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These screencast lectures are for non‐profit, educational use only

• These screencast lectures cover material you are already supposed to be familiar with, from Biology 204 and 205.

• These screencast lectures are NOT OPTIONAL –you will be examined on the material they present

Sometimes referred to as “Classical Genetics”

For text problems, please see syllabus

Screencast Lecture: Introduction to Transmission Genetics

What is Genetics?• Experimental science of heredity

• Plant and animal breeders needed a better understanding of inheritance of economically important traits

• Gregor Mendel: discovered principles of heredity

• Today, genes are explained in molecular terms

Transmission Genetics

• Transfer (“transmission”) of observable traits from one generation to the next

• Observable “traits” can be physical, chemical, behavioral – this is known as the phenotype

• These “traits” are encoded by genetic information, which we now refer to as the genotype

What is the relationship between genotype and phenotype?

• To what extent do your genes determine your (insert subject here)– Behaviour– Intelligence– Temperament– Susceptibility to disease– Hopes, dreams, nightmares, habits…….etc?

Is it genetic?

• There is a complex interplay between genes and the environment• Genes provide potential; environment plays a role in determining how that

potential is realized

Molecular basis of genetics• Genetic material is usually DNA, a double helix of complementary

polynucleotides.• Genes are segments of DNA encoding the amino acid sequence of

proteins.• The DNA of a (eukaryotic) cell is broken up into a series of (usually)

linear pieces complexed with proteins – these are the chromosomes.

• In diploid organisms chromosomes come in pairs.• Hereditary variation is caused by variant forms of genes known as

alleles.• Since alleles are different forms of the same gene, they occupy the

same locus (place) on the chromosome.• Alleles, like chromosomes, come in pairs in each individual

(although there may be MANY variant alleles in a population).• Alleles arise due to changes (mutations) in DNA sequence.

This is a mutant gene

T

PHENOTYPEpostaxial polydactyly type A1

GENOTYPEGLI3‐/‐

GLI‐Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome)

GENE LOCUS

Genetic Methods• Isolation of mutations (natural or induced)• Analysis of progeny of controlled matings(crosses)

• Genes mapped to positions on chromosomes• Biochemical analysis of underlying cellular processes

• Microscopic analysis of chromosomes (cytogenetics) and phenotypes

• Direct analysis of DNA– genomics: sequencing and annotating genomes– bioinformatics: extraction of information from DNA

Mutant vs. wild‐type (according to Google)

Mutant vs. wild type (according to genetics)

• Wild type alleles are the most common in a population (does this necessarily mean the “best” allele?)

• Mutant alleles are less common in a population (and usually detrimental)

Genetic notation

• Classical (Mendelian)– Wild type: yellow pea. Mutant: green. So call the gene Y for yellow,

capitalized b/c dominant, so y stands for the recessive allele which is green. MOST INTUITIVE but not for someone actually DOING genetics!

• Experimental (Mendelian)– Same as above BUT name after the mutant phenotype. So G is yellow and g is

green.

Genetic notation

• Experimental (e.g. C.elegans)– Three letter code describing some aspect of a gene’s isolation, phenotype,

required function with a dash and a number: unc‐5 is the fifth gene isolated that shows uncoordinated movement, and wild type would be unc‐5+ or just +

• Experimental (e.g. Arabidopsis)– Three letter symbol, upper case is wild type, lower is mutant, e.g., ARB1 or

arb1

• Experimental (e.g. Drosophila)– Gene name given based on mutant. Wild type is designated by a superscript

+; mutant either a superscript – or nothing. So g+ = yellow, and g = green. Note lower case for recessive; upper case would be given to a dominantmutant: example Sb = stubble (mutant, dominant) and Sb+ is wild type (recessive).

Genetic notation

• Sometimes whimsical…… e.g. in Drosophila, what do you think the function of Ken and Barbie is?

Mutant vs. wild type (according to genetics)

• Wild type alleles are the most common in a population (does this necessarily mean the “best” allele?)

• Mutant alleles are less common in a population (and usually detrimental)

w+ = “white plus” = wild‐type w = w‐ = “white minus” = mutant

How did Mendel infer the existence of a gene in the 1860’s?

