Lecture 1: Introduction: Mendelian Genetics plus -Genetic Linkage
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Simplistically, Genetics is a study that analyses the factors that underpin the rhythm of change and potential variation in all living organisms -the mechanisms by which these rhythms are maintained, how they came about, how similar they are to each other and how they are distinct.

As such, it blends mathematical approximations of observed phenotypic traits, and to a large extent data based informational analysis with a keen determination of the very fabric of organismal organization.

Curiously, in pursuit of this global appreciation of how life functions the study of Genetics has raised -and continues to raise- questions about our true understanding of our genetic world.

Even so, In the last thirty to forty years or more this understanding of Genetics has given rise to dramatic break throughs in medicine... and, indeed, how our very genomes are arrayed and structured.

 

1978 first "test-tube baby" is born...             2016 First "3 parent" baby is born...        Bioethical concerns abound...

genes                genes genes         genes

1984 DNA Fingerprinting...                   1997 first E.coli genome sequenced...       2001 - 03 Human Genome sequenced (?)...

 

                                                                        genes

 

2010 first synthetic organism (Mycoplasma)      2015- micro RNA's and editing genomic DNA in situ (CRISPR).

      genes                 genes         genes

Genetics continues to challenge many of the tenets that have been the mainstay of the science for the last 60 years, daring to suggest that -at the very core of our genetic makeup- the classical genetic dogma of DNA replicating and being able to give rise to transient RNAs that interact to produce proteins which provide most of the important functions in the cell -while important- is potentially a "side show" to the true mechanisms of gene expression in many cells.

Classical Geneticists, and now Molecular Geneticists are able to address the consequences of genetic activity at the genotypic level. Thus, they infer mechanism and genetic order from an "understanding" (rationalization) of gene function and (as we have discussed) can even begin to effect changes in the genetic makeup of higher organisms, including humans, to affect changes in phenotypic consequences of gene expression.

The aim of this lecture series is:

(a) to enhance/replace your understanding of Genetics (knowledge that was hopefully gained in Bio3900 -or its equivalent) with a more in-depth, genetic appreciation of the world,

(b) to complement this knowledge with a more molecular based understanding of classical genetic concepts, with some understanding of the technology used

and

(c) to allow you to become a little more informed than the average biologist on the topic of just how our genetics works.

 

-that's IF.... WE succeed.

To understand what has changed in Genetics over the years, you have to have a firm appreciation of "Classical Genetics" so, we will begin by quickly outlining/reviewing(?) the foundations of Classical Genetics -where and how its dictates still apply and where recent advances have modified our appreciation of these accepted norms.

In this lecture series I assume/know that we have a rather mixed population of students.... ranging from those who have recently taken Bio3900 (for whom terms like linkage, test-cross , expressivity etc. are fully understood, every day terms that "trip off the tongue"... and that they can explain at the "drop of a hat"......??) to those of you who haven't really thought of Mendel and his dividing peas for quite some time (if ever).

Thus, the novelty aspect of some of the lectures (especially the first series) will vary from individual to individual -ranging from a review of known material to a new (hopefully more in-depth) introduction into the various, and diverse aspects of gene function, gene expression and the interaction(s) of the consequent gene products.

Nomenclature:

To pamper you all a little bit -and to clear up (hopefully) any concerns about the naming of genetic traits...

Essentially there are two predominantly used methods.

The first is the simple adoption of an initial letter, which symbolizes the genetic trait under investigation (e.g.. "H" for Huntington's disease). Then, knowing that in diploid cells there are potentially two alleles (one dominant one recessive) and defining the presence of one as a capital letter "H" (dominant allele of the trait) and the other "h" (the recessive form of the trait). Thus: "HH" = homozygous dominant , "Hh" = heterozygous , and "hh" = homozygous recessive .

This nomenclature is simple, and (to a first level of understanding) provides a quite effective appreciation of how genetic traits can effect phenotype and how they are able to be passed on from generation to generation.

A second system, however, allows for a greater variety of traits to be listed (and also gives more information as to which allele of the particular trait is normally seen in the population). This system uses the "+" sign to denote the normal or "wild-type" allele.

By way of an obviously absurd example......

