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There are many sources that say that genes that are "linked" by being on the same chromosome assort with each other -- that when an allele is passed on that the gamete containing said allele will also contain every allele from the chromosome rather than simple allowing everything to assort independently.

There are also many sources that say during meiosis there is recombination, hence, why aren't all genes completely random?

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    $\begingroup$ The previous title of this post had a negative and some imprecise terms. In the interest of clarity I modified it to read "Why does meiotic recombination disrupt the independent assortment of genes on the same chromosome." It originally said "Why doesn't gene recombination maintain the law of independent assortment for genes on the same chromosome?" Hopefully I have preserved the sense of the OP's query. $\endgroup$
    – mdperry
    Apr 20, 2016 at 1:28

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Recombination does not make any two genes completely independent because there will not systematically be a recombination event between two given loci (=position on the chromosome).

Distance between loci

Consider two scenarios that describe the position of two loci on a chromosome.

  1. Tightly linked loci

Consider two very closely linked loci. Let's say that a recombination event occurs somewhere in the chromosome. It is very likely for this recombination event to occur somewhere else than between these two loci. These two loci are essentially linked and do not segregate independently

  1. Distant loci

Consider now two loci on the same chromosome. Each locus (=singular of loci) is found at one end of the chromosome. If a recombination event occurs, it is pretty sure that it will occurs between the two loci. As a consequence, the two loci will segregate (quasi) independently.

Conclusion

As a conclusion, recombination allows to break down the linkage between two loci but it does so at a given rate that depends on the physical distance between the two loci and on the per nucleotide recombination rate.

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  • $\begingroup$ Doesn't recombination always occur between two alleles on homologous chromosomes of the same gene? Also, doesn't a recombination of one gene not effect another? $\endgroup$
    – john01dav
    Apr 20, 2016 at 0:57
  • $\begingroup$ I don't understand what you mean. You say "recombination of one gene". What does it mean? A recombination (or cross-over) is the process by which homologous chromosomes exchange genetic material. This process allows for higher independence of assortment of linked loci. The more closely linked are two loci, the less likely it is that a recombination event will separate them. $\endgroup$
    – Remi.b
    Apr 20, 2016 at 1:34
  • $\begingroup$ Recombination has nothing to do with genes. The genes happen to be genetic markers arrayed along the physical chromosome. Meiotic recombination, in general, occurs after a double-stranded break has been formed in one of the chromosomes. One way to repair this break is to form a crossover. When crossovers are repaired by the cell this can result in recombination (alternatively it can result in gene conversion). If you have several heterozygotic genetic markers on the chromosome then you can score the progeny and possibly map where the crossover occurred. $\endgroup$
    – mdperry
    Apr 20, 2016 at 1:38
  • $\begingroup$ By "two loci" Remi.b means two loci on the same chromosome. Simple example: (a) ------------X--X----------------- compared to (b) -X----------------------------X- , if Xs denote genes, it is much more likely for the genes in (a) to remain on the same chromosome than for the genes in (b) assuming a random choice of recombination point. Although recombination is not actually random, this example holds in vivo. $\endgroup$
    – Luigi
    Apr 20, 2016 at 1:51
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    $\begingroup$ Yes, recombination has nothing to do with genes. Not however that recombination rate per nucleotide tend to be lower in regions of high gene density. Two closely linked loci (might be genes at these loci) are less likely to segregate independently as it is less likely that a recombination event occurs in between them (you seem to say the opposite in your comment). $\endgroup$
    – Remi.b
    Apr 20, 2016 at 2:35
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Imagine that mom's chromosome is blue, and dad's is red. If crossing over was happening hundreds of times per chromosome, sure, you could make chromosomes to pass into gametes which were very a very highly shuffled combination of paternal and maternal alleles. It would be blue, red, blue red, blue, red, all up and down the chromosome.

But it doesn't. It generally only happens once on a chromosome. So you can get a chromosome where the "top" 30% is red, and the rest blue, or the "top" 65% is blue and the rest red. When genes are unlinked, the odds of getting both alleles from the same parent is 50%, and the odds of getting one from each parent is 50%. If two genes are close together on the same chromosome, the odds of the break happening between them is small, so the odds of one being blue and one being red is much lower than 50%.

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