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Title: Introduction to Genetics Reading: Freeman, Chapter 13 (read twice, do all the questions at the back of the chapter), also Chapter 12 (to review meiosis, mostly)


1
Introduction to GeneticsReading Freeman,
Chapter 13 (read twice, do all the questions at
the back of the chapter), also Chapter 12 (to
review meiosis, mostly)
2
Information
  • Genetics is, quite simply, the study of the
    process by which information is transmitted from
    one generation of living things to the next.
  • Every living thing is organized via coded
    information, called its genetic material.
  • Reproduction involves duplication and
    transmission of an organisms genetic material.

3
WHAT IS A GENE?
A gene is an information entity. It is a
sequence of DNA that codes for a single genetic
instruction. Usually, this instruction is the
sequence of a protein, but a gene may also serve
to activate or deactivate other genes, in a cell,
or in neighboring cells. Every aspect of our
species is constructed based on information
encoded in genes. The genes themselves do very
little, they are information storage molecules.
It is the cytological machinery of our cells,
passed from one generation to the next, that
translate these instructions into a living
organism. The effects of every gene depend both
upon other genes, and upon the environment.
4
What is an allele?
  • An allele is ONE variant of a gene. Many genes
    have two, several, or many different variants of
    the same basic genetic information.
  • Some alleles are minor differences that to not
    significantly affect the organism, others cause
    profound changes.

5
Example
  • Nucleotide substitutions in the third codon
    position often produces no change at all, because
    they code for the same transfer RNA and thus the
    same protein is produced.
  • In humansCCU CCA does not cause a change,
    both triplets code for proline.
  • Other substitutions may produce profound effects,
    sickle cell anemia is caused by a single
    nucleotide substitution GAG GUG changes
    normal hemoglobin to hemoglobin that sickles
    under low oxygen concentrations.

6
  • Prokaryotes, which include the archaea and
    bacteria, are the simplest, oldest, and most
    common organisms on the planet.
  • A typical prokaryote has a much smaller genome
    than a typical eukaryote.
  • Nearly always, it is in the form of a simple loop
    of DNA (with associated proteins).
  • This loop is attached to the cell membrane.
  • Even though the structure simple, there is a lot
    of DNA in a single bacterium. .
  • Stretched out, the DNA in an E. coli would be 500
    times longer than the cell itself.
  • Prokaryotes do not have sexual reproduction,
    though they have several forms of gene exchange.
  • These include swapping plasmids

7
  • The various genes, about 1200 in a typical
    bacterium, are arranged along the length of the
    chromosome, like beads on a string.
  • There is no particular functional grouping to
    their order, it is mostly evolutionary chance
    that determines their location
  • In prokaryotes, the DNA loop replicates before
    fission, with both loops still attached to the
    cell membrane

  • During fission, as the cell membrane splits in
    two, one loop of DNA ends up in each new
    daughter cell

Thanks to/stolen from fig.cox.miami.edu
8
(No Transcript)
9
  • Most eukaryotes have several orders of magnitude
    more DNA than a typical prokaryote.
  • Like prokaryotes, eukaryote genes are arranged
    along the length of a chromosome like beads on a
    string.
  • There is no particular functional reason for
    their location, either within a chromosome, or
    with respect to what chromosome they are on, it
    is mostly an evolutionary accident.
  • Eukaryote DNA (except plastid DNA, which is very
    similar to bacterial DNA because of its
    evolutionary origin) is usually linear, not
    circular.
  • These strands are long, and extended (thus,
    invisible to microscopes) during the normal life
    of the cell.
  • These linear strands of DNA are called
    chromosomes and packed into a nucleus (or nuclei,
    in some cases).
  • In multicellular eukarotes, every cell has the
    same DNA, though in any given cell, only a
    fraction of the genes are active, others are
    permanently turned off during development.

10
  • The increased amount of DNA necessitates a means
    of condensing these long strands into compact
    structures that can be sorted into separate
    daughter cells during cell division.
  • Histones are important and very evolutionarily
    conservative proteins. Loops of DNA are wrapped
    around one histone (like thread around a spool),
    and locked in by a second, forming a structure
    called a nucleosome.
  • These structures further supercoil into a
    condensed configuration, to form the familiar
    shapes that scientists have viewed under light
    microscopes.

Thank you/stolen from www.geneticengineering.org
11
Mitosis
  • Mitosis, the duplication of the genetic material
    within a eukaryote cell, is worth mentioning here
    because of what it IS and what it IS NOT.
  • A cell gives rise to two, smaller but genetically
    identical copies of itself.
  • It IS a duplication of the genetic complement of
    a eukaryote cell. Since it is usually followed
    by cell division, it can lead to growth, in a
    multicellular organism, or asexual reproduction,
    in a single-celled organism.
  • It IS NOT a means of producing gametes. In
    sexual organisms, mitosis is peripheral to sexual
    reproduction, it serves to give rise to cell
    types which ultimately kill themselves off by
    splitting and splitting again, into four, very
    different, cells.

Do not bother to memorize the phases of
mitosis/meiosis, I do not care
12
Sexual Reproduction
  • Sexual reproduction is a particular type of
    reproduction, a sharing of genetic material, to
    form an individual with equal contributions from
    two separate parents.
  • This involves
  • The formation of haploid sex cells, called
    gametes, from a diploid cell, a process called
    Meiosis.
  • Syngamy (or, fertilization), a combination of
    genetic information from two separate cells to
    form a diploid cell, called a zygote.
  • Gametes usually, but not always, come from
    separate parents female produces an egg and male
    produces sperm. (In some organisms, the haploid
    phase of the life cycle is multicellular, and
    haploid individuals simply grow together during
    the process of syngamy.)
  • Both gametes are haploid, the resulting zygote is
    diploid.
  • Sex probably evolved as a means of producing
    variable offspring in the face of an uncertain
    future, though its evolutionary origins are
    obscure.
  • It is virtually ubiquitous among eukaryotes,
    though many can produce sexually or asexually.
  • It has the potential to produce enormously
    variable sets of genetic information, something
    that can be crucial to the survival of a species.

