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Suppose you have two variants from the same species, which have slightly different chromosomes I's to each other. Genes may be in slightly different positions on the chromosome, and the lengths of the chromosomes might be somewhat different. Suppose these are crossed to produce offspring. If a crossing over event occurs in the offspring during meiosis, what happens to the positions of the genes?

A concrete example of what I'm asking is the following. Suppose that in the above scenario, the first chromatid is 1Mb long and the second is 1.05Mb long. "Gene A" occurs between 6kb-8kb on the first chromatid and 10kb-12kb on the second. If the crossing over occurs and replaces the first 9kb on the first chromatid, what happens to gene A there? Does it cease to exist? Or does the crossing-over process somehow know to grab DNA from above 12kb from the second chromatid?

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    $\begingroup$ Are we talking purely about the natural process here, or also about the artificial? In the latter, making cuts and realignments is possible. $\endgroup$
    – Mast
    Mar 9 at 20:06
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It depends on the regions of sequence homology between the two chromosomes. Crossing over occurs through pairing of homologous regions. If there's a substantial stretch of chromosome without a matching homologous region on its pair, that non-homologous region should loop out and not be involved in crossing over. Crossovers will occur only in paired homologous regions. For example, if you have a chromosome I and I' as follows: I ABCDEFG I' ACDEHFGM They should pair as:

  • A-(A)
  • B
  • C-(C)
  • D-(D)
  • E-(E)
  • (H)
  • F-(F)
  • G-(G)
  • (M)

Crossovers should not happen in the B, H, or M regions lacking homology with the other chromsome. Crossovers in a homologous region will just result in a new chromosome containing the left end of one crossover partner and the right end of the other. Using I and I' above, a crossover in region E would produce either: ABCDEHFGM or ACDEFG Now, if you have repeated regions of homology in one or both chromosomes, or regions inverted on one chromosome vs. the other, pairing possibilities expand rapidly and all kinds of weird things can happen (and do in real life).

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If a crossing over event occurs in the offspring during meiosis, what happens to the positions of the genes?

Most of the time, things do not line up right, so the gametes do not contain the full information needed to make a complete organism, which is why when species are able to cross breed, usually the hybrids are sterile.

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    $\begingroup$ I've made a small edit to my post, but I actually meant to write that the variants are from the same species. In that case, is there a mechanism to make things line up? $\endgroup$
    – Jabbath
    Mar 9 at 7:35

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