What's in a name?

Names are handles to help us organize information.  We can use given names or nick names to identify particular people.  We use species names or common names to identify particular types of organisms.  Names help us find locations:  house numbers and streets, intersections, landmarks.  Sometimes names give us insight into details about a specific edifice.  For instance, if I'm told of a building and its name is St. Andrews, I have a good idea that it's a church or part of the Separate School system in my city.  The words "University", "College", or "High School" tell us that we're looking for an educational venue.
Geneticists don’t work in isolation – they are part of a wider community of fellow geneticists.  Many geneticists tend to communicate most often with other researchers working on their same organism. To make things easier, they agree on how to name mutant loci so that it's faster and more clear when they communicate their findings.  Choosing a good naming convention can save an immense amount of time. You'll see that the naming convention described here allows you to just look at a gene symbol and you can tell if it's X-linked, autosomal, dominant, or recessive.  If you see two gene symbols, you can tell if they're on the same chromosome (linked) or on separate ones.  It's a powerful, efficient system.

Pretend we are a community who will all explore a hypothetical organism:  a groo.  To do this we will use a common naming and symbolic system.  We’ll call it the “Groo Convention”.  Groos are dimorphic (males look different from females), are brick-red in colour, and have a blue, furry surface.  Here's what wild type groos look like (guess which is the male and which is the female!):

 Because the groos above are well-described by their researchers, the normal phenotypes (those most often found in the wild, and hence "wild type") are taken for granted.  Deviations from these - mutations - are therefore interesting and are likely to be studied to determine the genetic nature of these.  Thus our first rule:

• 1)  The "normal" groo phenotype is described as wildtype, and this is the "base state" or "reference organism".

• 2)  Any change from the wildtype phenotype is a mutation and must be named.  For example, a trait that makes a groo appear as very pale could be named “pale groos.”  Note that names should be descriptive: cute puns/jokes might work (maybe you want to call the mutants below jaundice), but the name provides a clear description of the mutant trait.
  

• 3) The gene symbol must be 3 letters derived from the trait name.  Underline the letters to show that they belong to a single trait.  For example, you might want a "p", an "a", and a "g" from pale groos.

• 4)  Dominant mutant trait symbols must have the first letter capitalized. Recessive mutant traits must be all lower case.  Mutants are not always recessive!!   Sometimes they are dominant!  For example, if one determines that the pale groos trait is due to a dominant mutation, we write:

Pag

            Or, if the pale groos trait is found to be recessive, we would write:

pag

• 5)  The allele that is not mutated in this locus uses the exact same letters as the mutant, only a superscript ‘+” is added to the symbol.  For example, assuming the pale groos mutation is dominant, the wildtype allele of Pag is:
  Pag⁺
   
• 6)  Homologous chromosome pairs are indicated with a ‘/’ (slash) symbol.
  For example, a groo that was heterozygous for the pale groos mutation, write: 
  
  Pag / Pag⁺ 

• 7)  Genes on nonhomologous chromosomes are separated by a ‘;’ (semicolon) symbol. For example, a groo that was homozygous for the pale groos mutation and heterozygous for a different trait, blue, on a different chromosome, write: 
  
  Pag / Pag ; blu / blu⁺

*this image was from another resource where I named a locus "Paf".  Please note it should be "Pag" for this example.

 

• 8)  Linked loci (loci that are on the same chromosome) are listed together on the same homologous chromosome. For example, if pale groos and being bald were linked traits, they would be on the same chromosome, and thus a groo that was homozygous mutant for Pag but heterozygous for blu would be described as:
  
  Pag blu⁺ / Pag blu

*this image was from another resource where I named a locus "Paf".  Please note it should be "Pag" for this example.

• 9)  For X-linked traits (sex-linked), the trait is written as a superscript to the letter X.
  For example, if vermillion was a dominant sex-linked trait, write:
  
  X^ver (mutant) or
  X^ver+ (wildtype allele of vermillion)
  

  
  

  *note:  the underline for "ver" should be IN the superscript.  The web editor does not force this for every browser.  Here's what it should look like:
  

  

   

• 10)  If the groo is hemizygous (i.e. male), use a ‘Y’ in place of the homologous chromosome.  For example, if there was a male groo with the X-linked trait, vermillion, write:
  
  X^ver /Y

• 11)  If the groo has two X-linked genes, add the loci to the superscript only.  For example, if there was a female groo heterozygous for two recessive X-linked traits, there are two possible genotypes:
  
  X^{ver+ pub+}/ X^{ver pub}
  X^{ver+ pub} / X^{ver pub+}
  … and let’s look at a female who is heterozygous for a dominant mutant allele and a recessive mutant allele.  The genotypes could be:
  
  X^{Glu+ pub} / X^{Glu pub+} or 
   X^{Glu+ pub+} / X^{Glu pub}
  
  What phenotypes would you write down for these?  The first would be a wild type female (het for two recessive mutants) and the second would appear to be a female Glu groo.

Let's try this out with some examples. 