13
Diploidy
  • Diploidy is the state of having two copies of
    every single gene-like pairs of shoes, pairs of
    gloves, pairs of stereo speakers.
  • Humans, and many of the organisms with which we
    are familiar (flies, zebras, potatoes), are
    diploid.
  • We have two copies of every gene in our bodies.
  • For many genes, these copies are identical
    matches (they are homozygous).
  • For others, there are subtle differences between
    the two copies (they are heterozygous).
  • Not all organisms are diploid as adults, some are
    haploid.
  • For sexual reproduction to occur, there must be
    both a diploid and a haploid phase of the life
    cycle.

14
Meiosis
  • Meiosis is that process by which a single diploid
    cell gives rise to four, genetically different,
    haploid cells.
  • It works like this (forget the phases)
  • The diploid progenitor duplicates its genetic
    materialthus, every chromosome is composed of
    two, identical, chromatids, joined at the
    centromere (this happens before meiosis starts)
  • Each chromosome finds its match, to form
    matching pairs of homologous chromosomes. This
    process, which occurs during the first of the two
    meiotic divisions, is unique to meiosis, it does
    not occur during mitosis.
  • Four strands (two homologous chromosomes,
    composed of two identical strands each) cluster
    in structures sometimes called tetrads, along a
    plane in the center of the dividing cell. A
    process called crossing over may occur at this
    time.
  • First division, homologous chromosomes separate.
  • Spindle fibers drag them to opposite poles of the
    cell. The cell then divides. Which chromosome
    ends up where is completely random and is not
    influenced by the fate of the other chromosomes
    around it. The cell then divides.
  • Second division, chromatids separate.
  • - Spindle fibers drag them to opposite poles of
    the cell. The cell then divides.
  • This gives you four, genetically different,
    daughter cells from a single parent.

15
www.biologycorner.com
The ancestral sexual species Probably had a life
cycle similar To that pictured above.
Meiosis results in 4 daughter cells Daughter
cells are haploid Daughter cells have unique
combinations of chromosomes Daughter cells do
not have homologous pairs Meiosis creates
gametes (sperm and eggs) Meiosis ensures
variability in offspring
16
Errors in Meiosis
  • Errors in meiosis have the potential to produce
    unusual phenotypes in the offspring.
  • The most common meiotic error is nondisjunction,
    where an entire homologous pair of chromosomes
    migrates to the pole of a cell, without
    splitting.
  • If this happens to a single pair, it causes
    either a trisomy, or a monosomy, in the resulting
    offspring.
  • If it happens to the entire genome, it can
    produce triploid or even tetraploid offspring.
  • The human condition of Downs syndrome results
    from a trisomy at chromosome 21, a trisomy at
    chromosome 18, 13, or the sex chromosomes (23),
    is also survivable. In humans, trisomies for
    other chromosomes are not usually viable.
  • In other organisms, triploids and tetraploids may
    be viable.

17
How Meiosis, and Sex, Produce Variation
  • Meiosis starts with a single diploid cell with
    two redundant sets of DNA, and produces four
    haploid cells, each with a single set of DNA.
  • These four cells all have DIFFERENT sets of
    alleles, although they have the same genes (one
    copy of each, not two).
  • Meiosis produces variation in two ways.
  • By randomly selecting one, or the other,
    chromosome from a diploid set, to form a haploid
    set, an enormous number of potential gametes
    arise. In an organism with 23 pairs of
    chromosomes, for instance, 223 potential gametes
    can be formed this way. This phenomenon is
    called assortment.
  • By the process of recombination, which is a
    result of crossing over, new combinations of
    alleles on chromosomes may arise.

18
  • Crossing over is a cytological phenomenon that
    occurs during the first of the two meiotic
    divisions.
  • Two strands of DNA from complimentary chromosomes
    cross over each other, and a break forms.
  • The break is quickly repaired, switching
    stretches of DNA among the two compliments to
    create two new chromosomes.
  • A pair of chromosomes can cross over once,
    several times, or not at all. The farther apart
    two genes are on a chromosome, the more likely it
    is that crossing over will create recombination
    between the two of them.
  • Crossing over creates new combinations of alleles
    on chromosomes, and permits favorable alleles to
    combine together on the same chromosome.
  • The genetic result is called recombination.

19
  • When geneticists speak about genes, they prefer
    to use the word locus. The two are virtual
    synonyms, but locus means location, and it refers
    to the place where variation can occur. Using
    the word gene emphasizes its information content.
  • Thus, as you might be able to intuit from the
    diagram to the left, the more distant the loci
    (plural), the more likely it is for a particular
    recombination event to switch them between
    chromosomes.

20
The Patterns Inherent in Mendelian Genetics
Result from the Nature of the Eukaryote Genome,
and the Events of Meiosis
  • The preceding information explains the
    cytological and evolutionary reasons why genetics
    works the way it does in eukaryotes.
  • Meiosis does not produce new genes, or new
    alleles
  • The genetics that follow have their cytological
    underpinnings in the events of meiosis.
  • It does, however, create new combinations of
    chromosomes, and new combinations of alleles on
    chromosomes
  • For example
  • Segregation is the process by which a gamete
    comes to have only one of the two alleles its
    parent possesses, for every gene. It is random,
    and it occurs because of the separation of
    homologous chromosomes during the first meiotic
    division.
  • Assortment accounts for the fact that most
    eukaryotes possess many pairs of chromosomes, it
    is segregation at two or many loci
    simultaneously. Assortment is responsible for
    the variation in gametes created by the random
    selection of chromosome from each pair into
    gametes..
  • Example via assortment alone a human with 23
    pairs of chromosomes can produce 223 potential
    gametes, far more than every person who has ever
    lived.
  • When genes are on separate chromosomes, it is
    said that they assort independently. When they
    are on the same chromosome, they tend to get
    passed on as a unit, which can only be broken up
    by recombination, this is called linkage.

