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I know that for a given mammal, half the chromosomes come from father and half from mother. This is typically denoted as x-y. I've recently read about "toolkit" genes that control how a cell develops into an embryo into an organism. I'm interested which set of chromosomes(x,y or both) contains these toolkit genes for development of an organism from a fertilized cell?

In other words, does an X chromosome know how to build a female and Y chromosome how to build a male, or is it some "overriding" of developmental instructions that Takes place when Y is present?

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Can you clarify what "toolkit" genes you are referring to? Do you have a link/citation for the source you read about them from? I'm guessing you are not referring to the toolkit genes listed here, so a bit more clarity might be helpful. –  Steve Lianoglou May 9 '13 at 0:30
    
That sounds like the toolkit genes I'm referring to –  Alex Stone May 9 '13 at 10:18
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up vote 2 down vote accepted

First, while half the chromosomes come from each of the two parents, these two sets of chromosomes are not termed X and Y (they would usually be called maternal and paternal). The terms X and Y refer to potential members of just one pair of the 23 pairs (in humans) of chromosomes, and X chromosomes can come from either the mother or the father. The presence or absence of a Y chromosome determines sex in mammals.

The Y chromosome contains one gene, SRY, which determines sex, and almost no nother genes. SRY simply switches on the "make a male" program in the cells.

Essentially all other genes, including any toolbox genes, come from both parents, one copy from each. (An exception, in males, are those genes on the X chromosome, which in males are present in only one copy and which came from the mother. Another exception is mitochondrial genes.)

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In addition to @mgkrebbs response, I'd add that many genes are controlled by epigenetic mechanisms which may mask one of the parental copies by methylation. This can be a specific effect where, the active gene is specifically from either the father or the mother. Mosaicism, where one copy of gene is randomly inactivated in any given cell, is also possible. The classic example of this is X chromosome mosaicism, where the entire X chromosome in each cell of a female is silenced. (At least in the case of humans and animals like humans)

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There's also this really cool example of a gene for a voltage-gated potassium channel, in which the paternal copy is methylated by a paternally-expressed ncRNA from the same locus (that site is methylated maternally). If this is disrupted, it results in developmental defects. <Shameless plug for an unanswered question of mine that has the relevant links.> –  dd3 May 11 '13 at 4:38
    
There are surveys of such genes from mouse studies, my favorite is MEST. I took a shot at that one @dd3 :) –  shigeta May 11 '13 at 14:52
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