• He inferred the existence of a hereditary factor

• He didn’t make the rules, he just helped to explain them

• Chose a useful model organism• Used scientific methodology (large

numbers, quantification, reproducibility)

• Developed symbolism to represent abstract hereditary determinants

• Applied the basic rules of probability to explain transmission of phenotypic ratios

Model Organisms• genetic analysis is carried out on a small number of representative species.

• selected for particular aspects of their life cycle or biological/genetic features that make them especially useful. (short life span, inexpensive, lots of progeny etc.)

• most principles of inheritance and gene and cell function can be extended to other organisms e.g. humans.

http://www.dnalc.org/resources/animations/model_organisms.html

Summary of criteria for model

• Can be raised easily in the lab• Can produce large numbers of progeny through controlled matings–Why are large numbers important?

• Short generation time• Phenotypic variants readily available• Extension to other organisms

How can flies or mice or plants tell me anything about myself???

Fraction mice share with other mammals

Fraction mice share with other multicellular organisms

Mouse genome:

Rodent specific genes: ~14% only!!!

So, model organisms are useful. Why did Mendel choose peas?

Pea Plant (Pisum sativum)•Used for Mendel’s classic experiments.

•Possesses a number of well‐defined, true‐breeding characteristics

So, model organisms are useful. Why did Mendel choose peas?

• All the usual reasons (easily available, cheap, easy to propagate etc)

• Reproduction of the pea can be artificially manipulated

• Pea plants will self pollinate (=self =self fertilize) unless the anthers of the flower are removed by the experimenter before they release pollen

• Mendel could thus artificially cross‐pollinate two different pea plants (controlled breeding)

• Also, he had many different varieties of plants available to him

Easy to score true‐breeding traitsFor each trait, he selected lines exhibiting one of two alternativevariations or forms. For example, for the trait of flower color, each of Mendel’s lines were true‐breeding for either purple flowers or white flowers. These are alternative phenotypes. A gene is defined by specific phenotypic differences.

What does true breeding mean?• Before starting his experiments, Mendel tested his lines for two years to ensure they were true‐breeding.

• Truebreeding line: a pure line, when “selfed” or cross‐pollinated within the same breeding line, will only give rise to progeny identical to the parents.

• This important step demonstrated that the outcome of selfing (or crossing within) the various strains was predictable and consistent.

• Therefore, deviations following cross‐pollination between different strains would be scientifically significant.

Classical definition of a gene

• In classical genetic methodology, the existence of a gene controlling a trait is inferred from phenotypic variation between individual organisms or groups of organisms.

• The inheritance pattern of a specific trait can only be studied if phenotypic differences (mutant alleles) in the trait are available.

What questions did Mendel ask?

• Do males and females contribute equally to the appearance of their offspring?

• Are parental traits irreversibly blended in the offspring?

• Are there basic rules, which can be described mathematically, for the transmission of hereditary elements from one generation to another?

Parental generation

First filial generation

Second filial generation

yellow

yellow

green

What did Mendel observe when he crossed two true‐breeding lines that differed in a

single trait?

Green seed color disappears in the F1

But reappears in the F2

This 3:1 ratio appeared reproducibly for many of his traits

Mendel’s observations

• Mendel designated the trait that appeared in the F1 as dominant, and the trait that returned as a minority in the F2 as recessive.

• Recessive traits are masked by dominant traits in the F1…

• …but the traits remain distinct –there is no blending of inherited traits

• Results from reciprocal crosses (pollen from green on stigma of yellow or vice versa) were the same, so both parents contribute equally to the outcome of a cross

Green is recessive to yellow because it is masked by yellow in the F1

(but the hereditary factor for green seed color is still

there….)

This same pattern of inheritance holds (F1 all dominant phenotypes, F2 characterized

by a 3:1 ratio of dominant: recessive phenotypes) regardless of which sex donated pollen in the P generation

Mendel’s conclusions

• Mendel proposed that the hereditary determinants for each trait are discrete and do not become blended together in the F1, but maintain their integrity from generation to generation.

• Mendel also proposed that, for each trait examined, the pea plant contains two copies of the hereditary determinant (gene) controlling the trait, one copy coming from each parent.

Terminology and nomenclature• Mendel developed a simple symbolism to describe his genotypes.• Each hereditary factor was given a letter designation, and the

dominant trait was capitalized while the recessive trait was lowercase.– So the trait for yellow seed color was G for the dominant, g for the recessive

(green). OR, you could say the dominant is Y, and the recessive, green, is y. Just be consistent.