21
Variation is ubiquitous, all organisms exhibit
SOME variation
  • Look around the classroom and you will
    immediately notice a great deal of variation
    among members of this class.
  • Some of this variation is morphological hair
    color, height, eye color, etc..
  • Some is behavioral preference for certain foods,
    knowledge of languages, choice of clothing, etc..
  • Other organisms crayfish, salamanders,
    scorpions, exhibit similar amounts of variation
    (though we are not as sensitive to it at first
    glance).
  • For centuries, biologists have sought an
    explanation for this variation.
  • Much of this variation has its basis in our
    genes, a fact that is of tremendous biological
    significance.

22
Variation within the White-cheeked Rosella The
White-cheeked Rosella is made up of four
varieties, each with its own distinct color
combination and markings. The diagram shows
where these varieties are found. Question-Based
upon this information alone, can you Tell
whether the variation is genetic,
environmental, or both?
Stolen from-www.environment.gov.au
23
Types of Variation
  • Attributes, or qualitative variables, can be
    scored, but not fall into a continuum.
  • Examples human eye color, political party, blood
    type, gender, etc..
  • Quantitative, or measurable, variables fall along
    a measurable axis, and can be measured to observe
    their place relative to others.
  • Discontinuous measurable variables fall into
    discrete intervals. Examples shoe size, number
    of mates, number of arrests for drunk driving,
    etc..
  • Continuous measurable variables do not fall into
    discrete intervals, they exist along a continuum.
    Examples height, weight, age, etc..

24
Distributions of Values
  • A group of individuals has a distribution of
    values for every quantitative variable. This
    reflects the number of individuals possessing
    each value for the trait.
  • The group of individuals in question is the
    statistical population, the population has a
    distribution of values for the variable.
  • These distributions are frequently expressed as a
    histogram the range of values for the category
    is broken into intervals, and the number of
    individuals within that interval is expressed as
    the height of a bar.

25
A Histogram
26
Types of Distributions
  • Populations of actual organisms exhibit a great
    variety of distributions for different measurable
    variables.
  • Some common distributions are
  • Normal
  • Bimodal
  • Multimodal
  • Distributions may also be skewed, or exhibit
    kurtosis.

27
Normal Distribution
28
A Skewed Distribution
29
Bimodal Distribution
30
Mean, Median, Variance, etc.
  • The distribution of numerical values can be
    described by several statistics
  • (Arithmetic) Mean the average xSx/N
  • Median The value with the same number of
    observations preceding it, and following it
  • Variance s2 the variability of values in the
    data set, their tendency to depart from the mean
  • s2(S(x-x)2/N-1 )
  • Standard Deviation sthe square root of the
    variance.

31
Dominance
  • As you remember, diploid organisms have two sets
    of redundant genetic information-two copies of
    every gene.
  • An individual is homozygous at a locus if they
    have two alleles for a gene, and heterozygous at
    that locus if they have different copies.
  • Dominant alleles mask the effect of a recessive
    allele at that locus, they are expressed in the
    homozygous or the heterozygous state.
  • Recessive alleles are only expressed in the
    homozygous state.By convention, we usually use a
    capital letter to designate the dominant allele,
    and the lower case of the same letter to
    designate the recessive allele.

32
  • Example Alleles for albino coloration in many
    animals result from recessive alleles.
  • It is usually a defective protein that inhibits
    the metabolic pathway associated with the
    production of a protein, or (more often),
    inhibits its placement in the target tissue.
  • In most cases, even one copy of a non-defective
    gene at this locus restores the pathway.
  • Thus, for albino coat color in mice, Individuals
    with either one or two copies A (dominant) allele
    have brown fur.
  • Therefore AA and Aa have brown fur. Note that Aa
    individuals can pass on the a allele, even though
    they do not express it themselves, they are
    carriers.
  • Individuals with two copies of the albino allele,
    aa, have white fur.

media.ebaumsworld.com/..
33
Some Alleles of Medical Interest
  • Because, when rare, recessive alleles are usually
    in the heterozygous state, and not subject to
    natural selection, human populations harbor quite
    a few harmful, recessive alleles at low
    frequencies.
  • For instance, a rare, autosomal recessive allele
    on chromosome 7 disrupts the normal migration of
    neurons, leading to an abnormally thick and
    smooth cerebral cortex, and reduced cerebellum,
    hippocampus, and brainstem causing a condition
    called lissencephaly.
  • It is typical of these conditions for an affected
    individual to be born to normal parents.
  • Dominant alleles, by contrast, are generally
    manifested in the parents.
  • For instance, ectrodactly, a condition where the
    affected individual has severely deformed digits,
    is caused by a dominant allele.
  • It runs in families, conspicuously, and was
    passed from the famous circus performer, Grady
    Stiles Junior, to one of his offspring.

