Dogs, like humans, have three types of genetic code which behave uniquely and can thus have different measures of diversity: autosomes, allosomes, and the mitochondrial chromosome.
Autosomes are all the chromosomes that are present in equal numbers in both males and females in a species. They contain the most information among the three carriers of genetic code. Autosomes recombine with no deference to gender so an autosome that is inherited from a mother could contain a mix of material from both the maternal grandmother and grandfather. Same with genes inherited from the father, they would be equal contributions from the paternal grandparents.
As you can see from the diagram at left, Autosomes are the only genetic vehicle that is composed of DNA from all of your ancestors and in proportion to their relatedness to you. Half of your allosomes come from your mother and half from your father. Your grandparents each contributed 25% of the alleles in your allosomes.
Humans have 22 pairs of autosomes and dogs have 38 pairs of autosomes. The fact that autosomes come in pairs is what drives the mechanics of dominant and recessive alleles and heterozygous or homozygous status. Autosomes are the genes that are most likely to benefit from hybrid vigor for this same reason. For any given gene there two copies, one on each chromosome in the pair.
Genetic traits that are controlled by genes on autosomes are called “autosomal” as opposed to those on the sex chromosomes which are called “sex linked.”
When males produce sperm and females produce eggs, the autosomes they received from their parents recombine using a process called “crossing over” such that each sperm and egg will have one set of chromosomes that is a unique combination of the pair present in each parent. Sperm get half a pair and eggs get half a pair so when they combine the offspring have one complete pair.
This process of recombining and limited transmission of genes (children are only 50% related to their parents) for autosomes make tracing deep history using them very difficult. Without comprehensive genetic testing of your relatives, it’s hard to look at any given allele and know which ancestor it game from.
Allosomes are also known as “sex chromosomes” and are unique from autosomes in their structure and behavior. In humans and in dogs, there is a single pair of allosomes known as the X and Y chromosomes. Females are XX so they always pass along an X, and Males are XY so they can pass along either an X or a Y. It is thus the male’s sperm that determines the gender of each offspring in humans and in dogs.
The X chromosome is present in both males and females and is comprised of a very interesting pattern of ancestor contribution. Looking at the chart above you will see that men get their only X chromosome from their mother, but women receive one from each parent. Because the X chromosome can still recombine in gamete production, each X chromosome is comprised of DNA that was contributed from both male and female ancestors. Females can pass along an X chromosome that contains information from both their parents, but males can only pass along an X that is a virtual copy of the one they received from their mothers.
You can see from the funny tree that the inheritance path that goes through a female’s father continues to go back, but that any male’s father is always pruned from the tree. Like autosomes, the process of recombination and unique ancestor contribution makes X chromosomes unsuitable for deep ancestor tracing and information on X chromosomes is not highly conserved over time.
Like the Y chromosome, the X chromosome contains information vital to sexual dimorphism, but it also contains genes that are unrelated to gender. Because the Y chromosome does not impart full coverage of the genes that exist on the X chromosome, genes on the X that would otherwise be recessive and thus not expressed in women are expressed in men because there is not a second copy of the allele in males. The insufficient double coverage of genes on the X and Y chromosomes lead to a special class of diseases that behave uniquely in their transmission and expression. One example is hemophilia which is x-linked recessive. Females need to receive two copies of the allele to be affected, but males need only receive one copy from their mother.
Unlike dual X allosomes in women, the Y chromosomes show an aversion to recombination with their associated X chromosomes in men, so much so that only 5% of the chromosome recombines (basically the very tips) when men produce sperm. This means that almost the entire Y chromosome is conserved from generation to generation. This allows for analysis of the deep male line history using the genes on the Y chromosome and it means that men pass along the X chromosome they get from their mothers virtually intact.
Recombination is one method that allows for error correction (bad mutations can be bred out over time) and since the Y chromosome is mostly stagnant save for new random mutations, it’s susceptible to collect these new mutations with no means to remove them. This is known as Muller’s ratchet.
Lack of recombination also makes the Y chromosome a means to ascertain deep male-line ancestry. The “sire line” of an individual is best represented by the Y chromosome, because although offspring also receive genes from the sire line as autosomes, the sires are not unique in this manner. They are unique in their contribution of the Y chromosome however as each dog in the sire line has the same allosome save only de novo mutations which are rare overall but about 5 times more common on the Y chromosome than the rest of the genome.
Y chromosomes are puny little things without a whole lot of interesting genes, typically fewer than 100. The SRY gene activates male sexual differentiation in the embryo and there are a handful of genes which code for sperm production and other testis function.
Since females get along just fine without Y chromosomes, there are no universally vital genes that appear only on the Y, and there are few documented Y-linked diseases. The ones we currently know about are related to the testicles and fertility. Although predisposition to diseases like testicular cancer can lead to poor health outcomes in the male that carries the Y chromosome, issues leading to decreased fertility are perhaps the most problematic for dog breeders.
Mitochondria are very different than the autosomes and allosomes. They are only inherited from the mother as they are an organelle that is present in the ovum (egg) that the sperm fertilizes. They are self replicating and so the code which creates them and which they contain is not carried in the animal’s chromosomes.
Like the Y allosome, the mitochondrial chromosome doesn’t recombine material from both parents and is thus highly conserved over many generations. It is thus a means to ascertain deep matrilineal ancestry (although mitochondria play no part in sexual differentiation like the Y chromosome does). Because mitochondria are predominantly uniparental in inheritance without recombination they are also susceptible to accumulating deleterious mutations.
Functionally, a mitochondrion produces ATP which is the primary source of chemical energy within cells. Mitochondria also control cell growth and death, differentiation (simple cells become complex cells), signaling and coordination between cells, and they also contribute to the process of aging.
Because of their varied and essential functions and ubiquity in almost all cells, mitochondrial disorders come in many forms: diabetes mellitus, multiple sclerosis, neuropathy, vision degeneration, and dementia. Such diseases would be passed along to all children if present in the mother but none of the children if present in the father. Many of these diseases, however, also have non-mitochondrial causes making specific diagnosis a challenge. Mitochondria have also been implicated in autism spectrum disorders and a contributor to bipolar disorder.
Mitochondrial DNA is actually very similar to the bacterial genome and it’s theorized that an ancient eukaryotic cell might have encapsulated the first mitochondria (most similar to prokaryotes) and gained a symbiotic benefit from the energy production and varied proteins that the mitochondria can produce.
Unlike the rest of the genome which is best envisioned as a double helix wrapped up into X shaped chromosomes, the mitochondrial DNA is best thought of as a ring of DNA. Human and canine mitochondria have fewer than 40 genes, about half of which encode proteins and half of which deal with creating ribosomes and transfer RNA molecules.
Due to the straight forward and predictable nature of autosomes, plus the fact that the majority of genetic material is carried in autosomes, most basic treatments of inheritance and genetic modeling refer exclusively to the mechanics present in this part of the genome. Calculations like Coefficient of Inbreeding and Relatedness between an organism and one of its ancestors almost always assume autosomal mathematics and ignore the small percent of the genome that is present in the the mitochondria and sex-chromosomes given their more unique inheritance patterns.
Given their role in both desireable and undesireable traits, dog breeders should still acquaint themselves with the sex-allosomes and the mitochondrial dna to appreciate how they differ in function and inheritance and enact breeding strategies that appreciate these differences.
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