Grass is normally green. This colour can result from the production of a variety of structures (chlorophyll springs to mind) whose synthesis is dependent upon any number of genes.  Let us assume, however, that there is only one gene that governs the colour of this particular species of grass. Now, If in a field of green grass a geneticist finds a blade of pink grass and, through a series of fundamental genetic experiments, determines that this colouration is the result of a single genetic factor she/he first needs to label the genetic trait, usually by a description of the variation in phenotype -which in this case would be its colour, green to pink.

Thus, the alleles of this particular gene would possibly be designated as "pk".

Now, the next thing the geneticist would normally do is to define whether this variation in grass colour is a dominant or a recessive trait. By undertaking a series of Mendelian crosses (which we will detail in a few minutes) it can be determined that the trait is recessive and, therefore, the lowercase "pk" is used to designate the particular "colour locus" (if the trait were dominant a capital letter could be used, "Pk").

Everyone knows that grass is not normally pink. Therefore, there must be two forms of this pink allele, the one which gives rise to the pink colour and the one which is normally present and gives rise to a green colour. Using the "+" symbol to denote the normal or wild-type allele, this allele is designated as "pk + ", with the mutant allele being given the simple "pk" symbol.

While this adoption of a modified nomenclature seems to be straight forward, it can give rise to a number of consequential interpretations of the genetic complement of cells that might not be.

Thus: "pk + / pk + " = homozygous "wild-type" (green grass), "pk + / pk" = heterozygous (green grass), because the trait is recessive), and "pk / pk" = homozygous mutant (pink grass).

If, for some reason the trait had been "DOMINANT" the different strains would be designated as..."Pk + / Pk + " = homozygous wild-type (which in this case would still give rise to green grass), "Pk + / Pk" = heterozygous (pink grass, because the trait is now dominant), and "Pk / Pk" = homozygous mutant (pink grass).

N.B. One cannot assume that, just because the normal (wild-type) colour of grass in any given population is green that the pink trait is "recessive". A classic example of this is one that we have just seen, Huntington's disease, which has three temporal variables -two of which are fatal, one gives rise to late onset and one early onset of the disease.

Having established the nomenclature for labelling the locus that would affect the grass colour in our example, there are potentially additional, alternative variations of the gene that may replace the "+" symbol, which we will get to in a few minutes.

In addition to all these variables there are also "qualitative" differences amongst the pehnotypic effects of different mutations, which we will begin to address in a little while, and deal with more heavily at later stages in the course. These phenotypic variables differ as a consequence of the severity of the mutation on the function of a given gene -as well as potential differences in gene expression.

Complications of interpretation abound, however, and the fact that genes reside on chromosomes, and that the chromosomes come in all shapes, sizes and numbers.. (at least in plants) causes an awful lot of additional variations for inerpretation. Thankfully the majority of chromosomes per organism are usually either one or two. Even so, there are still any number of causes for genetic variation....

Penetrance The proportion of individuals in a population that manifest the genotype at the phenotypical level due to the presence of different alleles and the influence of a variety of other possible external factors that would affect their expression. eg. BRCA1 and BRCA2, their prevalence giving rise to potentially different degrees of breast cancer risk -environmental, genetic background and other factors.

Expressivity , which is the "degree" to which the genotype is expressed in the individual, due to outside influences (the number of yes/no’s coming out as maybe’s/possibly’s and probably’s in the individual?? -environmental, genetic background and other factors giving rise to subtleties of phenotype and gene expression).

a red ball

 

How did we come to appreciate the "singularity" (and "duplicity") of nature (at least in our diploid world)?

All about "perspectives" on types of GENEs.

genes

 

Sometimes the consequences of genetic changes give rise to major changes... gain of function vs. loss of function mutational phenotypes... one more often giving rise to dominant traits, the other -more often recessive. e.g. of a gain of function mutation could be an overactive oncogenic factor, the Ras protein.

genes

 

...but we are getting ahead of ourselves.

 

Gregor Mendel's hypotheses:

1. Hereditary determinants are of a particulate nature. Each genetic trait is governed by unit factors , which "hang around" in pairs within individual organisms.

2. When two different unit factors governing the same phenotypical trait occur in the same organism, one of the factors is dominant over the other one, which is called the recessive trait.

