HMB265

Historical puzzle of inheritance (lec 2)

* artificial selection was the first applied genetic technique (purposeful control of mating by choice of parents for next gen)
* domestication of plants and animals was a key transition in human civilization
* domestication of dogs from wolves
* domestication of rice, wheat, barley, lentils, and dates from weed-like plants

2 Hypotheses to explain inheritance (lec 2)

1. one parent contributes more to an offspring’s inherited traits
2. blended inheritance: traits of parents are blended in their offspring explained single offspring, but not siblings/next gen

Gregor Mendel (lec 2)

* discovered of basic principles of genetics
* 1st scientist to combine data collection, analysis, and theory to understand heredity
* inferred __**laws of genetics**__ that allowed __**predictions**__ about which traits would appear, disappear, and then reappear
* “experiments in plant hybrids” became __**cornerstone of modern genetics**__
* had the right mind, proper equipment, and appropriate biological material, and INTERDISCIPLINARY EDUCATION

Appropriate model system to study genetics (lec 2)

Need to identify organisms that are more amenable t genetic analysis:

* short generation time
* can be inbred (self-fertilize)
* simple reproductive biology
* small size (easy to grow/breed)
* large numbers o progeny

Why Pisum sativum was a good choice (lec 2)

* well characterized, cultivated plant, grew well in Brno
* breeding could be done by __**cross-fertilization/selfing**__ to allow __**inbreeding**__
* could obtain and maintain pure-breeding lines (these always bred true producing the same trait gen upon gen)
* Cross-fertilization enabled reciprocal crosses (to rule out the effect of one parent vs other)
* Large numbers of progeny produced w/in short time (enabling statistical analysis)
* traits remained constant in crosses w/in a line

Inheritance of alternative forms of traits (lec 2)

* study of antagonistic pairs (qualitative and discrete traits)

Simple reproductive biology of plants (lec 2)

Traits that Mendel investigated (lec 2)

* one of the two traits is dominant (2nd one)


1. seed colour: green or yellow
2. seed shape: wrinkled or round
3. flower colour: white or purple
4. pod colour: yellow or green
5. pod shape: pinched or round
6. stem length: short or long
7. flower position: at tip of stem or along stem

Reciprocal crosses (lec 2)

* __**refutes the one parent theory of inheritance**__ because dominant trait still appeared no matter which parent had it
* also revealed that traits could be dominant

Genetic terminology (lec 2)

* P: parental generation
* F1: 1st Filial generation (offspring from parental generation)
* F2: 2nd Filial generation (offspring from F1 gen)
* Self: inbreeding cross that involves individuals that are genetically identical

Monohybrid cross (lec 2)

* crossbreeding two parents w/ just one different trait
* refuted blending hypothesis in F1 generation, all peas were yellow not yellowish green or greenish yellow
* refuted uniparental hypothesis in F2 gen, because both parents (F1 gen) were yellow peas but F2 gen still had green peas (showing not one parent contributes to offspring)

Units of inheritance (lec 2)

* mendel proposed each plant carries 2 copies of a unit of inheritance
* traits have 2 forms:


1. trait in F1 gen is in __**Dominant**__ form
2. trait that is hidden in the F1 gen is in __**Recessive**__ form
* progeny inherit one unit from each parent
* *now known as* __*“genes*____”__

Classical genetics terminology (lec 2)

* Locus: genetically defined location (behaves like single gene but don’t know if it’s only one)
* Alleles: alternative forms of single locus
* Dominant: allele that manifests itself regardless of other allele that is present ==(indicated using upper case letter)==
* Recessive: allele whose effect is “masked” when dominant allele is present. __**Appears only when other alleles are recessive**__ ==(indicated using lower case letter)==
* Homozygous: when both alleles at given diploid locus are the same (could be dominant/recessive)
* Heterozygous: has 2 diff alleles present at diploid locus (dominant allele w/ - represents unknown genotype, ex: A-)
* Hybrid: derived from 2 diff parents
* monohybrid: 1 hybrid locus
* Dihybrid: 2 hybrid loci
* True-breeding: homozygous at the loci/locus in question

