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This illustration says that if the two homozygotes pr+ pr+ vg+ vg+ and pr pr vg vg are crossed to produce a heterozygous offspring (pr+ pr vg+ vg), then:

this cross gives us exactly what we need to observe recombination: a fly that's heterozygous for the purple and vestigial genes, in which we know clearly which alleles are together on a single chromosome.

(My emphasis.)

Source: Khan Academy - Genetic Linkage & Mapping

Crossing two homozygous fruit flies to produce a heterozygous offspring

I can't see the logic of this: surely if there were four chromosomes involved instead of two, wouldn't we get the same result via independent assortment?

In this scenario, the red-eyed, long-winged fly would have pr+ on chromosome 1, pr+ on chromosome 2, vg+ on chromosome 3 and vg+ on chromosome 4.

Conversely, the purple-eyed, vestigial-winged fly would have pr on chromosome 1, pr on chromosome 2, vg on chromosome 3 and vg on chromosome 4.

As the mother and father are both homozygotes (the mother for the dominant alleles and the father for the recessive alleles) the offspring couldn't fail to inherit pr+ and vg+ from the mother and pr and vg from the father, and the offspring would be the same as in the illustration.

I can't see how we can get any information as to whether genes are on the same chromosome or not from this crossing (unless we know they are on the same chromosome before we do the cross!).

I'm sure I've got my own logic wrong - can anyone enlighten me?

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  • $\begingroup$ I think they assume that the two genes are on the same chromosome. The question is, given a situation where the individual is known to be pr+,pr and vg+,vg which of the following two configurations is the case: pr+ vg on chr1 and pr vg+ on chr2 vs pr+ vg+ on chr1 and pr vg on chr2 $\endgroup$
    – stochastic13
    May 22, 2021 at 15:30
  • $\begingroup$ I'll read the full text again, and see if that assumption is implied anywhere, thanks. $\endgroup$
    – Naj
    May 22, 2021 at 18:41
  • $\begingroup$ With reassortment you would only get proportions of the F1 with that genotype. If the genes are on the same chromosome, then all the offspring will have the given phenotype...though it has been 20+ years since I last did basic genetics so I could easily be wrong. $\endgroup$
    – bob1
    May 22, 2021 at 21:24

2 Answers 2

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(moved from comments)
We don't know from the pictured cross that the genes are linked. However, IF they are linked, we know from that cross which alleles are together on a single chromosome.

Thus, the description should have something like

", if indeed they are linked."

added to the end of

"this cross gives us exactly what we need to observe recombination: a fly that's heterozygous for the purple and vestigial genes, in which we know clearly which alleles are together on a single chromosome."

It's the further crosses of the F1 offspring that tell us if the genes are linked and if so, how closely. The original cross is necessary but not sufficient to determine this.

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Your headline question:

How can we know which alleles are together on a chromosome?

is not quite the same as the question at the bottom of the body of your post:

how we can get any information as to whether genes are on the same chromosome or not from this crossing

These questions are different in two ways that matter: (1) the second question is asking about a single crossing, the one shown in the diagram, and (2) the second question asks about knowing if the genes are on the same chromosome or not, whereas the first asks if the genes (I presume, it says "alleles") are "together on a chromosome" (depending on how you take that phrase).

On difference (1): the single crossing in the diagram does not give information about distinguishing gene locations, but the Khan Academy page you got this from goes on to describe further crossings using the flies created in the first crossing, and those crossings can show information about gene locations.

On difference (2): I would take the genes being "together on a chromosome" to mean "linked to each other", that is close enough to each other on a single type of chromosome to tend to stay together during recombination events. Maybe you meant "on the same chromosome", but that is, importantly, a different thing. Recombination testing cannot tell you if genes are on the same or different chromosomes; it can only tell you if they are on the same chromosomes and are close enough together that recombination will not sort them randomly, but rather tend to sort them together. If they are far apart, the genes will stay together or be separated by recombination with equal probability, which is the result that also happens when genes are on different chromosomes.

So, the full procedure that is described on the Khan Academy page will show how much recombination you get in the fly grand-offspring. If you get few recombinant forms compared to the number of parental forms, then the genes are close together on the same chromosome. If you get equal numbers of recombinant and parental forms, it indicates that is not the case, and therefore the genes are either on separate chromosomes or so far away on one chromosome that recombination has full effect and randomly separates them.

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  • $\begingroup$ Hello. I'm aware of what the rest of the article goes on to say. However, my problem is with the statement accompanying (and printed on) the illustration: "this cross [a double heterozygote] gives us exactly what we need to observe recombination: a fly that's heterozygous for the purple and vestigial genes, in which we know clearly which alleles are together on a single chromosome." HOW could we "clearly" know from "this cross" "which alleles are together on a single chromosome"? $\endgroup$
    – Naj
    May 23, 2021 at 7:00
  • $\begingroup$ @Armand Thanks for the confirmation - the penny has finally dropped - not helped to do so by the ambiguous language used in the article plus the way the genes are shown as linked for both the parents and the offspring in the illustration. $\endgroup$
    – Naj
    May 23, 2021 at 13:40
  • $\begingroup$ @Armand If the parents are homozygous dominant and homozygous recessive for two alleles then the F1 offspring will all be double heterozygous. Crossing this offspring with a "Tester" which is homozygous recessive will give us a mix of parental and recombinant offspring (The F2 generation). By looking at the actual numbers of parental vs recombinant offspring in the F2 generation we can determine whether the genes are a) linked (recombinant % is low) b) on same chromosome but far apart * (yes, if the recombinant % is high) or c) *on different chromosomes altogether (if recombinant = 50%). $\endgroup$
    – Naj
    May 23, 2021 at 13:51
  • $\begingroup$ @Armand - would you agree with that last comment? $\endgroup$
    – Naj
    May 23, 2021 at 13:52
  • $\begingroup$ @Naj (b) and (c) are one category -- independent assortment means either on different chromosomes or far apart on the same chromosome. In practice, one uses a "scaffold" of linked genes/markers on every chromosome to map an unknown gene. If neighboring genes in the scaffold are all linked to their neighbors, any unknown gene will show linkage to at least one of the scaffold markers. $\endgroup$
    – Armand
    May 23, 2021 at 14:00

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