3. During the formation of gametes the "paired" unit factors separate or segregate randomly so that each gamete receives either one or the other of the two traits, but only one .

4. The union of one gamete from each parent to form a resultant zygote is random with respect to that particular characteristic.

 

Mendel's First Law: Two members of a gene pair segregate from each other into the gametes, whereby one half of the gametes carries one of the traits, the other half carries the other.

 

Mendel's Second Law: During gamete formation the segregation of one gene pair is independent of all other gene pairs

 

Punnett squares can easily be used to demonstrate how these factors assort themselves in the offspring.

 

-made ever more complex by a dihybrid cross.

-and even more complex by a trihybrid cross.. but with the same principles.

 

Mendel's Laws and the uses of Probability:

The product rule; two independent events occurring simultaneously is the product of each of their respective probabilities.

Roll of the di(c)e ---> 1/6 x 1/6 = 1/36. 

The sum rule; the probability of either one of two events happening is the sum of their individual probabilities.

Roll of the di(c)e ---> 1/36 + 1/36 = 1/18.

This idea gives rise to understand the probability of passing on one of the two traites...."Branch diagrams", where "R-" equals the presence of any of the "R" (or dominant) genotypes. 3/4 x 3/4 = 9/16

 

   

Know how to test for Mendel's laws.

 

While Mendel could not comprehend any of the genetic intricaies that his laws might suggest, his determination of his abstract "unitary" traits had far reaching implications in understanding inheritance of these genetic traits and how they could be inherited.

As we have discussed, each of the gene variants is termed an Allele and ALL variants of a given gene reside at a specific locus on a given chromosome.

Variation in allelic types arise by mutation or change in the DNA sequence. An allele, therefore, can arise due to a mutation at a given locus, and can be analyzed through classical genetics once that variation has been incorporated

Alleles can be randomly mutatagenized to become a different allele, depending on DNA sequence changes and maintained or lost -again in a random manner- unless acted upon by a selective pressure.

"Wild Type", as we have discussed prevously is a term used for the most common allele in the population. (again, being the "most common" in a population does not always mean that the wild-type allele will be the dominant or "superior" allele.

However, some definition of "normalcy" in in the genetic expression of traits provides an incredible advantage in the understanding of how genes work in the whole organism... Indeed, in the early twentieth century, G. H. Shull crossed two varieties of corn, and the yield went from 20 to 80 bushels per acre, thus defining a now common agricultural practice to increase production in plants.

This is called either hybrid vigor or heterosis, whereby crossbred strains show superior qualities, and it is a result of the fact that continued genetic "in-breeding" leads to deleterious traits becoming "fixed" in the gene pool. The use of such hybridization techniques, therefore, has been a common agricultural practice ever since -to increase production in crops and cattle etc...

A hypothesis called overdominance even proposes that the heterozygous condition -in certain important genes- is often considered to be selectively "superior" or have a higher fitness to either homozygote. This occurs far more frequently in a single trait controls more than one phenotype. Such heterosis, would be slightly at odds with Mendel's idea of "independent" traits.

Even so, If all of Mendel's ideas were to hold true for his "particulate" mechanism of genetics which suggests that one gene in any given gene pair is simply dominant over the other.

Perhaps, Mendel wasn't perfect... he was also only observing, NOT deducing.

 

EXTENSIONS or Modifications to Mendelian Genetics -tend to vindicate Mendelian Genetics at the genotypic level.

Same basic scheme, but different phenotypical expression......

 

Incomplete dominance : eg. Four o' clocks, carnations, snap dragons. BLENDING 1:2:1
Codominance : eg. M and N blood groups on chromosome 4 having specific antigens M and N

1: 2: 1 but where the heterozygotes (MN) gives rise to a distinct phenotype

Multiple alleles ABO blood types, A and B are dominant to O , but A and B codominant to each other
Lethal alleles eg. Yellow colouration in mice coats. 2 : 1 . Pleiotropy(?)
Several genes/same character Coat colour in mammals,

eg. mice

A (agouti), B (black/brown), C, (colour) D (intensity), S. (distribution) genes

Epistasis essentially "eliminates" or masks phenotypic expression of other genes,

eg. albino gene

Complementary gene activity eg. Pea plants, purple colouration. 9 : 7
Duplicate gene activity eg. Shepherd's purse, Round over narrow fruits, where

both A 1 - and A 2 - can cause heart shape 15 : 1

Recessive suppression eg. Case of purple eye colour in the fruit fly. 13 : 3

 