Mendel’s law of segregation (lec 2)

* 2 alleles for each trait segregate during gamete formation
* 2 gametes, one from each parent, unite at random at fertilization

Punnett square (lec 2)

* simple way to visualize allele segregation and random union
* mendel’s first law incorporates the fact that his results reflected basic rules of probability

Basic rules of probability (lec 2)

Product rule:

* probability of 2 __**independent events**__ occurring together is the product of their individual probabilities
* Probability of event 1 __**AND**__ event 2 occurring?
* P(1+2) = P1 x P2

Sum rule:

* probability of either of 2 mutually exclusive events occurring is the sum of their individual probabilities
* probability of event 1 __**OR**__ event 2 occurring?
* P(1/2) = P1 + P2

F3 further confirming predicted ratios (lec 2)

* law of segregation was inferred from these crosses

Genotypes + Phenotypes (lec 2)

* Genotype: pair alleles present in individual
* Phenotype: observable characteristic of an org

Testcrosses (lec 2)

* reveals unknown genotypes
* used to discriminate btwn homozygotes dominant and heterozygotes
* testcross = unknown genotype x homozygous recessive

Dihybrid crosses (lec 2)

* reveals law of independent assortment
* mendel asked whether all the F2 progeny would be __**parental types**__ (yellow round and green wrinkled) or would be some __**recombinant types**__ (yellow wrinkled and green round)

Mendel’s law of independent assortment (lec 2)

* during gamete formation, diff pairs of alleles segregate independently of each other
* Y is just as likely to assort w/ R as it is w/ r
* y is just as likely to assort w/ R as it is w/ r

Law of independent assortment

* phenotype ratio: 9:3:3:1

Testcross on dihybrids (lec 2)

* testcross dihybrids to individuals that are homozygous for both recessive traits

Law of probability for multiple genes (lec 2)

* Loci assort independently, so we can look at each locus independently to get answer
* very helpful for determining likelyhood for bigger punnet squares

Predicting proportions of progeny from multihybrid crosses example (lec 3)

Summary of Mendel’s 1865 paper (lec 3)

• inheritance is particulate (not blended)

• there are 2 copies of each trait in cell

• gametes contain 1 copy of trait

• alleles (diff form of trait) segregate randomly

• alleles are dominant/recessive- thus diff btwn genotype and phenotype

• diff traits assort indendently

Mendel’s traits are encoded in DNA (lec 3)

• flow of genetic information in cells:

  • DNA to RNA to Protein

• allelic diff at DNA lvl can influence mRNA expression and/or protein func, thus the phenotype

Mutations, source of allelic variation (lec 3)

• mutation is the process where genes change from 1 allelic form to another, the creation of entirely new alleles can occur

• genes mutate randomly, at any time and in any cell of an org

• can arise spontaneously during normal replication/can be induced by a mutagen

• only mutations in germline cells can be transmitted to progeny, somatic mutations can’t be transmitted

• inherited mutations appear as alleles in populations

• human genomes ~99.9% identical

• most genetic variations created by SNPs (single nucleotide polymorphism)

• Wild-type (+): most common allele (frequency >/= 1%)

• mutant allele: rare allele (frequency < 1%)

• mutations affecting phenotype occur very rarely

• major cause of genetic diversity

• can also be detrimental

Single Nucleotide Polymorphisms (SNPs) are allelles (lec 3)

• each SNP can be tracked back to genome change that occurred in single ancestral genome

Types of mutations (lec 3)

• point mutations (SNPs):

  • ATGCAGT to ATCCAGT

• Deletion/insertion (indel mutations):

  • Deletion: ATGCAGT to AT CAGT

  • insertion: ATGCAGT to ATGGCAGT

• Change in repeat number:

  • CGGCGGCGG (3) to CGGCGGCGGCGGCGGCGG (6)

• Chromosomal rearrangements:

  • Inversion: ATGCAGT to TGACGTA

  • duplication: major drivers in evolution (extra copy of gene)

