variance
• Narrow-sense heritability (h²): proportion of phenotypic variance due to additive genetic variance
• Genetic variation: additive genetic variance, dominance genetic variance, epistatic variance
• Response to selection: change in average trait from selection
• Selection differential (S): difference between average trait in selected individuals and overall population
• Quantitative Trait Loci (QTLs): regions of a chromosome containing genes that influence a quantitative trait
• Estimated Breeding Values (EBVs): estimates of an individual's genetic merit

Mutations + Horizontal Gene Transfer

• DNA repair mechanisms
• Tautomers and Non-standard base pairing
• Mismatch repair
• UV damage
• Photoreactivation
• Silent mutations
• Missense mutations
• Nonsense mutations
• Frameshift mutations
• Consequences of mutation

Meiosis & Genetic Analysis

• Recombination frequencies: calculate map distances between linked genes
• Recombination: separates linked genes, increases genetic variation
• Dihybrid/Trihybrid test crosses: determine if genes are linked, gene order, map distances; parental and recombinant phenotypes observed
• Meiotic error: non-disjunction, trisomy/monosomy, translocation, inversion
• Molecular markers (SNPs, RFLPs, microsatellites)
• PCR (Polymerase Chain Reaction)
• Positional cloning: gene "location", identify "suspect" DNA sequencing
• GWAS (Genome Wide Association Studies)

Genomics

• Genome size and structure - differences in life forms
• mRNA, rRNA, tRNA, miRNA (non-coding RNAs)
• DNA sequencing methods (Sanger, Next-Generation, Third Generation)
• Genome assembly - from fragments to whole