Heterozygotes may show an intermediate phenotype.
For example, red-flowered snap dragons when crossed with white snap dragons will generate pink-flowered plants.\

   gametogenesis gametogenesis

While this phenotype (on the surface) might tend to support the blending theory that Mendel was so avidly trying to overcome, the F2 progeny, of a "selfing" of the pink flowers admirably demonstrates, Mendelian "particulate" geneticsThe reason for the change in colour results from a penomenon called "incomplete dominance".

Another example, where Mendelian Genetics apparantly falls down, can be seen in blood types. In this instance, however, Mendel’s laws are also not compromised -at the genetic level.

These blood-types are said to exhibit codominance, where both alleles are expressed. Note that in codominance the phenotype of the heterozygote is completely different (not just a "blend" of the two homozygotic phenotypes).

Mendel made a series of artful choices in choosing traits in peas that "just happened" to be examples of complete dominance

Consequently, Mendel analyzed his "units" in terms of dominant and recessive traits, there are many examples, where variations at a single locus, gives rise to multiple phenotypic effects.

So, let's look a little closer at the behoaviou of genes and their alleles.

Alleles and their Interactions
Differences in alleles of genes are often slight differences in the DNA sequence at the same locus, which result in slightly different products, and can give rise to different phenotypes.

Many "genes" can have "multiple alleles".

In rabbits, coat color is determined by one gene with four different alleles. Five different colors result from the combinations of these alleles.

      

Please note, even if more than two alleles exist in a population, any given individual can have no more than two of them: one from the mother and one from the father.

Again, as can be observed, Dominance need not be complete

Another example The AB of the human ABO blood group system. Moreover, the ABO blood groups are another example of multiple alleles.

The alleles for blood type are IA, IBand IO. They all occupy one locus.
These alleles determine which antigens (proteins) are present on the surface of red blood cells.

These "antigens" react with proteins called antibodies in the serum of certain individuals and cause the blood to clot.

   antigen   genes

The "ABO" blood-type system or "ABH-antigens" are not primary gene products but instead the enzymatic reaction products catalyzed by the enzymes called glycosyltransferases. The ABO system is now known to be a polymorphism of complex carbohydrate structrures of glycoproteins and glycolipids expressed at the surface of red blood cells.

Blood Type Genotypes ABO Enzymes
Present
RBC Antigens
Present
Serum Antibodies
"A"
AA, Ai
"H", "A" A, H
anti-B
"B"
BB, Bi
"H", "B" B, H
anti-A
"AB"
AB
"H", "A", "B" A, B, H
none
"O"
ii
"H" H
anti-A, anti-B

 

Chart Of A-B-O Blood Donor & Recipient Compatibility

 

RECIPIENT
D
O
N
O
R
Alleles &
Antibodies
  O
anti-A
anti-B
  A
anti-B
  B
anti-A
  AB
None
O
None
None
None
None
A
Clump
None
Clump
None
B
Clump
Clump
None
None
AB
Clump
Clump
Clump
None

 

 

A population might have more than two alleles for a given gene.

The result of mixing blood from each of the different ABOtypes can result in red blood cell agglutination, or clumping, which may prove to be fatal.

Multiple Alleles:The "ABO" blood-type system" or "ABH-antigens" are not primary gene products but instead the products of an enzymatic reaction catalyzed by the enzymes called glycosyltransferases. The ABO system is now known to be a polymorphism of complex carbohydrate structures of glycoproteins and glycolipids expressed at the surface of red blood cells.

Note that blood-types A and B can be considered to be "codominant", as the presence of both alleles AB gives rise to a completely different phenotype, when compared to a homozgous AA or a BB equivalent.

The alleles for blood type are IA, IB and IO and are true Alleles, because all three variations can be found at one locus.

These alleles determine which antigens (proteins) are present on the surface of red blood cells.

