Alpaca with tuxedo pattern
Dear Ingrid,
I've read several articles on genetics and am still somewhat confused. What is a locus? Also, what is an allele? Can you explain these terms very briefly in layman's language?
Sincerely,
Not A. Scientist
I'll try, but not in two or three sentences, as the breeder above has requested. Clarifying complex concepts to anyone just beginning to study and research a subject is difficult.
Comprehension of basic genetic principles is crucial, however, to the understanding of more complicated issues such as inheritance of genes coding for fleece color and patterns. Most breeders of fiber producing animals are very much interested in that aspect of genetics.
Let's explore the functions of a locus. In A Dictionary of Genes (1974), author Robert C. King defines a gene as "the hereditary unit that occupies a fixed chromosomal locus." In plain language, a locus is a gene's specific location on a chromosome. The nucleus of an alpaca's cell contains 74 chromosomes or, to be more precise, 36 pairs and two sex chromosomes. In mammals, thousands of genes are grouped on each chromosome. The exact number of loci is not known for most species.
Fellow alpaca breeder Dr. Patricia Craven explained to readers in Basic Molecular Mechanisms in Genetics (2000): "A gene is a sequence of DNA which encodes a single protein." Once a gene is identified as contributing to a particular trait, scientists label its locus for the simple purpose of communication. Sometimes they use a word. For example, the Agouti locus controls the distribution of black and red pigment in horses, dogs, and other mammals. The Extension locus interacts with the Agouti locus to either allow for full expression of these pigments or complete suppression of black pigment.
You may compare this to Dave Belt (gene), whose function is to produce Alpacas Magazine (trait). The location where he performs this function is at his desk at 678 Dichoso Street (locus) in Pagosa Springs (chromosome) in the U.S.A. (cell). Sorry Dave! At times, a locus is only identified through a letter. After you have studied color inheritance in mammals for some time, you recognize that the letter D usually refers to the D locus. Its genetic action dilutes black pigment to blue and red pigment to fawn. If you read, for example, that a specific dog breed carries the dominant form of a gene at the G locus, you know that it describes the gene which slowly turns a puppy's black coat a solid gray.
Sometimes, scientists combine letters and numbers to name a locus. An imprinted gene found in mice is identified as Igf2 in the scientific community. (Don't ask me at this time what an imprinted gene is. That'll take another article.) Various geneticists have described a locus as a genetic address, an excellent visual. It helped me, the non-scientist, understand the basic workings of a cell.
As I've recently mentioned, each pair of genes residing at its locus has a specific job to do. Occasionally, a gene pair acts by its lonesome self to produce a trait. The genetic mechanisms at single loci determine the inheritance of polydactyly (extra digits) in dogs and brittle ear wax in humans (no kidding!). In sheep, the devastating Spiderleg Syndrome can be traced to genetic action at one locus.
Most of the time, however, genes at two or more loci must work together to produce the many traits making up an animal's phenotype (the observable properties of an organism). Conformational traits such as length of muzzle, angulation of hind quarters, angle of croup, length of back...none are determined by only one gene pair residing at a single locus. Such polygenic inheritance patterns also apply to, for example, cardiac defects or hip dysplasia.
Pleiotrophy, "the phenomenon of a single gene being responsible for a number of distinct and seemingly unrelated phenotypic effects" (King), results in inheritance patterns which are extremely vexing to scientists involved in genetic engineering. When a pleiotropic gene is deleted from an organism's DNA in order to remove and undesirable trait, it may result in the disappearance of a desirable feature as well. As breeders, we must be cognizant that selecting against one specific trait may therefore have unforseen repercussions.
To sum it up:
Genes coding for coat or fleece color present another example of polygenic inheritance, albeit one with a subtle difference. For example, it does not take a cluster of genes to produce a pinto pattern in an animal, although the final phenotype of an animal described by breeders as pinto is determined by many genes.
What do I mean by that somewhat confusing statement? Let's use an alpaca to clarify this concept. While one locus directs the alpaca's cells to produce pigment, a second locus orders them to keep the pigment black rather than modify it to chocolate brown. A third locus codes for lack of dilution, a fourth determines that the fleece will not be streaked with white - the black fiber thus remains solid black. The genetic action at the fifth locus finally prevents asymmetrical areas of the body from producing melanin. The black alpaca is now pinto!
Additional loci will modify the extent of the white patches. Although a single pair of genes at one locus codes for white areas, the animal's color phenotype is the result of an entire genetic package.