  • Translocations: exchange of genetic material btwn 2 diff chromosomes

Types of mutations in coding sequence of genes (lec 3)

• silent mutation: mutation that doesn’t change amino acid sequence

• missense mutation: mutation that changes amino acid sequence (can be detrimental to protein depending on amino acid replaced)

• nonsense mutation: mutation that causes there to be early stop codon (UGA, UAG, UAA)

• frameshift: change in reading sequence (bc codons read in 3 nucelotides)

Gene expression and alleles (lec 3)

Gene expression and alleles: missense mutation (lec 3)

Gene expression and alleles: Splicing mutations (lec 3)

• Splice donor/acceptor site mutations:

  • disrupts splice donor/acceptor site, resulting in incorrect retention/excision

  • often leads to large additions/deletions that may cause frameshifts

• Leaky mutation: protein still functions but at worse level

How mutations affect phenotype (lec 3)

• think of central dogma of molecular bio (DNA to mRNA to Protein to organismal traits

• allelic differences at DNA level can influence mRNA expression and/or protein function, thus affecting the phenotype

Genetic basis of single-gene disorders: PKU

• PKU: phenylketonuria (chromosome 12)

• missing enzyme leads to mental deficiency

• in 1/10000 Caucasians

• Phenylalanine (Phe, F) → Tyrosine (Tyr, Y)

• without proper pH phenylalanine produces phenylpyruvic acid

• build-up of phenylpyruvic acid can interfere w/ nervous system development

• many possible sites for allelic diversity (PAH gene)

• mutations in both exons + introns (interfering w/ splicing) can inactivate gene, causing PKU

Gene basis of Mendel’s antagonistic pairs (lec 3)

• gene responsible for pea shape (Sbe 1)

• Wrinkled allele: R disrupted by insertion to r

• gene responsible for pea colour (Sgr1 YY)

  • functions in pathway involved breaking down chlorophyl during pea maturation = yellow peas

  • y allele is null allelle = no Sgr1 protein product = green peas

Loss of function mutations (lec 3)

• result in reduced/abolished protein activity

• usually recessive

• Null (amorphic) mutations:

  • completely block function of gene product (ex: deletion of entire gene)

• Hypomorphic mutations:

  • gene product has weak, but detectable activity

• understanding recessiveness for ‘null’ alleles: for many genes, 50% of protein product is sufficient to give wild type phenotype

• single WT (wild type) allele is Haplosufficient

Incomplete dominance (lec 3)

• phenotype varies w/ amount of functional gene product

• ex: white and red rose, would lead to shades of pink when genes are mixed

Haploinsufficiency (lec 3)

• one WT allele isn’t enough

Some nonfunctional mutations can be dominant-negative (lec 3)

• usually occurs in genes that encode multimeric proteins (made of >/= 2 subunits

• mutant subunits block activity of normal subunits (mutant toxic to WT)

Gain of function mutations (lec 3)

• enhance a function/confer new activity

• usually dominant

• Hypermorphic mutations:

  • generate more gene product/same amount of more efficient gene product

• Neomorphic mutations:

  • generate gene product w/ new function/is expressed at inappropriate time/place

  • ex: antennapedia gene of fruit fly causes ectopic expression of leg determining gene in structures that normally produce antennae

Determining inheritance patterns in humans (lec 4)

• tricky process due to:

  • long generation time

  • small numbers of progeny

  • no controlled mating

  • no pure-breeding lines

  • complex traits

Solutions to humans not being genetic models (lec 4)

1. use other organisms as models

2. follow pedigrees: an orderly diagram of family’s relevant genetic features extending through multiple generations

• pedigrees help us infer if trait is from single gene and if the trait is dominant/recessive

• Diagram: shows disease is recessively inherited

Mendelian inheritance and humans: autosomal inheritance (lec 4)

• humans autosomal traits are located on non-sex chromosomes (1-22)

• may be inherited as:

  • autosomal dominant

  • autosomal recessive

Mendelian inheritance and humans: same principles apply (lec 4)

• thousand of examples are described in database

• idea of dominant/recessive traits

Mendelian inheritance and humans: autosomal inheritance (dominant) (lec 4)