34
Typical manifestation of lissencephaly
Grady Stiles Junior, as a young man
35
Codominance
  • Codominance (sometimes called incomplete
    dominance) is the allelic interaction where, in
    the heterozygous state, both alleles are
    expressed (for attributes), or the heterozygote
    is in between the phenotypes of the homozygous
    individuals for those alleles (in the case of
    measurable characters).
  • Thus, the heterozygote has a unique phenotype.
  • For example, in chickens, black feather color is
    codominant with white feather color.
    Heterozygous chickens have black and white
    feathers in a checkered pattern.
  • FBFB is black, FWFW is white, and FWFB is
    checkered. Note that the notation uses
    superscripts, which makes it clear that neither
    allele is dominant.

36
Human Blood Type
  • The human ABO locus has three loci, which exhibit
    both dominance and codominance.
  • Human blood types are encoded by a single locus
    with three alleles IA, IB, and i0.
  • IA and IB code for two different proteins, cell
    surface antigen A, or antigen B. i0 codes for
    the lack of that particular protein.
  • Since we are diploid, we have a blood type, a
    phenotype, that depends upon the proteins on the
    surface of our blood cells.
  • IA IA and IA i0 are A, IBIB and IB i0 are B,
    i0i0 is O.
  • IA and IB are therefore CODOMINANT with respect
    to each other, and both are DOMINANT with respect
    to i0.

37
  • Most traits are not coded by a single genethe
    Rh/Rh- status of an individual is coded by at
    least two loci, RhD and RhCE..
  • Having a dominant allele at either of these loci
    makes a person Rh, having recessive alleles at
    all the Rh loci makes a person Rh-

38
Phenotype vs. Genotype
  • An organisms PHENOTYPE is its observable
    characteristics.
  • An organisms GENOTYPE is its genetic composition
    of alleles.
  • Thus, an organism heterozygous for a recessive
    allele, such as albinism, would exhibit the
    dominant trait, yet would possess the
    heterozygous genotype.

39
How Many Loci are There?
  • Bacteria have about 1,200 genes
  • Yeast have about 5,000,
  • Drosophila melanogaster have about 10,000
  • Human beings have approximately 29,000.
  • Do all loci have multiple alleles?
  • No, only a small percentage of loci have multiple
    alleles, perhaps 1-5 or less, depending upon the
    species.

40
Genes Interact with the Environment to Produce a
Phenotype
  • A gene does not act alone, it gives instructions
    to other aspects of the developing organism, or
    it produces a protein that is put to use in
    various metabolic pathways and processes.
  • Nearly every gene interacts with the environment
    to some extent. Sometimes the contribution of
    the environment is small, sometimes it is very
    significant.
  • This is no mere nature vs. nurture dichotomy, it
    is a complicated interaction and interplay.

41
Geographic Variation in Yarrow-A Norm of Reaction
  • The norm of reaction describes the pattern of
    phenotypic expression of a particular genotype
    across different environments.
  • For example, in yarrow, tall plants grow at low
    elevation roadsides, and much shorter plants grow
    in the mountains.
  • A naive researcher might conclude that the
    mountain plants simply had genes for growing
    short, or that the cold conditions in the
    mountain dwarfed them.
  • Grown under identical conditions, at low
    elevations, the mountain plants grow a little
    taller, but not nearly as tall as low-elevation
    plants.
  • Grown under identical conditions, in the
    mountains, the low-elevation plants grow VERY
    small, or die.

42
In fact, the mountain plants have a variety of
alleles at different loci coding for aspects of
dealing with cold winters and short summers, but
the cost of these alleles is reduced growth under
friendlier conditions. Differently adapted local
varieties of a species are called ecotypes. An
ecotype that performs well in one situation might
perform very poorly in another environment.
43
Genetics Problem
  • A chicken with black feathers is mated to a
    chicken with white feathers.
  • (by convention, this generation is called the P1)
  • This cross produces 9 offspring, all of which
    have checkered, black and white feathers.
  • (by convention, this generation is called the F1)
  • Two of these offspring (the F1) are allowed to
    mate and produce offspring of their own.
  • Diagram the cross, including the
  • genotypes of the parents
  • the genotypes of the GAMETES each parent produces
  • the genotypes of the F1 offspring
  • and the gametes the F1 can produce
  • and the genotypes of the various F2 offspring.
  • Predict the phenotypic composition of this next
    generation, the F2.

44
  • Answer.
  • Start by listing the genotypes of the P1s, this
    is part of the answer, and you will get nowhere
    if you skip right to a Punnet square.
  • The P1s are FwFw and Fb Fb
  • The white parent can produce one type of gamete,
    Fw, the black parent can produce one type of
    gamete, Fb. Note, gametes are always haploid.
  • The F1 are all FwFb, this is the only possible
    genotype, given the two parents. Note, adults are
    always diploid.
  • These F1 can produce two types of gametes, Fw and
    Fb.
  • To produce an F2, these two gametes can unite in
    four possible ways.
  • The male F1 parent can produce a Fw or a Fb
  • The female F1 parent can produce a Fw or a Fb
  • This gives
  • Fw from the male parent x Fw from the
    female-white chicken
  • Fb from the male parent x Fb from the
    female-black chicken
  • Fw from the male parent x Fb from the
    female-checkered
  • Fb from the male parent and Fw from the
    female-checkered
  • The colors in the offspring are ¼ black, ¼ white,
    ½ checkered.
  • If you answered ¼ to ¾, you should consider that
    this is a codominant system.

45
Much of what we know about genes was first
discovered by Gregor Mendel
  • Gregor Mendel was one of those rare historical
    geniuses who seems to exist in a vacuum (he
    didnt he lived at a monestery with a tradition
    of science). His work was not well known until
    after his death.
  • He conducted experiments on the garden pea, Pisum
    sativum, a species that exhibits variation for
    several interesting characters pod color, seed
    color, flower color, height, etc.. These differ
    because of alleles at a single locus.
  • Garden peas also produce a large number of
    offspring, a key to Mendels success.
  • Mendel was among the first scientists to think in
    quantitative, rather than strictly qualitative
    terms.

