Linkage
by C. Williams

Earlier in the tour, we touched on the concept of "crossing over"... where bits and pieces of the chromosome pairs exchange places. That is, the allele that is on one side of a chromosome, may exchange places with the allele on the other side. This is mostly random, which results in many gametes (sex cells) that are all unique and different from each other. This is what causes all individuals, except identical twins, to be unique individuals genetically.

However, the process of crossing over, is not quite that random in reality. It turns out that the chromosomes may "cross over" each other and "swap parts" in sections and segments... causing groups of genetic code (series of alleles) to be swapped together, rather than just random individual units.

As a result, alleles at loci that are very close to each other on the same chromosome physically, tend to be "transferred" together as a group more often. This phenomenon is referred to as Gene Linkage. Also, scientists have established that some chromosomes tend to "break" at certain points more often than at other points.

Linked traits can mean three things:

1. If the loci are very close to each other on the same chromosome, they are very likely to be transferred together more often than not. If it turns out that a known locus, such as that for Roan coloring is very near another locus that sometimes possesses a lethal allele... the result would be that the two alleles, R and a lethal ?L would nearly always be transferred together in tandem. There is a small chance that at some point, a "break" in the chromosome strand would happen between those two loci... and separate them. (Scientific evidence has yet to establish whether the Lethal Roan condition is caused by the R locus or by another locus that is very close to it on the same chromosome)

2. A recognizable phenotype (such as Roan color) that you can see, can be used as a visible marker, so you know what you are dealing with regarding a lethal allele that is almost always associated with it.

3. The expected outcomes among the offspring regarding probabilities and numbers born can be seriously skewed.

Sponenberg, in his book Equine Color Genetics, offers one example of a fairly tight linkage group, between the Extension and Roan loci. He cites the case of a Bay Roan (Ee, Rr) being crossed to Chestnut (ee, rr) mares. If we chart up the expected probabilities, the results look like this:

Bay Roan X Chestnut		Sire Rr Ee
		R E	R e	r E	r e
Dam rr ee	r e	Rr Ee Bay Roan	Rr ee Chestnut Roan	rr Ee Bay	rr ee Chestnut
	r e	Rr Ee Bay Roan	Rr ee Chestnut Roan	rr Ee Bay	rr ee Chestnut
	r e	Rr Ee Bay Roan	Rr ee Chestnut Roan	rr Ee Bay	rr ee Chestnut
	r e	Rr Ee Bay Roan	Rr ee Chestnut Roan	rr Ee Bay	rr ee Chestnut

The results are:

• 25% (4) Bay Roan
• 25% (4) Chestnut Roan
• 25% (4) Bay
• 25% (4) Chestnut

However, the results that were observed in the field were:

• 14 Bay Roan
• 1 Chestnut Roan
• 1 Bay
• 15 Chestnut

Figures such as this indicate that some type of "linkage" is going on with at least one of the parents. In this case, the E and R alleles appeared to be transferred together from this particular sire far more often than not.

It is quite likely that the singular Chestnut Roan offspring from this actual sample may be just as likely to pass on its genes in groups like above... but because it is chestnut... you won't be able to see this particular linkage in the offspring, and charts of it's own offspring are more likely to be closer to representing the "expected" probable results.

What linkage means, is that when two loci are close to each other-- they are going to be transferred together as a "team" more often than not. Every now and then, the "team" is "broken up" so to speak, and different combinations then become possible.

In this particular sample, the loci on one chromosome strand on the Bay Roan parent were E and R. On the other chromosome... the loci featured e and r. Most of the time, both alleles were transferred together as the sample shows.

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Here I'll offer you a good "brain twister". Assume 13 of the Bay Roan offspring inherited a ER combination. Assume that 1 of the Bay Roan offspring, instead, inherited a eR combination on one chromosome. (The other chromosome, having a Er combination. )

If you were to cross this "odd" individual to a group of chestnut mares-- the result would be that the offspring were primarily Bay and Chestnut Roan. (the reverse of the example above.)

In the above example, the loci were close enough for the alleles to be transferred as a "team" most of the time, but not so close that a "break" in the chromosome "chain" was very unlikely to happen between the loci (which it did a couple of times). If the loci were closer together on the chromosome, a "break" between the two loci would tend to be much more rare.

From this, one can infer that the closer the loci are to each other on a chromosome, the more likely they will be transferred together as a "team". The farther away, the less likely. Loci that reside on different chromosomes, are not considered to be "linked" to each other.

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It is currently believed that the Frame Overo patterning locus is the same one responsible for the Lethal White/Atresia Coli condition in foals. At the present time, geneticists are trying to establish whether or not any foals homozygous for the Frame Overo gene, do not have the atresia coli condition. If such individuals exist, it would establish the fact that there are two loci involved which are likely very close together on the same chromosome, rather than a single locus that controls both traits.

Since current technology now allows geneticists to identify the particular amino-acid sequence that occurs in horses who carry the lethal white gene and those foals born with it, in time they should be able to establish whether or not homozygous Frame Overo individuals without the atresia coli condition can and do exist. If so, this would make it possible to breed future generations that would be free of this lethal allele.

Of course, such scientific evidence will also make it possible in the future to more clearly identify many alleles in this manner, and eventually allow owners to know what genotypes their horses are carrying, both in terms of color as well as health issues in order to make better educated breeding choices.

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Views expressed herein are those of the writers and compilers of the various information. Reference sources are cited where applicable. Copyrights are the property of the respective authors.