• autosomal dominant:

  • homozygous dominant and heterozygotes exhibit affected phenotype

  • males and females are equally affected and may transmit the trait

  • affected phenotype doesn’t skip a generation

Mendelian inheritance and humans: autosomal inheritance (recessive) (lec 4)

• autosomal recessive:

  • only homozygous recessive individuals exhibit affected phenotype

  • males and females are equally affected and may transmit the trait

  • may skip generations

Anatomy of pedigree (lec 4)

Anatomy of pedigree: Huntington’s disease (lec 4)

• vertical pattern of inheritance indicates rare dominant trait

• alters human neurodevelopment

• people who carry mutation can live healthy lives for 4+ decades(~40) before onset of symptoms

Mendelian inheritance of Huntington’s disease (lec 4)

Recognizing dominant traits in pedigrees (lec 4)

• 3 key aspects of pedigrees w/ dominant traits:

  1. affected children always have at least one affected parent

  2. as a result, dominant traits show a vertical pattern of inheritance: trait shows up in every generation

  3. 2 affected parents can produce unaffected children, if both parents are heterozygotes

Horizontal pattern of inheritance (lec 4)

• indicates rare recessive trait

• parents are unaffected but are heterozygous (carries) for recessive allele

Recognizing recessive traits in pedigrees (lec 4)

• 4 key aspects of pedigrees w/ recessive traits:

  1. affected individuals can be children of 2 unaffected carriers, particularly as the result of consanguineous matings

  2. all children of 2 affected parents should be affected

  3. rare recessive traits show horizontal pattern of inheritance: trait first appears among several members of one generation and is not seen in earlier generations

  4. recessive traits may show vertical pattern of inheritance if trait is extremely common in the population

Consanguineous mating (lec 4)

• pedigree w/ Consanguinity (inbreeding) frequently “uncovers” traits that are recessive

• can give rise to “inbreeding depression” (offspring that are less fit than their parents)

Solving genetics problems (lec 4)

• list genotypes and phenotypes for the trait

• determine the genotypes of parents

• determine parents’ possible gametes

• determine possible genotypes of offspring

• repeat for successive generations

• is the trait rare/common in population?

Solving pedigrees: deducing mode of inheritance and associated genotypes question 1 (lec 4)

• what is known at the level of the phenotype: affected individuals coloured in

• recessive trait bc skips generations

Solving pedigrees: deducing mode of inheritance and associated genotypes question 1 (lec 4)

• parents of gen V and VI should be heterozygous bc has affected child but also unaffected children

Solving pedigrees: deducing mode of inheritance and associated genotypes question 1 (lec 4)

• carriers of disease should be found in family because trait is rare

Solving pedigrees: deducing mode of inheritance and associated genotypes question 2 (lec 4)

• shown is autosomal dominant bc disease shows up in every gen

• therefore, if not showing disease means individual is homo recessive

• disease individuals are hetero bc disease is dominant, if diseased was homo dominant, then all children should be affected

Reaction to mendel: Two Camps (lec 5)

1. exception to Mendel’s rules show that they aren’t general (some form of blending inheritance applies)

2. Try to explain exceptions in Mendelian terms of segregation and independent assortment

Dominance isn’t always complete (lec 5)

• phenotype of heterozygote defines dominance relationship of 2 alleles

• Complete dominance: only one trait shows (blue or white)

• Incomplete dominance: mix of 2 traits show (white and blue mix to form sky blue)

• Codominance: both traits show (white and blue form blue w/ white dots/stripes)

Exceptions to 3:1 ratio: incomplete dominance in Antirrhinum (lec 5)

• crosses of pure-breeding red w/ pure-breeding white results in all pink F1 progeny (snapdragon flowers)

• phenotypes reflect genotypic ratios

• ratio signifies alleles of single gene determine these 3 colours (just a mix up of 3:1 shows monohybrid cross)

Incomplete dominance - familial hypercholesteraemia (lec 5)

• heterozygote phenotype is distinct from either homozygous phenotype (intermediate phenotype)