46
Mendels Laws
  • Through experiments, Mendel deduced some basic
    patterns.
  • Inheritance is particulate particles called
    genes carry the information that makes parents
    tend to resemble their offspring.
  • This was a huge departure from the previous
    scientific paradigm, believed for centuries, that
    inheritance was somehow carried in the blood and
    blended together every generation.
  • These particles segregate, so that individuals
    with two particles produce gametes with only one
    particle, the law of segregation.
  • The particles for each gene segregate
    independently of each other, the law of
    independent assortment.
  • This law is, of course,not universal. It applies
    only to the special case where genes are on
    separate chromosomes. It was not until decades
    later that the relationship between chromosomes,
    and Mendels particles, was discovered.

47
A Classic Mendelian Experiment
  • Two lines of garden peas have been grown
    separately for a long time, they are called true
    breeding lines because the parents always
    resemble the offspring. One line has purple
    flowers and one line has white flowers. A parent
    is chosen from each line. These are called the
    P1.
  • When they are artificially crossed (garden peas
    normally self-fertilize), the resulting offspring
    (called F1) are all purple.
  • Two individuals from the F1 are crossed.
  • The resulting offspring (the F2) are 75
    purple-flowered and 25 white flowered. WHY?
  • DIAGRAM THIS CROSS in a similar way to the way
    you diagrammed the last one.

48
(No Transcript)
49
Questions
  • 1. What is the probability that any given pollen
    grain from the white flowered line contains an
    allele for white flowers?
  • 2. How about a pollen grain from the F1?
  • 3. What about a pollen grain from a white
    individual taken from the F2?

50
Answers
  • 1. 1.0
  • 2. .50
  • 3. 1.0

51
Another Experiment
  • One of F1 from the cross above is mated to an
    individual from the white-flowered line.
  • DIAGRAM THIS CROSS
  • What would be the phenotypic composition of the
    resulting offspring?
  • What would be the genotypic composition of the
    resulting offspring?

52
Independent Assortment
  • The segregation of alleles into gametes follows
    the laws of probability therefore an Aa
    individual would produce 50 A gametes and 50 a
    gametes.
  • If you consider two loci, with independent
    assortment, the chance of a particular allelic
    genotype is a product of the probabilities of the
    alleles at each locus.
  • Ie., an AaBb individual would produce 25 AB
    gametes, .50 is the probability of a A in the
    gamete, and .50 is the probability of B in the
    gamete, .5 x .5 is .25
  • An AaBbCc individual would produce 1/8 ABc
    gametes, for analogous reasons.
  • If genes are on different chromosomes, alleles
    assort independently of each other. This is
    called independent assortment. The chance of an
    allele at one locus being in a particular gamete
    is independent for each locus.

53
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54
  • The number of potential, different, gametes a
    parent can produce is equal to 2N, where N is the
    number of loci assorting (do not count homozygous
    loci).
  • Thus, a heterozygote for three loci Aa Bb Cc
    could form EIGHT different gametes
  • ABC, ABc, AbC, aBC, Abc, aBc, abC, abc
  • By contrast, AA BB Cc can form only two different
    gametes, ABc and ABC, because only one locus is
    assorting
  • For N independently assorting loci, there are 2N
    different gametes that can be created. If they
    are truly assorting independently, they will be
    present in equal numbers.
  • Departures from independent assortment are most
    often caused by LINKAGE, when two loci are close
    to each other on the same chromosome.
  • Linkage causes certain combinations of alleles to
    be over-represented in the gametes.

55
Sample Problem
  • Albinism is a condition that results from the
    lack of normal pigmentation. In humans,
    individuals with two recessive alleles at the
    ALBINO locus are albino,
  • therefore AApigmented
  • Aapigmented
  • aaalbino
  • Attached earlobes result from two recessive
    alleles at the EARLOBE locus.
  • therefore EEnon-attached earlobes
  • Eenon-attached earlobes
  • eeattached earlobes

56
  • Imagine an albino man with non-attached earlobes
    marries a pigmented woman with attached earlobes.
  • They have 23 children, none of them twins.
  • All of their children are pigmented with
    non-attached earlobes.
  • QUESTIONS
  • What is the most likely genotype of the man?
  • What is the most likely genotype of the woman?
  • What alleles for pigmentation will HIS gametes
    carry?
  • What alleles for pigmentation will HER gametes
    carry?
  • What alleles for earlobes will HIS gametes carry?
  • What alleles for earlobes will HER gametes carry?
  • What are the possible GENOTYPES of their
    offspring?

57
SOLUTION
  • Since all their offspring are pigmented with
    non-attached earlobes
  • The man is almost certainly aaEE
  • The woman is almost certainly AAee
  • (otherwise, at least one of the children would
    have been albino, had attached earlobes, or both
    )
  • Their offspring are all AaEe.
  • The mans gametes carry a SINGLE a allele for
    pigmentation, and a single E allele for earlobes.
  • The womans gametes carry a SINGLE A allele for
    pigmentation and a single e allele for earlobes.

58
  • (Based on their phenotypes, you cannot
    distinguish parental phenotypes aaEe from aaEE,
    or AAee from Aaee, but since none of their
    children exhibited the recessive phenotype, it is
    a pretty good bet the parents were both
    homozygous at both loci).

59
Now, imagine two of their children interbred and
had a child.
  • How many types of gametes can their children
    produce?
  • What would be the possible GENOTYPES and
    PHENOTYPES of their offspring?
  • Assuming independent assortment, what is the
    probability that their first child will be an
    ALBINO with ATTACHED EARLOBES?

