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I am studying recombination in Meiosis and the idea of crossing over doesn't make sense. My understanding is that 46 chromosomes in our germ-cell (23 from mom + 23 from dad) line up next to each other and recombine (swap areas of DNA). My confusion is that, since, for example, Chromosome 1 from mom is same as Chromosome 1 from dad, how is swapping areas of DNA going to exchange any information. Brown eye gene from dad would just be swapped with brown eye gene from mom. How will have any affect on the offspring? OR is it that if mom has brown eyes, the brown eye color gene in mom has something attached to it? OR is my understanding of genes incorrect and not every nucleus has all possible genes? (except the difference of X and Y chromosome.)?

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    $\begingroup$ The chromosomes are not equal. Read about alleles first before you start reading about recombination. $\endgroup$ – Adrian May 28 '17 at 19:05
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    $\begingroup$ And please change your title since it bears no relation to your actual question. $\endgroup$ – Alan Boyd May 28 '17 at 19:22
  • $\begingroup$ @adjan thank you for your suggestion! So, one person has a form of a gene and not ALL forms of all genes. This clarifies a lot. $\endgroup$ – Singh May 28 '17 at 19:33
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There is quite a few misunderstanding in your question. So, I'll shortly give you some (simplified) definitions and then point you to another post.

Definitions and Basic Concepts

A locus (plur. loci) is a position along a chromosome. A some loci, there are genes. To make things easy a gene is any sequence which is transcribed into RNA and translated into proteins.

Now at any locus, you might see different individuals having different variants. For example an individual may have the sequence ATTCT while another individual may have the sequence ATTGT. Those different variants are called alleles. It is key to understand that there is genetic variation in populations. This genetic variation is a big part of the reason why people around you look different and why you ressemble more your siblings (if you have any) than a random person in the population.

How does recombination have any impact?

To understand the effect of recombination you necessarily have to picture a several loci model. As you now understand the above definitions you will find your answer at this post: Why do we need two markers to measure a recombination rate?

Further readings

The following posts will also be of interest to you:

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  • $\begingroup$ Thank you. My main misunderstanding was that same chromosomes in all individuals is exactly the same. I now understand that there can be different forms of a gene (allele). Not all people have all forms of a gene. $\endgroup$ – Singh May 28 '17 at 19:58
  • $\begingroup$ Cool. There is indeed genetic variation in the population. This is a big reason for why we look different. Note that have understanding the existence of genetic variation and its maintenance in populations is key to have a basic understanding of evolutionary processes. If you think I answered your question you can check the checkmark to the left of my answer. $\endgroup$ – Remi.b May 28 '17 at 20:00
  • $\begingroup$ My question now is, "Do all genes get transcribed then?" I remember reading that only a percentage of DNA is transcribed. When I read that, I thought maybe if you have blue eyes, only blue eye gene would be transcribed and genes for all other eye color would be "trash DNA". But since you only have one gene for eye color, and same with all characteristics, what part of DNA does not transcribe? I hope my question is not too confusing. $\endgroup$ – Singh May 28 '17 at 20:02
  • $\begingroup$ We typically define a gene as a sequence that gets transcribed. So, by definition, yes all genes get transcribed. But most of DNA is not made of genes. There are regulatory sequences and introns (~24%), there are pseudogenes, there's loads of transposons and retrostransposons (~60%) such as the ALU sequences. "Junk DNA" is some kind of an undefined term that encompass all the non-coding DNA (~ 98.5%) but the term "Junk" has been very misleading to the large public. Of course all of this is not so specific to humans. Plants typically often have very large genome with loads of transposons. $\endgroup$ – Remi.b May 28 '17 at 20:15
  • $\begingroup$ Anyway, your follow-up question is very broad. You should just follow an intro genetic class or read some wikipedia articles and try to come back with a more narrow and accurate question. Good luck exploring this fascinating field of knowledge! $\endgroup$ – Remi.b May 28 '17 at 20:16

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