– Note: this symbolism has not stuck in Real World Genetics!• Now we call a hereditary factor a gene, and the different forms

are dominant and recessive alleles.• Genotypes with identical alleles (G/G or g/g) are homozygous,

and genotypes with different alleles (G/g) are heterozygous.• The slash (/) shows that the alleles form a pair (think about

where they might physically reside).• A MONOHYBRID CROSS is a cross between two true‐breeding

lines for a given trait

Parental generation

First filial generation

Second filial generation

yellow

yellow

green

Monohybrid cross (a cross between two true breeding lines for a trait)

Green seed color disappears in the F1

But reappears in the F2

Mendel’s law of segregation• The genotype of the F1 generation from a

monohybrid cross between homozygous dominant (yellow seed) and homozygous recessive (green seed) parents will all be heterozygous, and display the dominant (yellow seed) phenotype

• When an F1 individual forms gametes(*remember gametes are formed by meioses) the the paired G/g alleles will separate (segregate) into different gamete cells (there will be LOTS of these)

• About 1/2 of the gametes will carry the dominant G allele and 1/2 will carry the recessive g allele.

• This is true for both the male and female gametes

• During the formation of the F2 zygote, gametes combine randomly

½ G ½ g ½ G ½ g

G/G X g/g

All gametes G All gametes g

G/g

G/g X G/g

½ G x ½ G

¼ G/G

½ G x ½ g

¼ G/g

½ G x ½ g

¼ G/g

½ g x ½ g

¼ g/g

P:

F1:

F2:

3 1:

Mendel and probability

• Mendel assumed that the male and female gamete cell would combine at random, so, a given G or gmale gamete would have an equal chance of fertilizing an G‐bearing or an g‐bearing ovule.

• First element of chance: the chance that a gamete is G vs. g.

• Second element of chance: the random (with respect to genotype) combination of male gametes with female gametes.

• Therefore, we can the rules of probability to make predictions about the genotypic and phenotypic composition of the F2 progeny.

Rules of probability

• A probability is a measure of the likelihood or chance, that an event will have a particular outcome.

• A probability is usually expressed as a fraction between 0 and 1.

• 1: the event is certain to occur• 0: the event is certain not to happen• In all other cases the chance that a particular event will occur increases as the probability approaches 1

• The probability of two independent events both occurring is the product of each of their respective probabilities.

• To use the product rule, the events must be independent: the occurrence of one event cannot affect in any way the probability of the other event occurring

• This rule can apply to multiple independent events

The product (both/and) rule

What is the chance that an F2 progenyshows the recessive phenotype?

• According to the product (both‐and) rule of probability, the probability that a given zygote (that’s the cell that results from fertilization) received an g allele from both the male and females gametes is 1/2 X 1/2 or 1/4

G/g X G/g

½ G ½ g ½ G ½ g

½ g x ½ g = ¼ g/g

F1

gametes

Probability F2 is homozygous recessive

What is the chance that an F2 progenyshows the recessive phenotype?

(This is Mr. Punnett)

G/G g/g

G/gG g

G g

½ G

½ g

¼ G/G ¼ G/g

¼ G/g ¼ g/g

¾ G/‐ yellow¼ g/g green

Punnett square

The sum (either‐or) rule

• The probability of either one of two mutually exclusive events occurring is the sum of their respective probabilities

• In other words we are determining the probability of one event OR another event (either‐or rule)

• This rule applies to multiple events

What is the chance that an F2 progenyshows the dominant phenotype?

• To show a dominant phenotype, the genotype of the F2 can be either G/G or G/g.

• The probability of a dominant phenotype = (1/2)(1/2) + 2(1/2)(1/2) =3/4

(G/G) (G/g)

What is the chance that an F2 progenyshows the dominant phenotype?

(This is Mr. Punnett)

G/G g/g

G/gG g

G g

½ G

½ g

¼ G/G ¼ G/g

¼ G/g ¼ g/g

¾ G/‐ yellow¼ g/g green

Monohybrid

Punnett square

How does this translate to large numbers of progeny?

• Large numbers of progeny represent many independent fertilization events.