60
SOLUTION
  • Their children, the F1generation, are
    HETEROZYGOUS at TWO loci.
  • They can produce FOUR different gametes
  • AE aE Ae ae
  • Since the children have interbred with each
    other, their are SIXTEEN possible combinations of
    male and female gametes

61
Punnet Square

  • male gametes
  • AE
    aE Ae ae
  • AE AAEE
    aAEE AAeE AaEe
  • aE AaEE
    aaEE AaeE aaeE
  • female gametes Ae AAEe AaEe
    AAee aAee
  • ae AaEe
    aaEe Aaee aaee
  • Note that there are only NINE different genotypes
    and FOUR different phenotypes for the offspring,
    because several combinations of male and female
    gametes give the same genotype, and several
    genotypes give the same phenotype.

62
  • The chance their first child will be albino with
    attached earlobes is 1/16, since only one of
    sixteen combinations, ae vs. ae, gives the aaee
    genotype which results in the albino attached
    phenotype.

63
QUESTION
  • The mother from the cross goes on the Jerry
    Springer show for having an illicit affair with
    her first born son. She claims to have given
    birth to ANOTHER child, this one is normally
    pigmented with attached earlobes. What are the
    potential genotypes, and phenotypes, of that
    child?
  • Assuming independent assortment, what is the
    chance that a child from this type of union will
    be albino with non-attached earlobes?
  • Is that child her husbands, or her sons?

64
ANSWER
  • Remember, the F1 male (her son) can produce four
    gametes
  • AE, Ae, aE, ae
  • She can produce one gamete, Ae
  • therefore

  • male gametes
  • AE
    aE Ae ae
  • female gametes Ae AAEe AaEe AAee
    aAee
  • Note that there are four potential genotypes, and
    TWO potential phenotypes, pigmented with attached
    earlobes and pigmented with non-attached
    earlobes, 50 chance of each.
  • The child could be her sons, but it couldnt be
    her husbands.

65
Testing Independent Assortment
  • A TEST CROSS is used to determine whether two
    loci are linked.
  • Cross two true-breeding parental lines, such as
    Sepia vs. Black Drosophila melanogaster
  • se se BK BK x SE SE bk bk
  • to create a heterozygous F1
  • SE se BK bk
  • Now, INSTEAD of crossing the F1 to ITSELF, cross
    it to a line which is HOMOZYGOUS for RECESSIVE
    alleles at BOTH LOCI

66
Test Cross
  • SE se BK bk x se se bk bk

  • male gametes

  • se bk
  • SE BK
    SEse BKbk
  • se BK
    sese BKbk
  • female gametes SE bk SEse bkbk
  • se bk
    sese bkbk
  • Note that this cross yields FOUR different
    Genotypes, each with a distinctive PHENOTYPE,
    they should be in equal numbers.

67
Test Cross Ratios
  • Eyes Body Expected Ratio
  • Red Normal 1/4
  • Sepia Normal 1/4
  • Red Black 1/4
  • Sepia Black 1/4
  • If the two alleles are linked, the PARENTAL
    phenotypes will be OVER-REPRESENTED.

68
The Chi-Square Test
  • The Chi-Square test is a good statistical tool to
    test a hypothesis with distinct OBSERVED and
    EXPECTED values.
  • Imagine we did the cross above and counted 400
    offspring. We observed the following numbers.
  • Eyes Body Number Observed
  • Red Normal 101
  • Sepia Normal 99
  • Red Black 106
  • Sepia Black 94

69
This is how we would do a Chi-Square test
  • if the expected ratio is 1/41/41/41/4, we
    expect 100 flies with each phenotype.
  • Eyes Body Number Observed Number
    Expected
  • Red Normal 101
    100
  • Sepia Normal 99
    100
  • Red Black 106
    100
  • Sepia Black 94
    100
  • The Chi-Square (Written c2) S(O-E)2/E, is in
    index of how far your observed numbers are from
    your expected numbers.
  • QUESTION What is the Chi-Square value from the
    cross above?

70
Answer
  • Eyes Body Observed Expected O-E
    (O-E)2/E
  • Red Normal 101 100
    1 .01
  • Sepia Normal 99 100
    1 .01
  • Red Black 106 100
    6 .36
  • Sepia Black 94 100
    6 .36

  • S(O-E)2/E.74

71
What the _at_!?? Does this Number Mean?
  • The c2 value for any given test represents the
    extent to which the observed values depart from
    the expected values.
  • The c2 distribution lists the probability of any
    given set of observed values departing from the
    expected values by chance, given the degrees of
    freedom-degrees of freedomN-1 where Nthe number
    of comparisons
  • QUESTION How many degrees of freedom were there
    for the cross we just did?

72
  • ANSWER N-13 degrees of freedom.
  • QUESTION What is the probability that the
    observed values from the cross above would depart
    from the expected values to the extent that they
    did? (see your lab manual, page 93)

73
  • ANSWER With three degrees of freedom, the
    probability of departure is gt.70. In other
    words, MOST data sets will depart by that much,
    or more, even if the hypothesis that generated
    the expected values is perfectly correct.
  • Why?
  • Because a certain amount of departure by random
    chance is part of the essential, probabilistic
    nature of genetics.
  • Why gt.70?
  • The table on page 93 gives a few rough
    benchmarks. For example, at 3 degrees of
    freedom, 50 of data sets depart to the extent
    that the c2 value is 2.37 or more (Plt.50). 5
    depart to the extent that the c2 value is 7.81 or
    more (Plt.05).

