Genetics and Mapping

Quiz and Packback Reminders

• Quiz view on Sunday, includes three-point mapping problems.

• Packback due on Sunday; no curiosity scores for this one.

Three-Point Mapping

• Explaining three-point mapping, how it works, and why it is used.

Recombination and Crossover

• Homologous pairs of chromosomes line up during meiosis (prophase I or prophase II).

• Crossover occurs between non-sister chromatids.

• Yellow and blue represent sister chromatids; pair forms a tetrad or homologous chromosome pair.

• Crossover involves DNA breaking, repairing, and rejoining.

• After crossover, parental gametes are still present.

• Purpose of meiosis: making gametes and maintaining chromosome number.

• Recombinant for gene 'b' occurs when 'b' and '+' switch places; small DNA piece exchange between blue and yellow chromosomes.

• Single gene crossover involves flipping one gene from one chromosome to another.

Double Crossovers

• With double crossovers (or triple/quadruple), outcome depends on crossover location relative to genes of interest (e.g., 'a' and 'b').

• Focus only on 'a' and 'b', ignoring other genes on the chromosome.

• If double crossovers occur between 'a' and 'b', there is no change in the relationship between 'a' and 'b'. Information in between might change, but we're not considering it at this point.

• Gametes produced are still parental types (e.g., ++ and ab).

• If crossover events occur on either side of 'a' and 'b', the relationship between 'a' and 'b' remains unchanged.

• A and B are moved from the blue chromosome and plus plus from the yellow one.

• The gametes produced are still ++ and ab.

• Critical factor: location of crossover events determines the outcome.

• Understanding meiosis is important.

Recombinants

• Recombinant are those where 'a' and 'b' relationship remains the same.

• In that situation, nothing changes.

• When considering double crossovers, triple crossovers, where they occur matters.

Crossover between two genes

• If a crossover occurs next to the a gene. a and b move down here and plus and pluses moved down here.

• If an next crossover event occurs between a and b, b and plus move back to where they were.

• We have true recombinants because we have plus plus and a b.

• Flipping either A or B results in the other being flipped as well.

Calculating Crossover Frequency

• Calculate frequency of specific crossovers similar to calculating probabilities.

• Example: frequency of rolling a six is 1/6.

• Frequency of rolling an 11 in craps (6 and 5) is about 1/6 \times 1/6 = 1/36 \approx 2.7\%.

• Apply this to crossover events: what are the odds of crossover events occurring between two genes?

• Linkage, centimorgans or map units, recombination frequency all refer to distances.

• What are the odds of an event between two genes this far apart?

• Example: fruit fly genes black (b), cinnabar (cn), and vestigial wing (vg).

• Consider a heterozygote. What is the possibility of a double crossover affecting all three genes.

• The possibility would be the chance of having that crossover event between b and cn.

• From the last lecture, that was 9\%.

• What are the odds of having both crossovers occur?

• One between b and cn, and the other between cn and vg.

• Odds of crossover between cn and vg is 8\%.

• Odds of both happening is 9\% \times 8\% = 0.72\%.

• These odds depend on how far apart the genes are.

• Example: 9 centimorgans and 8 centimorgans – close but not exact.

• Further apart the genes, the more likely a crossover.

Map distances versus Recombination Rate

• Graph of map distance vs. recombination frequency.

• Closer genes are (0-2 map units), less recombination.

• Further apart (100+ map units), approaching 50% recombination.

• 50% (1:1:1:1 ratio in dihybrid cross) is independent assortment which means no longer linked.

• Graph approaches 50% but never reaches it; reaching it means no longer linked.

• How to calculate 8% and 9% from the prior lecture: Number of recombinants divided by total offspring (always 4, 2 recombinants, and 2 parentals) gives recombination frequency.

• Independent assortment is a 1:1:1:1 ratio.

• Dihybrid cross (heterozygote crossed with homozygous recessive) will give four offspring.

• If offspring ratio is 25% each = independent assortment. The genes are not linked.

• 50% recombinants and 50% parentals = independent assortment.

• Graph is not from p = 1/2 equation, you don't have to know what that graph is showing.

• Further apart genes on a chromosome, closer to independent assortment.

• Genes on different chromosomes are by definition independently assorted.

• The closer you get to 50%, the less and less linkage there is.

Three-Point Crosses

• Using three genes to speed up calculations and determine distances quicker.

• Three genes = quicker than two at a time.

• Starting with pure breeding individuals (homozygous dominant and homozygous recessive).

• Mutant, mutant, mutant for a, c, and b: all + are considered wildtype, or normal fly.

• Looking at a cross happens between the a locus:

• C and b move.

• A recombinant is when they are compared together.

• What makes something recombinant A has changed, this makes it the recombinant.

• If you are crossing between C and B:

• Then the recombinant is B, with A and C parental.

• Crossing a and c and c and b:

• Creates c as a recombinant, as a and b stay on the same chromosome.

• First crossover takes C and B, which changes places with the plus and plus.

• Second Crossover flips the b back to where it originally was.

• That's a double crossover we are taking advantage of here.

Three-Point Test Cross

• Using fruit fly notation.

• Pluses are going to be wild type or normal.

• Letters are mutants.

• You do not always have to start with wild type wild type, mutant mutant flight, you have to start with a purebred and fly.

• Can have wild type wild type, mutant mutant for cross veinless wings are mutant mutant for cut edge wings.

• Cross veins are the little veins that you see here, cut wing is from a normal wing.

• Normal eye color, but mutant for cross vaneless wings, mutant for cut edge wings.