These "antigens" react with proteins called antibodies in the serum of certain individuals.

The result of mixing blood from each of the different ABO types can result in red blood cell agglutination, or clumping, which may prove to be fatal.

What about Rhesus factors?.......these are a whole new set of antigens, discovered when blood from rhesus monkeys was injected into guinea pigas (circa 1940's).  There are over 50 different types of Rh factors, but the most comomonly known one is the D antigen (Rho[D]), which -if it is present- indicates that that person is Rh-positive; if the D antigen is absent, that person is Rh-negative

In contrast to the ABO system, however, antibodies to Rh antigens aren't necesssarily inherent to the person's blood, and can develop as an immune response after a blood transfusion, or during pregnancy.

At a mother's first antenatal screening, blood tests are taken in order to determine her blood type (A, B, AB or O) as well as her rhesus status (Rh-positive or Rh-negative).

If the mother has the rhesus factor (which is a protein on the surface of her red blood cells) then she is said to be Rh-positive. If not, then she is Rh-negative. 85% of people are Rh-positive.

The rhesus state only really begins to play a role during pregnancy if the mother is Rh-negative, the father is Rh-positive and the baby is also Rh-positive.

Rh(D) positive cells contain the D antigen, which can stimulate Rh(d) negative blood to produce harmful antibodies that can destroy red cells. The harmful antibody is called ‘anti-D’ antibody, and can be produced by a mother who is Rh-negative carrying a baby who is Rh-positive.

Rhesus incompatibility doesn’t cause any problems with a first pregnancy because (unlike the AB antibodies) the rhesus antibodies aren’t inherently present in the mother’s blood.

However, in subsequent pregnancies, if the babies are Rh-positive, there may be a problem. The mother’s antibodies can / will cross over the placenta into the baby’s blood causing a reaction.

This causes problems with the baby’s haemoglobin levels (the iron-carrying element in the red blood cells) which could then fall, causing anaemia. Blood transfusion would then be necessary (see chart below) at birth and the babies could also be severely jaundiced.

Gene Interactions
Some genes give rise to gene products that alter the effects (phenotypes) of other genes.

Epistasis

Given that genes of any organism do not operate in total isolation from one another, but obviously are functioning in a common cellular environment. a phenomenon that occurs when the alleles of one gene covers up (or alters) the expression of alleles of another gene.

epistasis   epistasis

Labrador coat colour is an example of Epistasis in that there are two genes which affect coat colour -the "E" gene, which affects the presence of a dark pigment in the coat and the "B" gene, which governs the degree to which that pigment is present in the coat, where B_ gives rise to a "black lab", but only if the genotypes at the E locus are E_ or EE.

While blood groups would also be a more than adequate example of this phenomenon, a quite overt example of epistatic effect, albeit more indirect, would be life and death consequences! Some might even argue that it is not technically "true" epistasis... Why? what do you think?

 

 

In this instance the same gene that affects coat colour in the mouse also has some influence upon development of the embryo. Thus, one gene, does not always mean one function.   If, as in this case, It has more than one function and is therefore considerred to be pleiotropic.

 

Ratios: 3:1 and 1:1 (test cross) for monihybrid crosses and 9:3:3:1 for dihybrid crosses.

Extension of Mendelian Genetics:-

 

Another example is coat colour in mice in the example shown in the picture:

The B allele determines a banded pattern, called agouti.
The recessive b allele results in unbanded hairs.
The genotypes BB or Bb are, therefore, agouti.

The genotype bb is coloured solidly black .

Another gene, at an entirely different locus, determines if any coloration occurs at all.

The genotypes AA and Aa have color, whereas the double recessive aa are albino, which do not allow any colour to show through as the aa genotype blocks all pigment production.

Mice that are heterozygous for both genes are agouti.


An F2 phenotypic ratio of an initial parental cross between a BB, AA and a bb, aa would be: 9 agouti: 3 black: 4 white.

The corresponding genotypes are 9 agouti (1 BBAA + 2 BbAA + 4 BbAa):3 black (1 bbAA + 2 bbAa):4 albino (1 BBaa + 2 Bbaa + 1 bbaa).

