Pedigree Query

After reading the summary of the ENCODE findings that Bill from WA posted, which points out the importance of the non-protein encoding portions of the chromosomes, I now wonder about recombination in connection with that.

Specifically, where how does recombination work during the process with the "middles". Are there spots where disunion occurs and, after that, recombination? Are these spots in particular places so the DNA before and after them carries along what has heretofore been called "junk" DNA?

It's the genetic alleles on each chromosome that recombine, isn't it? Not whole chromosomes? If that's the case, there are millions, maybe billions of places where variation can occur if we take into account all the spots that the ENCODE project has pointed out that have an effect on the final genotype and phenotype.

The highly condensed version. No claim of expertise intended.

Meiotic recombination involves whole chromosomes and makes no distinction between coding and non-coding portions (formerly known as "junk"). Recombination normally happens at specific breakpoints that 'bookend' relatively large segments of the chromosome. This results in certain genes usually being inherited together - linkage disequilibrium (LD). But breakpoints themselves are heritable and subject to change. Ergo, LD decays over time. Measuring LD can be used to estimate how much time has passed since change occurred within a population at some point on a chromosome. For example, the 'speed allele'(C) in the equine myostatin complex was determined to be much 'younger' than the wild allele (T) by comparing the level of surrounding LD. It was high when the speed allele was present, low when the wild allele was present. Similar comparisons can be and have been made with non-coding recombinant DNA. ENCODE just formalized what has been suspected for much of the last decade, that what was once believed to be "junk" is pretty important.

I was trying to understand recombination and ran across this article:
http://www.plosone.org/article/info%3Ad ... ne.0025498

At least in dogs, the recombination process is not the same as for humans and mice, and the difference, they say, goes back millions of years--before the split between wolves and coyotes and before dogs were domesticated.

Do we know if similar work has been done in horses?