• The probabilities of dominant and recessive phenotypes translate into fractions of progeny.

• 3/4 of the F2 progeny should show the dominant phenotype and 1/4 the recessive for the single gene under study.

• This is Mendel’s famous 3:1 ratio.

How did Mendel know that the dominant F2’s consisted of two different genotypes?

• Self the F2 and examine the F3• The recessive phenotype should breed true• But now there are two classes of dominant phenotypes.• One class breeds true.• The other class recapitulates the 3:1 ratio.

Fraction of F2 Phenotype of F2 Phenotype of F3 Genotype of F3

1/4

1/2

1/4

dominant

dominant

recessive

ALL dominant

¾ dominant¼ recessive

ALL recessive

G/G

G/g

g/g

Role of chance: predict the phenotypes and genotypes of the F3

F3

¼ G/G ¼ G/g ¼ g/G ¼ g/gF2

Breed true: all dominant (G/G)

Do NOT breed true: recapitulate F2 ratios:

3 dominant (G/G; G/g; g/G) to 1 recessive (g/g)

Breed true: all recessive (g/g)

• Self the F2 and examine the F3• The recessive phenotype should breed true• But now there are two classes of dominant phenotypes.• One class breeds true.• The other class recapitulates the 3:1 ratio.

Fraction of F2 Phenotype of F2 Phenotype of F3 Genotype of F2

1/4

1/2

1/4

dominant

dominant

recessive

ALL dominant

¾ dominant¼ recessive

ALL recessive

G/G

G/g

g/g

Role of chance: predict the phenotypes and genotypes of the F3

Conditional probability• Sometimes we want to determine the probability of an outcome that is dependant on a specific condition related to that outcome.

• Example: in the F2 of a monohybrid cross between tall (dominant) and short (recessive) plants, what is the probability that a tall plant is heterozygous (NOT homozygous)?

• We have set a condition: consider only tall F2 plants (since we know that short plants are homozygous recessive).

Conditional probability

• P(F2 plant is heterozygous) = ½• P(F2 plant is tall) = ¾• So the probability of any tall F2 plant being heterozygous is P(outcome)/P(condition)

• P(A given B) = P(A and B)/P(B)• P(A|B) = P(A∩B)/P(B)• OR, P(F2 heterozygous)/P(tall)• OR (1/2)/(3/4) = (1/2)(4/3) = 4/6 = 2/3

Conditional probability

• P(F2 plant is heterozygous) = ½• P(F2 plant is tall) = ¾• So the probability of any tall F2 plant being heterozygous is P(outcome)/P(condition)

• P(A given B) = P(A and B)/P(B)• P(A|B) = P(A∩B)/P(B)• OR, P(F2 heterozygous)/P(tall)• OR (1/2)/(3/4) = (1/2)(4/3) = 4/6 = 2/3

¼ T/T ¼ T/t

¼ T/t ¼ t/t

1/3 T/T1/3 T/t

1/3 T/t

Mendel established dominant/recessive relationships for a number of traits

Does the principle of segregation hold for two different traits?

W/W; g/g w/w; G/G

Description of a dihybrid cross• Mendel also was interested in

knowing whether his principle of segregation held true when the parental lines differed with respect to two or more different traits.

• He crossed a parental line that had round, green seeds with a parental line with wrinkled, yellow seeds.

• As expected, all F1 seeds showed the dominant yellow and round phenotypes.

• Mendel then allowed the F1 plants to self‐pollinate and examined the phenotype of the F2 seeds.

W/W; g/g w/w; G/G

W; g w; G

W/w; G/g

F2 Phenotype # F2 progeny Fraction

yellow; round

yellow; wrinkled

green; round

green; wrinkled

315

101

108

32

9/16

3/16

3/16

1/16

Genotype

F2 phenotypic categories for a dihybrid cross



yellow; round

yellow; wrinkled

green; round

green; wrinkled

315

101

108

32

9/16

3/16

3/16

1/16

Genotype

416

140

3:1



yellow; round

yellow; wrinkled

green; round

green; wrinkled

315

101

108

32

9/16

3/16

3/16

1/16

Genotype

3:1

Conclusions?

• For each trait, the F2 seeds exhibited the 3:1 (dominant: recessive) ratio that he had observed previously when analyzing the traits individually.