Other examples of gene/allelic expression which differ from expected patterns of Medelian inheritance are:

Recessive Suppression

b  b  b b

 

Duplicate genes, occur when two distinct genes affect the same phentype in the same way.

One of the best examples of this would be the shape of the shepherd's purse pollen sac.

  

Polygenes also mediate quantitative inheritance.
Individual heritable characters are often found to be controlled by groups of several genes, called polygenes.

Each allele intensifies or diminishes the phenotype.
Variation is continuous or quantitative (“summation" or "adding up” of all the traits).
Examples of continuous characters are height, skin color, and (possibly) intelligence.

Nature vs. Nurture?
When thinking about the importance of either genotypes or phenotypes, one must always consider the immense importance of.....the environment , and how it can affect the action(s) of any given gene.

Variables such as light, temperature, and nutrition can dramatically affect the translation of a genotype into a phenotype.

For example, the darkness of the fur on extremities of a Siamese cat is affected by the temperature of that region. Darkened extremities normally have a lower temperature than the rest of the body.

Such colouration can be manipulated experimentally.

Bunnies

Chromosomes and Mendel:

Sutton and Boveri (at the turn of the century) independently linked Mendel's particulate theory (1866) to the behaviour of chromosomes, coining the term " allele" as being a variation of a gene. At this point the ideals of Genetics and Cytology began to merge.

 red ball

Because of the density of the DNA as the cell transitions into Prophase 1 red ball all of these features can be readily observed under the microscope.

Indeed, at the turn of the century the whole process of the "dancing chromosomes" was correllated to the behavior of Mendel's particles by Sutton and Boveri (1902) red ball.

Consequently, Mendelian genetics can, could be easily explained through a knowledge of Meiosis, and the predictable nature of chromosomal moviement -cellular activities and an understanding of Meiosis came togther beautifully.

      red ball

This was (and is) entirely True ....to a point.  That point being what?....

That any given organism has only a fixed number of chromosomes, far less than the number of potential traits governed by Mendel's particulate theory of hereditary should be a concern for Mendelian Genetics. Even so, random assortment of these numerous genetic "particles" still applies -for the most part......???

So, what about genes that are located on the same chromosome?   According to a cellular appreciation of meiosis, wouldn't that suggest that these genes could not randomly asssort relative to each other, and would be considered to be linked on the same chromosome?

At this stage you may want to revisit the fundamentals of Meiosis and carefully observe the process, and the formation of chiasmata, which were observed at diplotene and diakinesis phases in Meiosis I, where chromosomes appear to be interacting at "mobile nodes". These nodes apparently move toward the ends of the chromosome giving a distinctively unzipping-like aspect as the chromosome appears to "unzip" as the chromosomes move to the poles of the dividing cells....Potential for these interactions to give rise to crossover events?

  chiasmata

It turns out that the probability of these chiasmata (exchange of genetic information from one paired chromosome to another) are critical ingredients for the Mendelian school of thought. They appear to happen randomly -at least once per meiotic event.

Now, if that were true, then genes at loci that are far enough apart on a chromosome are highly likely to experience a chiasmatic event. which would have a dramatic effect upon their degree of "random assortment"?

 

The role of the sex chromosome:

Mendel did all his analyses with plants, which -like corn- exhibit both male and female reproductive structures in the same adult plant (termed monoecious, or "all in one house"). 

What about animals and plants, which have individuals that are either one or the other sex (termed dioecious, or having “two houses”).

In most dioecious organisms, the sex of the organism is determined by differences in the presence/absence of a set of chromosomes, or the presence/absence of discrete chromosomes.

In honeybees, for example, eggs are either fertilized -and become diploid females, or they are not fertilized -and become haploid males, drones.

Female grasshoppers have two X chromosomes, whereas the males have just one. Consequently, it is the sperm that determines the sex of the zygote. If a sperm (without an X) fertilizes an egg, the zygote becomes a male grasshopper.

As for humans...

Discovery of Linkage : This phenomenon was first hypothesized to exist by Bateson and Punnett, who observed "asssociation" of heritable traits.  However, it was really verified by Morgan (1909) working on non-autosomal or sex chromosome -linked genes of Drosophila melanogaster.

