[Young]

Hi,

I’m interested in a particular gene. Wang et al. (2009) found that the gene is in some linkage group that contains 43 genes (http://genomebiology.com/2009/10/11/r126). When you say a gene is in a linkage group, does that mean that most likely all the genes in the linkage group are inherited together regardless of a map distance (centimorgans)? Or is it that genes in the same linkage group are more likely to be inherited together than a gene in linkage group A is inherited together with a gene in linkage group B, and the closer genes are within the same linakge group, the more likely they are inherited together?

Sorry if it’s not clear. I would appreciate it if you could let me know that.

Thanks!

[jonmoulton]

The map distance tells you how closely linked the genes are. The shorter the map distance, the higher the probability of co-inheritance and the more tightly linked the genes are ("tightly linked" and "close map distance" are pretty much synonymous).

"the closer genes are within the same linakge group, the more likely they are inherited together?" Yes.

[wbla3335]

To be a bit more accurate, it’s the alleles of the genes that are of concern here. The order of the genes themselves will remain the same barring genetic events such as deletions, insertions, translocations, or inversions. You can get more information by searching for "linkage disequilibrium" and "genetic hitchhiking".

[Young]

Hi jonmoulton and wbla3335,

Thanks for your post! So those 43 genes (alleles of them) in the same linkage group are inherited together. But how likely are they inherited together? I know this is hard to answer. But some genes are only 1.5cM away and others are as far as 140cM away but still in the same linkage group!

When you have allele frequency data of a particular gene and know which genes are in the same linkage group and want to know if they are under the same or similar environmental selections, would you say that the gene of interest is in LD with "gene C" and they may be under the same selection even if they are 140cM away (*allele frequency of gene C is not known)? If it’s too far away from each other to come to a valid evolutionary inference, what is a maximum map distance (cM) where you would confidently say the genes are under the same selection? If there is any paper on this topic, please let me know!

Thanks

[wbla3335]

A centimorgan is the distance between two loci where the frequency of a crossover between the two loci per generation is 0.01. So the frequency of crossover between two genes 1.5 cM apart will be 0.015, and the frequency of a crossover between genes 140 cM apart will be 1.4. The alleles of the all genes within 1.5 cM will thus tend to be inherited together much more frequently than the alleles of the all genes within 140 cM. The physical distance (base pairs) represented by a centimorgan varies with species, so that the size of selective sweeps will also vary.

[Young]

Thank you!

[Author]

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