So yes, Robert Redford is the only horse whisperer in his movie, but there would have been no movie without the supporting cast. Dave Belt, working at his locus in Pagosa Springs, is not the only contributor to the publication of Alpacas Magazine. We also have Stephanie Pride at the Manhattan, Kansas locus. Steve and Annie Segal, laboring at their locus in Deer Trail, Colorado (another chromosome), add to the final product. Actually, Steve and Annie serve as the best example. A locus, if you recall, houses two separately inherited DNA sequences (genes).
Likewise, the locus producing the pinto pattern needs a supporting cast of other loci to create the "whole picture" (and yes, I admit my analogies are somewhat strange and entirely unscientific). There is always more than one locus coding for a black or red fleece with or without white spots, light silver gray, fawn, white, medium brown, or any of the other delightful colors and patterns we enjoy in our alpacas. Comprehension of color inheritance is greatly aided if a breeder grasps this basic concept.
The term pinto, by the way, refers to irregular white patches on a black or red animal. Piebald refers to black/white animals, skewbald to white spotting found in combination with any other colors. All are often confused with tuxedo (cape) pattern which may be under the genetic control of a totally separate locus. True pintos may be quite rare in alpacas. Many of the animals described as pintos actually express the tuxedo pattern. In the case of the "grays," it leads to speculation about possible close genetic linkage of two separate loci (roan and tuxedo).
Alpaca with tuxedo pattern
Since true pinto spotting is often the result of a recessive genetic mechanism in mammals, we may assume that both alleles (forms of the gene) at the Spotting locus must code for the pinto pattern in alpacas. Occasionally, species have two loci coding for such a pattern - one has the pinto allele under recessive and the other one has it under dominant genetic control. That's enormously difficult to sort out. We cannot rule out such an occurrence for camelids at the present time. Please be aware that nomenclature for some of the loci may vary from author to author. I like to refer to that phenomenon as genetic Alphabet Soup.
The function of an allele is not that difficult to understand. What is somewhat confusing to lay people is the fact that scientists use the terms gene and allele interchangeably. A pair of genes consists of two alleles, one inherited from the sire, the other one from the dam. Parental combinations may be homozygous (AA or aa) or heterozygous (Aa). It is crucial to understand that each allele carries the information needed for performing a specific function or for deleting that function. The possible parental combinations at the Spotting locus are therefore spotting-spotting, no spotting-no spotting, or spotting- no spotting. Think of the two alleles at one locus as a married couple. They work together, they affect each other, they create and live in a single home... but they are and will always remain separate entities.
Alleles are commonly referred to as alternate forms of a gene. Allelic combination can result in one allele being dominant over the other (the Segals remain mum on this subject). They can also be co-dominant, incompletely dominant, or show incomplete penetrance. Interested readers may wish to refer to Dr. Craven's article for more detailed information.
Dr. D. Phillip Sponenberg, well-known and highly respected for his research in mammalian color genetics, proposes the following alleles for alpacas at the Agouti locus. His proposal remains speculative at the present time. I have coded the alleles for easier referral.Agouti Locus Alleles
The Agouti locus offers a perfect example of a locus with multiple alleles. It's important to remember that the individual animal only carries two alleles at any locus. An alpaca may, for example, be AA, Aax, axa, atat, Aa, aa, or any other combination of two out of the four alleles. Geneticists will usually list multiple alleles in order of dominance.
Occasionally alleles are lost to a population. If breeders aggressively select against a dominant allele, the trait for which it codes may disappear forever. Selection for a dominant trait may result in the loss of all recessive alleles. Not all dog breeds, for example, still carry the five Agouti alleles identified for that species. Kerry Blue Terriers, to name one, only carry the dominant A allele in their entire population. A Kerry is always AA. In dogs, the dominant Agouti locus allele codes for black. It is good to remember that recessive alleles are "sneaky" and sometimes hide out for generations. They often survive all efforts to purge them from a breeding program. A trait under complete dominant genetic control therefore is certainly the easiest one to "lose" if you so desire.
Once a population is homozygously recessive at all loci coding for color (such as aa at the Agouti locus), breeders better be happy with what they have! Once vanished, dominant alleles cannot be recalled.
The important message here is the concept of one locus ->two genes (two alleles) ->two separate sequences of DNA - one inherited from the sire and one from the dam. All allelic combinations split up again in subsequent generations.
Mendel's Law of Segregation leads to the discomfiting discovery that we may not have inherited a single allele from the famous ancestor we took such pride in. I leave you to ponder this Mendelian tidbit as it pertains to your alpaca breeding program.
If you'd like to contact me for more information, you will find me at the usual locus. My alternate form will entertain you with hair-raisingly strong coffee (Husband's note: spoken by a woman who brews coffee so thin she could simply reuse my old grinds!). See you there!