This distinction was critical for the first analysis as a female that is heterozygous for two distinctively X-chromosomal traits will give male offspring that are hemizygous for these genes so that the gametic genotype -derived from the mother- will directly produce the male offspring's phenotype.

 

Morgan worked with a mutation in Drosophila melanogaster, which caused a white eye instead of the red eye normally found in his stocks of Drosophila

He crossed a white-eyed male fly with a normal, red-eyed female. ALL the F1's were red-eyed, as might be expected.... if the red-eye allele were dominant.

   

 

Subsequently, when he crossed a male and a female of this F1 generation (giving rise to  the F2) he got the expected 3:1 ratio. He then carried out, what he thought would be a series of test crosses with the equivalent to Mendel's "test cross" using an F1 red-eyed female with a white eyed male and he got the expected expected 1:1 ratio. He then did the same thing with an F1 red eyed male with a white eyed female and he again got the expected 1:1 ratio. The only problem with all this was that when he looked at the original F1 generation -there was a distinctive sex bias toward the white F1 generation, they were ALL MALE.

Eventually, Morgan figured out that these results could be explained if he assumed that the particular gene for eye color was located on the X chromosome.

An understanding of this phenomenon allowed for a special type of genetic inheritance......sex-linked inheritance.   In essence, while a female can be heterozygous for a particular gene that is present on her X chromosome, her male offspring will be hemizygous

Thus, if the allele on the X chromosome is a recessive of the trait it will ALWAYS show through in her male offspring. 

it is relatively easy to trace an X-linked trait that has an overt phenotype, as long as you have enough progeny or a well defined family tree.  One such trait, which has become somewhat infamous among genticists (especially in England) is the passage of Haemophilia within the English royal family.

  

On a less morbid note about another type of X-linked trait -Red Green Colour blindness.... -true story.

  b  b   b    b  b   b

While the X and Y  chromosomes normally behave according to the laws of meiotic cell division (and thus according to Mendelian genetics) the ability to "visualize" through genetic crosses the presence of each of the alleles that is located on either of the X-chromosomes of a mother directly challenges the ubiquity of Mendel's 2nd law).

Remember, that ... to equate Mendel with meiosis we had to invoke the role of chiasmata occuring between two gene loci on adjacent chromatids in paired chromosomes during prophase I of meiosis.   This CANNOT occur for X and Y chromosomes,

 

But what about ALL the genes on the other autosomal chromosomes.

Morgan then went on to analyze other genes and demonstrated that some genes -other than the ones that he had tracked to the X chromosome- also failed to behave according to Mendelian expectations, and appeared to retain some of the gene association traits that were present to one or the other of the parents.

Two such traits: purple eye colour (pr, purple and pr+, red) and vestigial wing (vg, vestigial and vg+ normal).

cross       pr+ pr+ and vg+ vg+  x   pr pr and vg vg

giving an -> F1 gen. of      pr+ pr / vg+ vg.

He then test crossed the females of these flies with male flies that were double recessive (i.e. recessive for both traits)

giving an -> F2 gen. of.......

pr+ vg+ 1339
pr vg 1195
pr+ vg 151
pr vg+ 154

.......demonstrating an apparent association of Wild-Type and mutant phenotypes, or "gene coupling"

Morgan then undertook a different cross using a

pr+ pr+and vg vg with a pr pr and vg+ vg+male

giving a similar -> F1   gen. of pr+ pr / vg+ vg .

Again he then took the females of these flies with male flies that were double recessive

giving an -> F2 gen. of.......

pr+ vg+ 157
pr vg 146
pr+ vg 965
pr vg+ 1067

..........seemingly demonstrating an abnormally overt lack of association or "gene repulsion", but having the same gene associations as the original parents.

Morgan explained the anomalies by proposing that the two loci were present and "linked" on the same chromosome.

He went further to suggest that such linkage was apparent because of the "proximity" of genes to each other on the chromosome, which modifed the possibility of chiasmata being able to completely randomize their assortment in to the gametes.......remember those "mobile nodes" or chiasmata???  When do they occur?

           Meiosisred ball.