74
Most scientists use an arbitrary criterion to
determine whether the departure of observed and
expected values was due to chance, or due to a
flaw in the hypothesis that generated the
expected values to begin with.
  • The arbitrary cutoff is Plt.05. If there is less
    than a 5 chance that the observed and expected
    values would depart to the extent that they did
    by chance alone, than we say that the hypothesis
    is falsified we reject it.
  • Otherwise, we accept it (this does not mean we
    have proven it, however, because an infinite
    number of hypotheses can be concocted to generate
    the same data).
  • QUESTION For the cross above, do we accept, or
    reject the hypothesis?
  • What does this mean?

75
  • ANSWER Accept the hypothesis.
  • The hypothesis that we used to generate the
    expected values was independent assortment.
  • Since we cannot reject independent assortment,
    this means that the genes are not linked.

76
Linkage
  • Linkage is the result of two loci being located
    close together on the same chromosome. It causes
    a departure from independent assortment (thus,
    Mendels second law is incorrect, but he didnt
    know about chromosomes).
  • In crosses involving two loci, linkage causes
    certain combinations of alleles to be
    over-represented in an individuals gametes.

77
Example of Linkage
  • In Drosophila melanogaster, the recessive allele
    for the sepia locus causes flies to have very
    dark colored eyes. The recessive allele at the
    ebony locus causes the fly to have very dark body
    color.
  • A male from a true breeding line of sepia
    eyed-ebony bodied flies is crossed to a female
    from a true breeding line of red eyed, tan-bodied
    flies (the wild type).
  • se se eb eb x SE SE EB EB
  • to create a heterozygous F1 SE se EB eb
  • Now, cross a female F1 to a male from the
    sepia-eyed, ebony bodied, line.
  • QUESTIONS What is the phenotype of the F1?
  • With no linkage, what is the expected proportion
    of sepia-eyed, ebony-bodied flies?

78
Answer
  • The F1 are Wild Type
  • With no linkage, the expected proportion of
    sepia-eyed, ebony bodied flies is 25.

79
Now, imagine we got this data
  • Eyes Body Number Observed
  • Red Normal 123
  • Sepia Normal 77
  • Sepia Ebony 119
  • Red Ebony 81

80
Are the loci linked?
  • Eyes Body Observed Expected O-E
    (O-E)2/E
  • Red Normal 123 100
    23 ?
  • Sepia Normal 77 100
    23 ?
  • Sepia Ebony 119 100
    19 ?
  • Red Ebony 81 100
    19 ?

  • S(O-E)2/E??

81
  • Eyes Body Observed Expected O-E
    (O-E)2/E
  • Red Normal 123 100
    23 5.29
  • Sepia Normal 77 100
    23 5.29
  • Sepia Ebony 119 100
    19 3.61
  • Red Ebony 81 100
    19 3.61

  • S(O-E)2/E17.8
  • The loci are linked.
  • QUESTION Why are there fewer SEPIA NORMAL and
    RED EBONY?

82
  • Answer Linkage causes the GRANDPARENTAL
    phenotypes to be over-represented in the progeny
    from a test cross.
  • MOM DAD
  • Egg
    sperm
  • F1
  • gametes (without recombination)
  • gametes (with
    recombination)

SE EB
se eb
SE EB
se eb
se eb
SE EB
SE EB
se eb
SE EB
se eb
EB
se
SE BE
eb
83
Linkage Mapping
  • You can tell how far apart loci are by the
    proportion of the F2 from a test cross that are
    recombinants. Simply take the number of
    recombinants and divide by the total, and that
    gives you r-the proportion of recombinants.
  • For instance, for the cross we just did, the
    recombinants were Red Ebony and Sepia Normal.
  • Thus, r (8177)/400.40
  • Hint-the recombinants are the F2 that do not
    resemble the grandparents.

84
  • From r, you can get the distance between loci.
    Simply multiply r by 100 and you get the distance
    in map units (Morgans).
  • Thus .40x 10040 map units.
  • Note that the more recombinants, the higher r,
    and the farther they are away in map units.
  • Loci that are very close together are said to be
    tightly linked, and produce few recombinants.

85
This is a linkage map of sorgum, which was a work
in progress when I wrote this slide. The linkage
groups almost always turn out to be
chromosomes the genetic markers are loci that
have been placed in order by a comparison of
their relative distances (this is from the
icrisat website)
86
An Interesting System, Heterostyly in Primrose
  • In Primula sp., an interesting genetic system
    maintains two distinct phenotypes in the
    population, and ensures the virtual absence of
    intermediate phenotypes.
  • It is called heterostyly, because each type of
    flower is well adapted to cross with its
    opposite, but unable to cross with itself.
  • This system encourages outcrossing, which can
    potentially maintain genetic diversity.

87
  • The dominant, G allele codes for short style (the
    female part of the flower), which reaches to the
    middle of the corolla tube, the recessive, g
    allele codes for a longer style, which reaches to
    the lip of the corolla.
  • The dominant, A allele codes for long anthers
    (the male part of the flower), which reaches to
    the edge of the corolla tube, the recessive, a
    allele codes for short anthers, which reach to
    the middle of the corolla tube.
  • The dominant P, allele codes for thrum pollen,
    the recessive, p allele codes for pin pollen,
    which is much smaller.
  • The three loci are very closely linked-so that
    crossing over rarely occurs

Thrum-left, pin-right
88
  • In normal populations, only two genotypes are
    present, GgAaPp, and ggaapp
  • The genotype ggaapp gives rise to the pin
    phenotype, which has long styles, short anthers,
    and pin pollen.
  • The genotype GgAaPp gives rise to the thrum
    phenotype, which has short styles, long anthers,
    and thrum pollen.
  • Even though other genotypes are theoretically
    possible, a combination of tight linkage, and the
    mechanical impossibility of thrum x thrum crosses
    keeps them from becoming common.
  • Thrum x thrum crosses are impossible, because
    thrum pollen cannot grow down a short style.
  • Pin x pin crosses are possible, but very rare.