From the genotype shown, determine

i.    How many mutant traits are being described in this groo?
ii.  The inheritance pattern of each trait (sex-linked, dominant or recessive),
iii.  The linkage, if any, of traits,
iv.   The phenotype (including sex) of the groo, and
v.    The zygosity of each trait (homozygous [dom/rec], heterozygous, hemizygous).

The genotype:

X^hel / Y ; grn / grn⁺ ; Brs / Brs⁺

 
Now let's go the other way.
Give all possible genotypes for a groo in which:

i.    Three traits are involved, tny, wht, and Eye
ii.    Eye  is X-linked; tny, wht are autosomal.
iii.   This groo is heterozygous for all loci.

 Bonus question:  What is the phenotype of this groo?

Here are more for you to chew on:

Exploring genotype:

Answer key:

Exploring Phenotype

Answer key:

Ratios, ratios, ratios

In classical genetics, phenotype and even genotype ratios are a mainstay for determining inheritance.  You can memorize the ratios, but it's important you understand what they're based on.

In this exercise, assume we're dealing with simple dominant/recessive relationships for two traits in a bean plant.  The bean can have yellow or orange pods and can be inflated or constricted.  Constricted or orange pods are novel (new) traits.  You cross a true-breeding orange, constricted bean line with one that is true-breeding for yellow, inflated pods.  The F₁ seeds are planted and all grow up to bear fruit which are yellow and inflated.  The F₁ are allowed to self-fertilize.
You have several tasks:

1. Design appropriate gene symbols.
2. Use a branch diagram to show the expected phenotypic distribution of the F₂ progeny.
3. Of the F₂ progeny, those with orange pods are selected and allowed to self.  What is the expected phenotypic distribution among these select F₃ progeny?
4. Demonstrate the expected ratios of progeny from a test cross for the original F₁ plants using a Punnett square.

Here's a full solution, but if you want to just see the solution for part 3 (as my students wanted) you can see a shorter version in the second YouTube video.

---

Here's just the answer to 3:

Another bacterial mapping exercise.

Here's another question you could practice with.  Sketch a single chromosomal map with the loci spaced out properly.  Include the site of Hfr insertion for each of the four strains, indicating proper polarity (direction in which it inserted).

The answer is here.

Replica Plating / Interrupted Mating Gene Mapping

In bacteria, gene mapping is accomplished differently from eukaryotes.  For one thing, they're haploid, and so we're not going to see nonparentals!

Replica plating is done to look for the genotypes of exconjugants, and this presentation doesn't talk about conjugation, F^-, F⁺, or Hfr strains.  You have to know those things before this exercise.  Your textbook probably doesn't go into replica plating too much, so the "Solution" to the problem below gives a bit of information on that.

Here's the exercise.  Try it before looking at the solution!

And now - the solution!

Deconvoluting a genetics question (branch diagram solution)

One of the common tasks for a genetics student is to break down a complex question and solve it systematically.  Here's the kind of question I often put on an exam.  There are several ways to solve it; I include one that uses a branch diagram to find the answer.

The theory behind the Chi2 test

Most textbooks do a pretty bad job in describing how the Chi² test works and how to apply it.

Here's my first video on the subject.  It goes into the theory behind the Chi² formula and when you would apply the statistic to your data.  The components of the Chi² formula are discussed so you should be able to get an idea what it measures.  

The Chi² test is commonly taught in Genetics courses to give students a tool to assess whether data could belong to particular ratios (e.g. 3:1, 1:2:1, 9:3:3:1). After viewing this video, you should:

•  recognize that the Chi² formula measures deviation of and observed value from a theoretical value for purposes of comparison
• be able to calculate the Chi² score from a set of data
• determine the degrees of freedom for a particular sample 
• be able to reject or fail to reject a set of data from a theoretical population by using the Chi² table

Actually doing the Chi²  test is quite simple.  I'll provide a few examples of calculating the Chi² value and interpreting it using the Chi²  table.

Determining Gene Order

I had a lot of office visits today regarding how to set up the F₁ chromosomes in order to figure out the gene order.  The textbook uses examples where all the wild-type alleles are on one chromosome and all the mutants are on the other.  This is called a coupling arrangement:

e.g.

 a+ b+ c+

==========

 a  b  c

However, it's certainly permissible to have an F₁ organism that has some alleles in repulsion:

e.g. 

 a+ b   c

==========

 a  b+  c+

You should note that in both cases, the genotypes of the F₁ are the same:  they both represent heterozygous creatures.  This will dramatically change the ratios from your testcross and which numbers represent the "parentals" (which actually just give the chromosomes for your F₁).

For the first case (all in coupling), if the het is derived from two true-breeding parentals, they might have the genotypes of:

 a+ b+ c+          a  b  c

==========   x    =========

 a+ b+ c+          a  b  c

The double crossover class from the testcross would be:

 a+ b  c+         a  b+ c

==========  or   ==========

 a  b  c          a  b  c      <=== This came from the testcross parent

For the second (some repulsion), the double crossover classes from the testcross would be:

 a+ b+ c         a  b  c+

=========  or   ==========

 a  b  c         a  b  c      <=== This came from the testcross parent

Here's an exercise to help you with this concept.

A solution is shown below (click on the YouTube icon to go to the YouTube site so you can view it in full screen and high definition).