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Gene mapping

Created by Efrat Bruck.

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  • leaf green style avatar for user J P
    How would you determine where a gene is on a chromosome if you're given the number of offspring with certain phenotypes?
    (8 votes)
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  • blobby green style avatar for user swathi.pakalapati
    Hi, Is the video on gene mapping complete? I cannot see the statistical analysis part. Please let me know.
    (7 votes)
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  • piceratops ultimate style avatar for user Phil Howlin
    At , the comment 'not drawn to scale' is made, but intuitively I don't think m.u. are a linear measurement of distance. For example, are the blue genes (B) and green genes (G) 31 (25+6) m.u. apart?
    Am I right to say that the probability of recombination is the "probability of the blue swapping with respect to the purple and the green staying still" plus "the probability of the green swapping with respect to the purple and the blue staying still"?:
    D(G->B) = ((1-0.06)*0.25 + (1-.25)*0.06)*100 = 28 m.u., which is not 31 m.u.
    Any thoughts from others? Am I off base here?
    (6 votes)
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    • aqualine tree style avatar for user Don Zhu
      If you consider double cross-overs leaving the 'same' genetic product and other advanced genetics concepts, the accuracy of a map unit is reduced as you near 50 being the theoretical max. Since higher order cross-overs can happen in the genes that are not labeled, but do exist in between the labeled genes in her video, there is statistical analysis you can perform to prove the non-linearity as you near 50 cM. The take home message is that linearity approximates well for genes that are not separated by huge distances. You are correct in saying that linearity is not likely applicable for estimating genes which recombine at 31%.
      (5 votes)
  • aqualine ultimate style avatar for user David Pedersen
    Thanks for a clear explanation in your video! I am looking for a more in-depth assessment of how map units relate to a specific % of progeny. e.g. if the resulting progeny is 4% (the # produced following crossing over*) Would the distance between loci = 8 m.u.? I read that the % of tetrads involved in an exchange b/t 2 genes = 2x the % of recombinant gametes produced. Is this the correct application of this formula, or am I confusing two related ideas?
    *The cross is made with Ar/aR x ar/ar and only 4% of progeny are aarr. Thanks!
    (4 votes)
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  • aqualine ultimate style avatar for user NicholasHoffman2004
    I'm still not sure how to calculate Recombination Frequency, and I can't find a video on it. When you go to the questions, it says that I should watch this video, but this video doesn't tell me anything, I've watched it twice.
    (3 votes)
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  • mr pants teal style avatar for user frehman
    When she says that recombination happens, is that something that occurs only during crossing over? Or are there other times this recombining can happen as well?
    (2 votes)
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  • blobby green style avatar for user Rashadul Islam
    I thing this video is confusing with centromere and gene number.
    (2 votes)
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    • purple pi purple style avatar for user Yeonjun Kim
      The centromere is the band on the chromosome, the one that holds the double chromosome together, though it is also present in the single chromosome. the Gene number is however, something entirely different, so no, the video is not confusing between the two terms.
      (1 vote)
  • duskpin sapling style avatar for user shehashope8
    Can the blue and green genes also recombine/separate?
    (1 vote)
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  • male robot hal style avatar for user Michael Natal
    Hi. Great video. I have a doubt regarding genetic recombination. Does genetic recombination occurs in non-coding regions, or it can happen anywhere in the chromosome? I think the latter would pose a problem if it occurs in the middle of a gene since the expression or the protein that it codes for could be compromised.
    (2 votes)
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  • starky sapling style avatar for user kaustubhshroff1
    When she says "x %" of times meiosis occurs, she means it out of every 100 times meiosis occurs right?
    (1 vote)
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Video transcript