Primula veris. Thrum is on the left, pin is on
the right
89
  • Each form is adapted to transfer pollen to a
    different part of the potential pollinator,
    thrums transfer pollen to the waist, which can be
    received by the styles of a pin flower.
  • pins transfer it to the insects head.which can
    be received by the style of a thrum flower.
  • Rare crossing over events, in thrum flowers,
    produce intermediate phenotypes, but these do not
    do not produce many offspring of their own, at
    least via animal pollinators.

90
Sex-Linkage
  • Sex linkage is not really linkage.
  • Sex linkage is the term for a locus being located
    on a sex chromosome, such as the X chromosome in
    humans or Drosophila.
  • Sex linkage causes a unique combination of
    inheritance.
  • For instance, in humans, males receive only ONE
    allele from each sex linked locus (from their
    mom).
  • Recessive alleles are therefore automatically
    expressed in the male, a state referred to as the
    hemizygous condition.

91
  • Homogametic sex that sex containing two like sex
    chromosomes. In most animal species these are
    females (XX).
  • Butterflies and Birds, ZZ males.
  • Heterogametic sex that sex containing two
    different sex chromosomes In most animal species
    these are XY males.
  • Butterflies and birds, ZW females.
  • Grasshopers have XO males.
  • In ants, bees, and wasps, males are haploid, in
    effect, every locus is sex-linked.

92
  • Examples of Sex-Linked Traits in Humans
  • Hemophilia
  • Duchennes Muscular Dystrophy
  • Red-Green Color Blindness
  • The above are all recessive, exhibiting a
    characteristic pattern of inheritance
  • A female can be a heterozygous carrier but a
    man cannot.
  • Males, since they always exhibit the trait, are
    much more commonly affected by it, though the
    allele occurs in equal frequencies in females.

93
A Genetic Cross With Sex Linkage
  • Red/white eye color in Drosophila
  • The white locus is on the sex chromosome, the
    white allele is recessive, therefore
  • W red, w white
  • In females
  • WW, Ww, red-eye female
  • w w white-eyed females
  • In males
  • W red-eye male
  • w white-eyed male

94
  • One key indicator of sex-linkage is that
    reciprocal crosses give different results
  • Cross (purebreeding) red-eyed females to
    white-eyed males
  • F1 All males and all females have red eyes
  • Reciprocal cross white females crossed to red
    males
  • F1 All males are white, all females red
  • WHY?
  • What would the F2 look like in each case?

95
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96
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97
X inactivation
  • In each female cell in mammals , one X is picked
    at random and inactivated.

98
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99
Epistasis
  • Epistasis occurs when a gene at one locus alters
    the expression of a gene at another locus.

100
Coat Color in Mice
  • In Mice, Black coat color (allele B) is dominant
    to brown coat color (allele b). Therefore, bb
    individuals normally have brown coats, BB and Bb
    normally have black coats.
  • A SECOND locus controls the way the pigment is
    distributed
  • Normal distribution (C) is dominant to inhibited
    distribution (c) . CC and Cc individuals
    therefore normally have black coats or brown
    coats (depending upon their alleles at the color
    locus), and cc individuals are WHITE no matter
    what they have at the other locus. This is
    because, if pigment is not deposited, the animal
    has a white coat, regardless of the potential
    coat color of the animal.

101
Question A BROWN mouse is mated to a WHITE
mouse. All of the resulting offspring are
BLACK.What is the genotype of the
offspring?What types of gametes can they produce?
102
Answer
  • The parents are bbCC (brown) and BBcc (white).
    We know the parents are homozygous because ALL
    the offspring had the dominant trait at each
    locus (if they were heterozygous, we would see a
    mixture among the offspring).
  • Their offspring are BbCc (black).
  • The F1 can produce four different gametes for
    these two loci BC, bC, Bc, bc.

103
Question
  • If these F1 mated with each other to produce an
    F2, what proportion of the offspring would be
    expected to be BLACK?. What proportion would be
    expected to be WHITE?

104
Answer.
  • 9/16 black, and 4/16 white.

105
Pleiotropy
  • Most genes exhibit pleiotropy, they have multiple
    affects.
  • The best examples come from genetic diseases in
    humans, such as Marfans syndrome.
  • Individuals with Marfans syndrome (a dominant
    allele, actually a deletion that behaves as a
    dominant allele) have the potential for very
    tall stature, elongated fingers, curved spine,
    problems with their retina, heart valve problems.
  • All these effects result from an allele that
    affects the distribution of the fibrillin
    molecule. Fibrillin fibers surround the
    important areas of connective tissue in the body,
    thus, alleles that modify fibrillin cause MANY
    changes in the growth of the human body.

106
Penetrance and Expressivity
  • When researchers perform genetic crosses, they
    take pains to make sure their strains are all
    genetically uniform EXCEPT for the alleles in
    question, and that the environment is identical
    from one generation to the next.
  • In the real world, alleles do not act alone, they
    act in concert with other genes and against a
    variable environmental background.
  • Having a particular genotype does not necessarily
    mean the individual will manifest it. Also, it
    is possible to manifest a trait to various
    degrees.
  • Penetrance describes the probability that, given
    a genotype, the individual in question will
    manifest it.
  • For example, Huntingtons disease is caused by a
    dominant allele. 95 of persons with this allele
    manifest the disease, 5 do not. It has 95
    penetrance.
  • Expressivity is the extent to which a trait is
    manifest, given that it is manifest in an
    individual. Many traits have variable
    expressivity.
  • For example, Marfan Syndrome, caused by a
    dominant allele, has highly variable
    expressivity. Some people develop a tall build
    and long fingers, others develop life-threatening
    conditions.
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