Dominance is not always complete: summary (lec 5)

• crosses btwn true-breeding strains can produce hybrids w/ phenotypes diff from both parents

  • Incomplete dominance:

    • F1 hybrids that differ from both parents express an intermediate phenotype. neither allele is dominant nor recessive to other

    • phenotypic ratios are same as genotypic ratios

  • Codominance:

    • F1 hybrids express phenotype of both parents equally

    • phenotypic ratios are same as genotypic ratios

Co-dominant blood group and lentil coat pattern alleles (lec 5)

• phenotype ratios reflect genotype ratios

Genes can have more than 2 alleles (lec 5)

• multiple alleles of a gene can segregate in populations

• although there may be many alleles in pop, each individual can carry only 2 of the alternatives:

  • ABO blood group gene: I

    • 3 alleles: I^A, I^B, and i

    • 6 possible ABO genotypes: I^AI^A, I^BI^B, I^AI^B, I^Ai, I^Bi, or ii

• Dominance relations are unique to pair of alleles:

  • dominance relations are always relative to second allele and are unique to a pair of alleles alleles

  • ABO blood group:

  • I^A/B is completely dominant to i but codominant to I^B/A

  • 6 genotypes generate 4 phenotypes: Type A/B/AB/O

ABO blood types in humans are determined by 3 alleles of one gene (lec 5)

• i is a null mutation because there is no sugar produced

Seed coat patterns in lentils are determined by a gene w/ five alleles (lec 5)

• Five alleles for C gene: spotted (C^S), dotted (C^D), clear (C^C), marbled-1 (C^M1), and marbled-2 (C^M2)

• reciprocal crosses btwn pairs of pure-breeding lines is used to determine dominance relations

• a 3:1 ratio in each cross indicates that diff alleles of same gene are involved

How do we establish dominance relations btwn multiple alleles of gene (lec 5)

Dominance relations btwn alleles don’t affect transmission of alleles (lec 5)

• type of dominance depends on type of proteins encoded and by the biochem func of proteins

• Variation in dominance relations don’t negate Mendel’s law of segregation

• Alleles still segregate randomly

• Interpretation of phenotype/genotype relations is more complex

one gene could affect multiple traits (lec 5)

• Pleiotropy: phenomenon of single gene determining several distinct and seemingly unrelated characteristics

  • EX: many aboriginal Maori men have respiratory problems and are sterile due to mutations in gene required for functions of cilia (failure to clear lungs) and flagella (immotile sperm)

• with some pleiotropic genes:

  • heterozygote can have visible phenotype

  • homozygotes may be inviable (causes lethality)

• alleles that affect viability often produce deviations from 1:2:1 genotypic and 3:1 phenotypic ratio predicted by Mendel’s laws

Lethality and Pleiotropy (lec 5)

• A^Y is dominant to A for hair colour but recessive to A for lethality

• cross yellow x yellow mice

  • F1 mice are 2/3 yellow and 1/3 agouti

• 2:1 ratio is indicative of a recessive lethal allele

  • Pure-breeding yellow (A^YA^Y) mice can’t be obtained because they aren’t viable

One gene, multiple phenotypes: Pleiotropy (lec 5)

• unusual ratios w/ only 2 phenotypes

Understanding Pleiotropy: One gene controls multiple phenotypes (lec 5)

Pleiotropy (lec 5)

• one gene has many symptoms or controls several functions

Extensions of Mendel’s laws: single genes (lec 5)

• summary of Mendel’s basic assumptions and comparison of these assumptions w/ 20th century contributions

Other alterations to Mendel’s laws: Genotype isn’t always deterministic: Penetrance (lec 5)

• For some genes, given genotype will give certain phenotype only some of the time (ex: 75% of homozygous recessive individuals will have disease)

• individuals w/ same genotype can differ in phenotype due to incomplete penetrance

• Penetrance:

  • is percentage of population w/ particular genotype that shows expected phenotype

• can be complete (100%) or incomplete

Incomplete Penetrance example: polydactyly (lec 5)

Other alterations to Mendel’s laws: Genotype is not always deterministic: Expressivity (lec 5)