Additional, physical evidence for these crossover events came much later, and were defined by Creighton and McClintock (1931) while trying to understand the gentic assortment of two genes in corn: Waxy [Wx] (starchy ) and colour [C] (colourless). These two genes were found to be linked on chromosome #9, and their crossover phenotypes were always reflected in the physical aberrations at the extremities on each of the chromosomes.

 

Morgan went further.  He proposed that the frequency of such cross-over events (occurring between two gene pairs) was a function of the genetic distance between the two loci....., BUT ONLY as the gene pairs were relatively quite close to each other on the chromosome.

 

 

He thus defined the unit of genetic distance as being:

 

one crossover event/100 products of meiosis = one map unit or 1 centiMorgan (cM)

 

If this were to be the case, then perhaps the apparent association or linkage could be used to define the order of the location of genes that were relatively close together onthe chromosome

The answer to this idea was Yes, because the probability of crossing over occuring between two loci that were relatively close to each other on the same chromosome appeared to be additive.

Thus, in the following linkage map the probability of a crossing over event pccuring between Y and M would be expected to be 35%.

 

Y-----W- -------------------------------------------M
     0.5 34.5

 

One of Morgan's students, Sturtevant, quickly realized that such information could be used to map genes.

Three point test crosses. Mathematically, two independent events happening at the same time-

However, to observe these traits.....

1. Organism producing the crossover gametes must be heterozygous for all three traits.

2. The cross must be constructed so that each of the phenotypic traits must reflect a change in the genotype at each locus.

3. A sufficient number of offspring must be obtained to get statistically viable results.

In determining the gene order among three genes. You will need to know how this can be achieved!!

eg.

F1:

a b c
A B C

 

This is equivalent to the required heterozygotic parental generation for all three traits.

Remember that this is the simplest case where all the wild-type alleles are dominant and, at least in this case, on the same chromosome.  Correspondingly, ALL the mutant alleles are iniitially on the other.

In the next generation these triple heterozygotes can be test- crossed with triply recessive testers (???)............

In so doing, any "crossing-over" events that have occurred in the formation of the gametes will show through against the triply recessive pairing.

F2: listed as gametic genotypes...Crossover Types

a b c = 230 = 467 = 42.1% = NCO
A B C = 237      
 
a B C = 82 = 161 = 14.5% = SCO
A b c = 79      
 
a b C = 200 = 395 = 35.6% = SCO
A B c = 195      
 
a B c = 44 = 86 = 7.8% = DCO
A b C = 42      

Thus, some vindication of the underlying linkage principle... but this all assumes the premise that the gene order is a b c

Another example: Cross of X/X y/y z/z with x/x Y/Y Z/Z is, however, not appear to behave is such an overtly simple manner, = -as there is now what is termed a mixed "association" of =Wild-Type and mutant alleles, giving:

F1    

X y z
x Y Z

                      

Now if this triply heterozygotic strain were to be test-crossed with a triple recessive...! yielding 1448 total offspring

X y z = 580 = 1172 = 80.9% = NCO
x Y Z = 592      
 
X y Z = 45 = 85 = 5.9% = SCO
x Y z = 40      
 
X Y z   = 89   = 183   = 12.6%  = SCO
x y Z   = 94      
 
X Y Z = 3   = 8    = 0.5% = DCO 
x y z   = 5       

 

But these problem only arise, however, if we assume the genes are in alphabetical order; that, with respect to x and y, the parent types are "X y z " and "x Y Z"

If they are not, then:

 

the first question would be....... What is the gene order?  We find this out by looking at the DCO's.

X y z
x Y Z

 

What would be the gene order that gives "X Y Z" as a DOUBLE cross over

The answer is ...."y     x      z".

Now both the single cross overs (SCO) and double crossovers DCO make sense.

It also allows us toe guage the recombinant distance between the outside genes pairs of y and zby adding up the SCO values between y --- x and x --- z = 268 / 1448 =18.5% to be the recombination frequency value (RF) between the outside genes pairs of y and z

If one does the same thing for the other two sets of gene pairs then one can obtain recombination frequency values (RF values) of 13.1%  for y and x, and 6.4% for x and z, respectively

But 13.1 + 6.4 = 19.5%, which is a little higher than the previously calculated 18.5% -because the DCO's also need to be considered when evaluating crossover frequency.

 

 


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