• Mutant for eye color, kind of a different red (mammalian color).

• Normal vein wings, normal wings.

• Both pure breeding.

• Doesn't matter whether they're homozygous wild type, it only matters that they are homozygous.

• Cross two pure breeding flies, get a heterozygote.

• Gametes can only pass a plus for eye color, a c for veins, a t for cut edge.

• Same with down here, only a v for the eyes and plus plus for the other two.

• Those jeans are listed in arbitrary order, do not know what order they in.

• Looking to find out what the order of those genes are.

Wildtype & Mutants

• Pluses can be thought of as Big A, little A, as long as you tell the note taker that A is eye color.

• If you think of it in these regards it makes it easier.

• Meaning you're making the assumption that these genes have some manner of linkage to them.

• Making the cross the assumptions are for complete linkage, but we'll address that in a moment.

• Have to know that piece of information, then you're going to do a process that deals with linkage.

• That cross is a test cross- Homozygous recessive.

• Going to cross to a homozygous recessive, this is the reason you will do this.

• Cannot assume male versus female as this is not dealing with sex linkage.

• You do not know if it is VCT, CVT, TCV, you just don't know.

• Know that wild type for eye color is on the same side of the chromosome as mutant for veins, and mutant for wing shape.

• Do not care about anything that is crossing over here, only care about this.

• The first set of offspring are going to be parenteral.

• They are going to be having the same set of set up on the genes as a heterozygous fly.

F1 Generation

• F1 is going to produce these offspring.

• Crossing this fly with a parent with VCT and VCT, makes this fly useful as is its easy to read.

• If you were to move the v fly, it acts just like the fly again.

• A cross over between the t's will give you a plus c and a v plus t.

• Where else can you have a cross over?

• Between two crosses, creating a plus plus t, and a b c plus.

• What is important is what's happening from that heterozygous cross.

• Why are you not considering crossovers with the other fly that only carries VCT allele?

• Well if you flip the v's you change anything.

• To make my life easier, I'm going to know that all possibilities can have a mutant down below.

• The mutants act as placeholders.

• Can you repeat how you got the parentals, they just look like that one fly that is all.

• Single crossovers, and then that last one a double crossover, this is assuming VCT are in a certain orientation.

• We will get to offspring to determine location information.

• Then will be able to tell what a single and double crossover is.

Offspring Grouping for Analysis

• Parental phenotype: most offspring due to cells conserving energy (not using energy for crossover).

• Flipping the v genes causes cells to use more energy.

• Double crossover less frequent because it uses the most energy.

• Determine single crossover one, single cross over two.

• If a VCT for instance it will equal +++.

• Because that crossover event is going to happen equally with each case, will have close to the same amount of offspring.

• What if the numbers were all close? Pick one and it will make a heterozygote, that pairs up then the other two pairing up.

• You cannot have VV or TT.

• They cannot match like that.

• Take any two of those genes.

• Where is your parental?

• Well its right there.

• I'm going to choose b and c, what is the distance?

• To do that, if this is my parental, the resultant of the recombination would be the flip of one of those.

• Flip c to the bottom.

• To go look what recombinant is for these, I'm going to only look for those values.

• Take the other one will give those genes in relation.

• Whatever the number is right here to always look at the result in recombinant.

• Plus plus VC -Right there

• Add them together, divide by the total number.

• How to get the total? You take all of those numbers and add them all together.

• Recombination frequency of 18.5 percent between those two

• Did the same thing for another pair

• Look for plus plus VT.

More Calculations with Genes

• I have the plus T v plus is the parental, means you have a plus plus v, and the plus again

• Adding those together, dividing by total by 13.2 percent.

• Between V and T.

• Calculating the T and C.

• Taking c and t.

• Parental the recombinant.

• Do the math again and that will come out for a frequency of 6.4.

• This ensures how the total distance is calculated.

• Alleles are correct, now know T is in the middle.

• VTC is known now.

• For test is asking for the order they want the true order, and if the other gene is in the middle.

• Doesn't matter how those genes will be written as long as T is in the middle.

• T is how you find where it is on that point.

• Can you tell that T and the middle, because it was the differential and the same on the Frontal etc?

• The distance between them is different

• If this is my map, when I calculated the distance between t and c, that was the 6.4.

• How to get those distances, and if I have the other one down there

• The 13.2 used to offspring to get to this point.

• Adding the double crosses.

• Making that 19.6.
  Have 34 is interference.

Interference

• Does the crossovers currently happen each other or dependently?

• Is the first crossover event have anything to do with the event?

• That's referred to as interference.

• That is if the two events occur independently.

• Calculating that is taking your two distances for vt.

• Taking it as point times point.

• Those two percentages equal where those events intersect.

• This is the expect double crossovers.

• What percentage of offspring should i expect happen?

• 1448 times 0.8 equals where around 12 of those crosses, so what you expect

• Those are expected double crossovers.

• Observe divide by total to calculate the results.

• Take that number and subtract it and that get this number, this is a percentage number, you times it by one

• What if more, you can have a positive coefficient.

• Where the event is encouraged and more can happen.

Four-Point Crosses

• You never have to worry, takes a lot of re combinants.

• Short cut- for the ones that are interested in making it easier.

• The changes of a cross are the one thing you add together

• The main difference of it here, is easy to find results. The easiest way to do for both crosses.

• B is there for Parental.

• Take those and compare and find the results that will come out.

• This makes the cross even with it. It gives the results that are perfect for people, the changes of making it even easier .