• phenotypes can be expressed to diff degrees

  • ex: severity of disease can differ w/ same genotype

• Expressivity: degree/intensity w/ which particular genotype is expressed in phenotype

  • can be variable/unvarying

Other alterations to Mendel’s laws: Phenotype isn’t always deterministic (lec 5)

• colour indicates level of expression (shades of green show varying expressivity)

Other alterations to Mendel’s laws: Environmental modification (lec 5)

Genotype vs. Phenotype (lec 5)

• Complicated relationships btwn genotype and phenotype can violate Mendel’s predicted 3:1 ratios

• Mendel’s Laws of Segregation and independent assortment still hold

Extensions to Mendel for single-gene inheritance dominance isn’t always complete (lec 5)

• crosses btwn true-breeding strains can produce hybrids w/ phenotypes diff from both parents

• Incomplete dominance: ex: snapdragon flower colour

• Codominance: ex: lentil coat patterns, ABO blood groups in humans, histocompatibility in humans

• Pleiotropy:

  • recessive lethal alleles (ex: Ay allele in mice)

  • delayed lethality

Do variations on dominance relations negate Mendel’s Law of Segregation? (lec 5)

• dominance relations affect phenotype and have no bearing on the segregation of alleles

• alleles still segregate randomly during gamete formation

• gene products control expression of phenotypes differently

• Mendel’s Law of Segregation still applies

• interpretation of phenotype/genotype relationship is more complex

Genetic interactions (lec 6)

• more than just a few genes in genome

• diff genes are likely to be interacting/dependent on each other to give rise to specific traits

• can that explain deviation from Mendelian segregation?

Reciprocal Recessive Epistasis (lec 6)

• purple F1 progeny of sweet peas are produced by crossing 2 pure-breeding white lines

• F2: 7 white:9 purple ratio

• indicates 2 genes at work

• purple: at least 1 dominant in both alleles (both enzymes must work)

• White: 1 loci must be homo recessive

Possible biochem explanation for Reciprocal recessive Epistasis for flower colour in sweet peas (lec 6)

Locus heterogeneity in humans: Ocular-cutaneous albinism (lec 6)

• heterogeneity: mutations in 2 diff genes but cause same phenotype

Inheritance of eye colour (lec 6)

• blue recessive to brown

• at least 12 genes affect eye colour, although 2 explain much of variation (H and O)

• need at least 1 dominant allele for both genes for brown eyes (H-O-)

Locus heterogeneity in humans: complementation (lec 6)

Complementation/Allelism (lec 6)

• diff null mutations in same gene can abolish function

• mutations in diff genes might also abolish function and give rise to same phenotype

• how to distinguish btwn these possibilities?

Heterogeneous traits and complementation test (lec 6)

• complementation testing used to determine if particular phenotype arises from mutations in same/separate genes

• can be applied only w/ recessive, not dominant, phenotypes

• “complementation group” synonymous w/ single gene

Complementation Test (lec 6)

• works when phenotype is recessive

• useful tool to determine how many genes contribute to trait (complementation groups)

• mutant phenotype = same gene

• no mutant phenotype = diff genes

Many ways to “knockout” a gene: allelic variation (lec 6)

• mutations can pop up in many places

WT alleles complement mutant alleles (lec 6)

• WT alleles complement in cases of haplosufficiency, phenotype is WT

When mutant alleles at same locus can’t complement each other: they are allelic

• 2 mutant alleles can’t complement each other so phenotype is mutant (indicator of allelism)

• Molecular vs Phenotypic visibility of allelism:

  • while locus appears hetero at molecular lvl, the individual appears homo at phenotypic lvl

Forward genetics (lec 6)

1. identify mutants that produce target phenotype

2. complementation test: Cross inbred lines to test whether mutations are in same/diff genes

3. do genes interact?

Complementation test: sorting allelic from non-allelic (lec 6)

• variety of molecular deficiencies, still allelic if in same gene

Complementation test: sorting allelic from non-allelic pt. 2 (lec 6)

• 2 loci = complementation