• It is possible to examine the inheritance of traits in a dihybrid cross separately.

How to explain the 9:3:3:1 distribution of progeny?

• If the traits are combining at random, then the product rule of probability can be used to calculate the expected frequency of round, yellow plants (both dominant phenotypes).

• For example: 3/4 (for round) X 3/4 (for yellow) = 9/16 (both round and yellow).

• You can do this for each allele.

• So the phenotypes are combined at random in the F2 progeny to give a 9:3:3:1 ratio of progeny.

Mendel’s law of independent assortment

• To explain the random combination of phenotypes in the F2 progeny Mendel proposed that during gamete formation, the segregation of one gene pair occurs independently of the segregation of other gene pairs.

• Does this sound familiar? (Think about meiosis…)

What predictions do Mendel’s principles make for the gametes of an W/w; G/g plant?

• Segregation:– ½ the gametes will carry W– ½ the gametes will carry w– ½ the gametes will carry G– ½ the gametes will carry g

• Independent assortment:– Gametes receive W or w independently of G or g

What kind of gametes can a W/w G/g plant produce?

• Mendel predicted then that a W/w G/g plant would produce four different types of gametes in equal numbers:

• 1/4 W, G = 1/2 chance of W X 1/2 chance of G• 1/4 w, G = 1/2 w X 1/2 G• 1/4 W, g = 1/2 W X 1/2 g• 1/4 w, g = 1/2 w X 1/2 g

1/16 W/W;G/G

1/16 W/w;G/G

1/16 W/W;G/g

1/16 W/w;G/g

¼ W,G ¼ w,G ¼ W,g ¼ w,g ¼ W,G ¼ w,G ¼ W,g ¼ w,g

Gametes: Gametes:

W/w ; G/g x W/w; G/gF1:

F2:

1/16 w/W; G/G 1/16 w/w; G/G 1/16 w/W; G/g 1/16 w/w;G/g

What kind of progeny can a W/w; G/g plant produce?

This is too much work……

How to explain the 9:3:3:1

distribution of progeny?

W/W; g/g w/w; G/GRound, green wrinkled, yellow

W/w; G/g: Round, yellow

W/W; G/G W/W; G/g W/w; G/g W/w; G/G

W/W; G/g W/W; g/g W/w; g/g W/w; G/g

W/w; G/g W/w; g/g w/w; g/g w/w; G/g

W/w; G/G W/w; G/g w/w; G/g w/w; G/G

W, G W, g w,g w, G

W, G

W, g

w,g

w, G

W, g w. G







W, G W, g w,g w, G

W, G

W, g

w,g

w, G

W, g w. G

Q: What is the probability of W/W; G/g?

1. Draw up the Punnett square and count up the number of times W/W G/g occurs in the Punnett square.

1/16 + 1/16 = 1/8







W, G W, g w,g w, G

W, G

W, g

w,g

w, G

W, g w. G

Q: What is the probability of W/W; G/g?

1. Draw up the Punnett square and count up the number of times W/W G/g occurs in the Punnett square.

2. OR, since the alleles are assorting independently, just use probability…







W, G W, g w,g w, G

W, G

W, g

w,g

w, G

W, g w. G

• Probability F1 parents produces an W/W progeny plant?

• (1/2)X(1/2) = ¼• Probability F1 parents

produces a G/g heterozygous plant?

• (1/2)(1/2) + (1/2)(1/2) = ¼ + ¼ = ½

• Probability for this particular combination for both genes?

• (1/4)(1/2) = (1/8)







W, G W, g w,g w, G

W, G

W, g

w,g

w, G

W, g w. G

¾ W/‐

¾ G/‐

¼ g/g

¼ w/w

¾ G/‐

¼ g/g

9/16 W/‐; G/‐

3/16 G/‐; g/g

3/16 w/w; G/‐

1/16 w/w; g/g

Branching diagrams

Cross between organisms heterozygous for genes exhibiting independent assortment

# heterozygous gene pairs

# different types of gametes produced

# different genotypes produced

# different phenotypes produced

n 2n 3n 2n

1 2 3 22 4 9 43 8 27 84 16 81 16

How to avoid carpel tunnel syndrome for multiple traits that assort independently


• W/w; G/g; S/s × W/w; g/g; s/s ‐‐‐> 2,000 seeds. How many do we expect to be round and green and produce tall plants?