- [Voiceover] One of the very interesting things about genetic recombination is that you can actually use genetic recombination to figure out the distance between genes on a chromosome. And if you were to do this to all the genes on a chromosome, you could actually map out the chromosome, figure out exactly where the genes are. And we're going to explore that concept. So we're looking at a pair of homologous chromosomes, and let's just say that the orange chromosome is the paternal chromosome, so it comes from the father, and let's say that the yellow one is the maternal chromosome. And, just to remind ourselves, these are sister chromatids. That means that they are identical chromatids, they have identical genes on them. So those colored circles that I drew represent just some genes that I randomly picked. And you can see that on the two sister chromatids I drew them in the same color, because they are the same. And for that matter, these are also sister chromatids. These two yellow chromatids are also sister chromatids. And I'm just gonna review a bit to give us some context. So normally in the cell, the paternal chromosome would just look something like that, with the centromere middle. And the maternal chromosome would also look something like that. But, during myosis or mitosis, when they replicate, this chromosome will turn into that. So it's gonna duplicate itself and each one of those strands is a sister chromatid. And so the maternal chromosome turns into something that looks like that. But, this is still considered one chromosome. And this is considered one chromosome. And that can be a little bit confusing, because how could this be one chromosome and this also be one chromosome? If this X has double the material as the original strand? And the answer to that question is because we count chromosomes by the amount of centromeres that are present. So this has one centromere, it's considered one chromosome. This X has one centromere, so it's considered one chromosome. However, they're not quite the same. This, on top, is just one chromatid. And the bottom chromosome has ended up with two chromatids. So try not to get confused, even though we're calling this one chromosome, it's really made up of two identical sister chromatids. But anyway, that was a bit of a digression. Let's focus again on our homologous chromosomes. So I picked a couple of genes, that I just put on, and we're gonna focus on three genes in particular. And to make this a bit more real or relevant, let's just say that the green genes represent I don't know, maybe complexion. Maybe like a dark complexion versus a lighter complexion. And on the maternal chromosome, I also drew it in green, to remind us that these are homologous chromosomes, they're homologous alleles, in other words, these are both alleles that code for complexion, but different shades of green, because they're probably different versions. So these green genes also code for complexion. And let's say that this darker purple, or magenta, gene codes for, let's say hair color. So that means that the lighter purple on the maternal chromosome also code for hair color. And then let's say that the blue genes code for eye color. So we have dark blue on the paternal chromosome and light blue on the maternal chromosome. And let's then focus on the sister chromatids where genetic recombination occurs. So these two strands are going to swap genetic information between them. Maybe like a chunk on bottom will swap, maybe something in middle will swap, maybe something on top will swap. Actually, genetic recombination also occurs between sister chromatids. However, sister chromatids are identical so it would be of no consequence. Anyway, so let's look at the two chromatids where genetic recombination is happening. The two that I circled. Let's take a closer look at those. So here are the two chromatids that are going to exchange genetic information and undergo recombination. And I want to ask you a question. So I'm gonna give you two choices. And I want you to try to figure out which one is more likely. So, for the first choice, let's look at the purple and green genes. And the question is, what's the what's more likely? Is it more likely that the purple and green genes undergo recombination? And when I say that, I mean that the genes that are originally on one chromosome separate. So I mean to say that, for example, this purple gene will get separated from that gene, and this lighter purple gene will get separated from that gene. So is it more likely that the purple and green genes recombine? Or the way I like to view it, get separated. Or, is it more likely that the blue and purple genes recombine or get separated? And the way to think about this is, well look at the distance between them. So the distance between the purple and green genes is something like that. So in order for recombination to occur with respect to the purple and green genes, it would have to happen somewhere over here. Or on the other side, it doesn't matter, it doesn't make a difference. So you have this whole distance, whereas if you wanted recombination to occur with respect to the purple and blue genes, you have a very smaller area to work with. It would have to happen somewhere here. So somewhere along this line of the chromosome. So, that means that it's much more likely for recombination to happen with respect to the purple and green genes. That is more likely because you have this entire distance to work with. If these two chromatids swap genetic information anywhere along this stretch of the chromosome, so the green and purple genes will separate and recombine. And the blue and purple genes are less likely to recombine because recombination would have to occur only in this little sliver of chromosome and that's just smaller than the other part of the chromosome that we were looking at. So, we just learned a very important concept and that is that the further apart two genes are, the more likely it is that they will recombine. I'm not actually not sure if that's the proper way to use the word, but I just use it that way. So I'm gonna put it in quotes. And again, when I say recombine, I mean that two chromosomes that were originally on the same, sorry, two genes that were originally on the same chromosome get separated. And then the next thing we learned is that the closer two genes are to each other, I'll abbreviate each other, just e.o., the less likely it is that they will recombine. And now i'm gonna introduce you to some terms. The centimorgan is the unit of measurement that we use to measure distance on a chromosome. And another way to say centimorgan is a genetic map unit. Or, m.u. which stands for map unit. And I'll give you the official definition of a centimorgan, because I think it's important and it kind of ties in distance to what it has to do with recombination. And so a centimorgan is the distance between genes, I'm just gonna abbreviate between like that, for which one product of myosis in 100 is recombinant. And to put that in simpler terms, it means that if two genes are one centimorgan apart, it means that one out of one hundred times, or one percent of the time that myosis happens, those two genes will be recombinant, or separate, or recombine. And we'll actually do an example of this to illustrate what this means. So here we have our two chromatids again and let's just say that the distance between the purple and green genes is 25 map units. Remember, a map unit is the same thing as a centimorgan. And let's say that the distance between the blue and purple genes is six map units. So this is clearly not drawn to scale very well, but it's just an estimate. So let's first focus on the purple and green genes. So if they're 25 map units apart, so remember if two genes are one map unit apart that means that one percent of the time they'll recombine, so these are 25 map units apart, so that means that 25% of the time that myosis happens, recombination will occur with respect to the purple and green genes. So let's see what that looks like. So we're gonna see that in this spot, right over here, the chromatids just swap information, So let's draw what that would look like. So let's draw our paternal chromosome, or at least part of it. And then we'll draw our, actually I'm gonna draw that a little bit higher, because we need more room. So here's our paternal chromosome. And then our maternal chromosome. Or chromatid. And then, since they kind of swapped in this spot, so I'm gonna draw yellow, right over here. That's the part that came from the maternal chromosome. And then I'm gonna draw orange over here. That's the part that came from the paternal chromosome. And now let's fill in our genes. So the blue genes will just stay where they were. So, we just leave them put. And the same goes for the purple genes. But then, we have that piece of maternal chromosome. So we get that hunter green gene over here. And then we get the lime green gene right over here. So this is what I mean by recombination being a separation of genes. So this purple gene and that lime green gene were on the same chromosome before, but they got separated. They're not on the same chromosome any more. And the same applies to these two genes. Now let's look at the blue and purple genes. So they're six map units apart. So that means that 6% of the time that myosis happens, the purple and blue genes will get separated. So, we're gonna see that upwards of this spot, the chromatids swap information. So, let's draw that. So here we'll draw a part of our paternal. that's the paternal chromosome and the maternal one. And they swapped somewhere like over here. So let's fill that in. So that's the part of the maternal chromosome that lands up, sorry, yeah, that's the part of the maternal chromosome that ends up on the paternal one. And the orange over here. And now let's fill in our genes. So lets's first fill in the ones that just stay put. So we have that lime green gene, then we have that hunter green gene. And our purples also stay put. But the blue genes swap chromosomes. So we have our dark blue gene over here and our light blue gene over here. And again, take note of how they swap places, or how the separate. So these two genes were together on the same chromosome before, but not anymore. And the same for these two genes. So let's just tie this back into the bigger concept going on. If we were to do a statistical analysis of how often certain recombinations happen, that can help us map out the genes on a chromosome.