By Loren Bolinger, November 18, 2007, copyright © Loren Bolinger, 2007

What causes expression of either the maternal or paternal alleles? What mechanism makes the choice between the sire’s and the dam’s allele at a particular location within the offspring’s genome? Conventional thought has been that most genes [with the exception of certain genes in early embryonic development, imprinted genes, and genes involved in x-activation] are equally expressed [or randomly activated] from the sire's and the dam's parental genomes [roughly, about half each from sire and dam]. "..This paper discusses the finding that the allelic contribution from either parent can be randomly [or, more likely selectively - lb] turned off or silenced in more than 5 percent of genes." The sex-based mechanism that preferentially causes the inactivation is currently unknown.

The November 15, 2007: paper, "Single Parent Genes," published in The Scientist, announced the discovery that a significant percentage of alleles in the nuclear genome are preferentially silenced. The occurrence of preferential silencing or inactivation of one parent’s allele by the other parent’s allele is both unexpected and stable. There is a higher likelihood that certain traits, both positive and negative as well as inherited disease not only may selectively and reliably reproduced from one of the parents, but may also have a greater chance to duplicate some characteristics of the parent.

What could this mean for horse breeders interested in improving chances of the expression of performance traits in their foals? Monoallelic expression at this frequency, previously unrecognized, may be a pathway that could reinforce or duplicate Mendelian nuclear inheritance and/or female mitochondrial inheritance, depending on which allele achieved activation or dominance at each location. Preferential inactivation, therefore, may aid in the process of selectively expressing traits of a particular sire or dam. Furthermore, inbreeding to prepotent female ancestors may have yet another path to activation of performance genes. Monoallelic expression may also explain what breeders term "prepotency," the ability for some breeding stock to strongly "stamp" their offspring with certain characteristics.

The effect of monoallelic expression may also help explain why getting performance from matings based on certain types of selection seems to be so random to a breeder who is frustrated at the unreliability of selective mating schemes that work in one instance and fail in others. If certain desirable genes inexplicability activate or inactivate and the mechanism causing such behavior is unknown, the process may seem random when, in fact, it is merely not yet known.

Over 300 genes out of 4000 in a clonal cell line used for the study made an arbitrary, allele-specific choice. In the future, "phenotypically characterizing a trait is going to be more complicated" said Marisa Bartolomei of the University of Pennsylvania School of Medicine of the research results. The mechanism of such monoallelic expression remains to be discovered. "Is there a genetic component to this epigenetic phenomenon [epigenetic asymmetry between parental genomes]?"

So, if a significant number of alleles have predetermined maternal or paternal copies expressed – that is, the maternal or paternal copies of some genes are preferentially silenced - I wonder if there is any relationship between genes that are maternally activated [the paternal copy is silenced] and the mitochondrial genome? Could this potential reinforcement be another pathway to matrilineal transmission and expression of performance traits? If certain matrilines not only have mitochondrial genomes that are favorable to athletic performance, but also maternal copies of alleles in the nuclear genome, could monoallelic expression be a mechanism contributing to matrilineal performance traits? Furthermore, could it also an independent Mendelian mechanism for a sire to contribute a form of matrilineal influence to the dam's mitochondrial genome. If an instance of inbreeding to a great matriarch lies in the paternal wing, Mendelian genetics would say it has no influence with a similar instance in the maternal wing, since the sire, not having cytoplasmic genes, cannot normally pass maternal inheritance from his dam's mitochondrial genome. However, if certain maternally activated nuclear alleles are passed from his dam (or from any other maternal ancestor in his pedigree) to his offspring where they might synergize with other maternally activated nuclear genes as well as genes encoded in the mitochondrial genome.

Certain maternal bloodlines may have been conferred with a slight evolutionary advantage for racing performance inherited from the founder mare of that matriline. Each matriline is likely to have unique variations in their ATP energy cycle, particular to its mitochondrial genome - a small number of polymorphisms cause differing efficiencies, utilization and conversions that contribute to the organism's overall athletic ability. Matrilineal expression of genes in some of the maternal families that confer superior/more efficient utilization of Adenosine Triphosphate compared to other matrilines, for example.

Excepting genetic disease, damage and/or mutations, the matrilineal evolutionary advantage is carried by nearly all matrilineal descendants of the founder mare [members of the maternally-related family] and is probably latent in most, if not all, members. In most individuals, it needs some external trigger to cause the expression of performance traits. Those exceptionally meritorious descendents exhibiting elite racing performance obviously have inherited the advantage in expressed form or have had it triggered by such nature- or human-directed selection as inbreeding, outcrossing, fortuitous environmental factors, etc.

1. Performance traits are polygenic in nature. Many individual genes are involved with each trait that is a component of racing performance. The portion of the nuclear genome specific to the individual [and not part of the "scaffolding" necessary and common to all mammals, to all equi caballus, to all Thoroughbreds] is likely of a scale somewhat similar to the size of the mitochondrial genome [in other words, they are comparable in size]. It is likely that a majority of the genes that make up an individual come from the nuclear genome. But importantly, the nuclear genome must interact with the mitochondrial genome, there are genetic processes unique to the mitochondria required for the nuclear genome to operate, and finally, the mitochondrial genome has non-nuclear genes that are only inherited from the mother.

2. The mitochondrial genome is a factor in performance. These non-nuclear genes are essential to the function of the ATP energy cycle of the cell, and therefore, of the creature. Their capabilities, efficiencies, etc. are directly involved with the creature's use of energy and therefore ability to perform and these characteristics are the characteristics of the maternal founder mare. Racing requires the expenditure of energy. Very slight differences in the ATP energy cycle have a direct bearing on ability of a horse to successfully race. The degree of racing performance is intimately associated with genotypic inheritance, its phenotypic expression as influenced by environmental factors. The bigger the biological engine or the more power produced and/or better utilization of the biological fuel by the more efficient engine usually means higher class performance.

3. Duplicating instances of a prepotent female ancestor in a pedigree increases the chance of the occurrence of duplicated alleles from that mare in the offspring's genome. Duplicate alleles of a significant [prepotent] female ancestor may increase the chances of the expression of her desirable traits in the offspring. Not all duplicate alleles have anything to do with performance and their existence in a pedigree is no guarantee that they will be expressed but it does increase the probabilities slightly.

4. Duplicating the mitochondrial genome of a prepotent maternal ancestor is one pathway. There is an increased chance of desirable or positive interaction between the nuclear and the mitochondrial genomes due to increased opportunity caused by monoallelic activation. There is an increased possibility that monoallelic expression represents another pathway in which maternally derived genes may activate and express.

 Note: The diploid human genome consists of 46 chromosomes, 22 pairs of autosomes, and 1 pair of sex chromosomes (the X and Y chromosomes), while the diploid horse genome consists of 64 chromosomes, 30 pairs of autosomes, and 1 pair of sex chromosomes. The diploid hamster genome consists of 44 diploid chromosomes, 21 pairs of autosomes, 1 pair of sex chromosomes.