• Translate to genotypes: expect how many W/_; g/g; S/_ ?• Three pairs of alleles segregate independently, so start by doing

each one separately.• W/w × W/w ‐‐> 3/4 W/_• G/g × g/g ‐‐> 1/2 g/g• S/s × s/s ‐‐> 1/2 S/s• P(W/_; g/g; S/_) = (3/4)(1/2)(1/2) = 3/16 = expected frequency• expected number = (3/16)(2,000) = 375


• How would you calculate the probability of getting EXACTLY 375 seeds of this genotype if you crossed these parents and collected 2000 seeds? This would involve a binomial calculation which we will not cover in 321 – though you will see it in other courses!

• We don't expect to get exactly the expected frequencies. But if they are very different we might decide that our expectations are wrong ... i.e. that we used the wrong model or hypothesis or explanation.

• How much can our observed frequencies differ from the expected frequencies before we decide that our model is wrong?

• An a priori probability is defined by a model or hypothesis, while an a posteriori probability is defined by measuring the frequency of an event.

• The validity of a model may be tested by comparing the a priori probabilities or expected frequencies defined by the model with the observed data. The comparison is made using a statistical test.

• Appropriate statistical test for many kinds of genetic data is chi‐square test which you will see and apply in other classes.

Use a TEST CROSS to show that W/w G/g gametes are produced 1:1:1:1

• Cross the genotype to be tested (here, W/w; G /g) to a plant recessive for the same traits

W/w G/g X w/w g/g

Test cross: if you are unsure of the genotype, cross it back to recessives for all traits

¼ W,G ¼ w,G ¼ W,g ¼ w,g ¼ W,G ¼ w,g ¼ W,g ¼ w,g

Gametes: Gametes:W/w;G/g x W/w; G/gF1:

Test cross results

• A testcross is informative about gamete ratios because the tester strain contributes only recessive alleles to the progeny.

• Therefore the gamete composition of the F1 parent can be directly inferred from phenotypic composition of the progeny.

Gametes from F1 parent

¼ W,G ¼ W,g ¼ w,G ¼ w,g

Gametes from tester strain

w,g¼ W/w; G/g ¼ W/w; g/g ¼ w/w; G/g ¼ w/w; g/g

round, yellow round, green wrinkled, yellow

wrinkled, green

Mendel’s findings

• Equal segregation of discrete, paired alleles into separate gamete cells.

• Independent assortment (segregation) of the paired alleles controlling different traits.

• Random fertilization of gametes.

Chromosome theory of inheritance

Early 1900s:(Sutton, Boveri)

Chromosome behavior resembles transmission of

Mendel’s “factors”

Early 1900s:(McClung, Stevens, Wilson)

Discovery of sex chromosomes

1910:(Morgan)

Sex linked inheritance: evidence for the

chromosome theory

Mendel’s factors and chromosomes

Mendel’s factors and chromosomes

• How do you fit approximately 2 meters (human diploid nucleus) into a space that averages maybe 5 millionths of a meter wide?

• How do you replicate, repair and transcribe tightly packaged DNA?

Chromosomes and chromatin

Chromosomes and chromatin

Chromatin = DNA + protein

Interphase (decondensed: why?)

Metaphase (fully condensed: why?)

Chromatin comes in two varieties: Heterochromatin and Euchromatin

• Stains darkly (highly condensed)• Repetitive sequences• Replicates later in the cell cycle• Little or no recombination• Transcriptionally repressive:

silences gene expression

• Stains lightly (decondensed)• Single copy sequences (genes)• Replicates early in the cell cycle• Recombines• Transcriptionally active:

permissive for gene expression

Heterochromatin and euchromatin in an interphase nucleus

Heterochromatin: repressed, repetitive sequences, condensed, virtually inactive with respect to gene expression

Euchromatin: where the action is – most of the genes are here…

Heterochromatin and euchromatin in a (lysed, treated) metaphase nucleus

horse

Heterochromatin is concentrated at centromeres (and telomeres)The Y chromosome

is almost entirely heterochromatic

Genes reside on chromosomes: evidence?

Chromosomes directly related to the sex of the organism: hence “sex chromosomes”

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