The basic unit of inheritance is called a gene. Genes that are located at the same site in the chromosome and which affect the same trait but in different ways, are called alleles. Genes are segments (pieces) of deoxyribonucleic acid (DNA). The whole strand of DNA is referred to as a chromosome. DNA is a very complex molecule that forms the genetic code for all living things. Chromosomes occur in pairs; one chromosome of a pair inherited from the sire (father) and the other chromosome inherited from the dam (mother). These pairs are known as “homologs” because while each one may contain different genetic information, they each affect the same traits and are of the same shape and composition.

The number of chromosome pairs is species-specific. All domestic goats have 60 (30 pairs) chromosomes in each body cell. When cells divide by mitosis (cell division) the number of chromosomes remains constant (60), and the genes associated with each chromosome regulate all aspects of the body biology. The major exception to this applies to the sex cells or gametes (sperm and eggs) which have half the number of chromosomes (30), or one of each pair. This is necessary so that at fertilization, when the sperm and eggs join, the outcome is the proper number of chromosomes. The half number “n” is produced through meiosis (reduction division) whereby the cells divide twice and reduce the number of chromosomes to half.

The location of any pair of genes on the strand of DNA (chromosome) is known as its “locus”; it is the site of a particular gene. At each locus there will be a pair of genes — one inherited from the sire and the other inherited from the dam. The genes at a particular locus are designated by a letter or a letter/number combination. Different “forms” of the same gene, creating different effects for the same trait, are known as “alleles”. These alternative forms of the gene are designated by the same letter but with different numbers or uppercase/lower case. Examples include:

• A1 and A2 for the alleles at one locus (the “A” locus), and perhaps B1 and B2 for the genes (alleles) at another locus.
• A and a for the alleles at one locus, and perhaps B and b for the genes or alleles at another locus affecting another trait or characteristic.

(For those of you who are inclined to jump ahead or to come to premature conclusions, the upper and lower case as used here have nothing to do with type of gene action, e.g. dominance/recessive. Here they are just used to designate alternate form of the gene)

Although there will be only two genes at a particular locus for each individual, those two may be a subset of a larger series of alternative forms of a gene. There may be “multiple alleles” involved such that A1, A2, A3 and A4 may exist even though only two of the four will be paired in the same individual, e.g., A1 A3. As an example, the extension of color pigment in the Labrador Retriever breed of dogs, is influenced by three alleles and the various combinations of two of them will suggest the amount of pigment in the hair coat. What little research evidence is available on “simple” traits such color or color pattern in goats suggests that even that inheritance involves several alleles.

Genotype

The combination of genes at a particular locus is referred to as a genotype, or a one-locus genotype. A one-locus genotype is considered homozygous if both genes at that locus are functionally the same, e.g. A1A1 or BB. One-locus genotypes containing functionally different genes are considered heterozygous, e. g. A1A2 or Bb. The terms occur because of the root “homo” meaning alike and “hetero” meaning different and “zygous” making reference to the zygote or living organism at time of conception.

The Basics in Biology – Mendelian Inheritance. What Mendel knew about meat goat genetics/what he did not, or, it ain’t all dominance and recessive. Coming back to our friend Gregor Mendel; there are two fundamental biological laws that he identified that apply to inheritance. The first was the law of segregation which states that in the formation of a gamete (sperm or egg), the two genes at a locus in the parent cell are separated and only one of the two becomes a part of each new germ cell or gamete. That process is quite complicated and today we know the process as meiosis. The process involves a number of intricate steps during which not only genes but entire homologous chromosomes are separated. Mendel knew nothing about the details but had the process reasonable right based on observation — that is, that sperm and eggs contain only one gene of each pair in the cell.

Mendel’s second law was the law of independent assortment. This means that during meiosis genes assort independently — they can assort with any other genes so long as all possible gametes are formed in equal proportions. For this to happen a given gene from one locus must have an equal probability of being present in the same germ cell with either of the two genes from some other locus.

As an example, consider a genotype like AaBb (two pairs of genes; two loci “A” and “B”). Meat goats with an AaBb genotype can produce four possible gametes (sperm or eggs) – AB, Ab, aB, and aa. If all four gametes occur in equal proportions then these genes have assorted independently. Mendel was lucky. Genes on different chromosomes controlled the traits he chose to observe, in his pea plants. He did not experience and knew nothing about linkage. Chromosomes assort independently so the genes on those chromosomes assort independently too. Because all the genes Mendel was studying did in fact assort independently, he came to believe that all genes assort independently.

We know now that there are exceptions to the law of independent assortment — these exceptions occur now and then, and Mendel knew nothing about them:

• Linkage – Two or more loci (the genes at two or more loci) are linked if they occur on the same chromosome. They are inherited together rather than independently. This is one basis of current efforts in genetic marker-assisted selection. During meiosis genes on the same chromosome tend to end up in the same gamete. This is not complete, because of the mechanism of crossing over.
• Crossing over – Involves a reciprocal exchange of chromosome segments between homologs, and occurs during meiosis prior to the time the chromosomes are separated to form gametes. In the crossover process mutual breaks occur at identical sites on each chromosome, and chromosome fragments are exchanged between the two homologs. These exchanges prevent linkage from being complete.

If linkage occurs then the actual number of gametes of each type will not occur in equal proportions, as would be the case under independent assortment, but at some level whereby two of the four possibilities in our example will occur at a much higher frequency as compared to the other two. Crossing-over may occur at only one point along the chromosome, but it is more common for multiple crossover events to occur. The longer the chromosome the more likely that multiple crossover will occur.

Expected outcomes in formation of new offspring

When new offspring (zygotes) are formed by the joining of a male gamete and a female gamete, they have the normal number of genes and chromosomes for that species. Half the chromosomes will be contributed by the sire and half from the gamete contributed by the dam. Determination of which sperm will join with which egg, is a random process. Nearly all gametes have an equal chance of contributing to a zygote.

A useful device for visualizing how this process works is the Punnett Square. Although an over-simplification for most traits, this tool can help you come to an understanding of how individual gene pairs contribute to the next generation in going from gametes to zygotes. In this example an A1,A2 B1,B2 male is mated to an A1,A2 B1,B2 female. Each parent can produce four distinct gametes (sperm or eggs), one from each pair, so there are four rows and four columns in the Punnett Square which then results in 16 cells as listed in the table, when they are combined.

By looking closely at the cells it becomes obvious that not all cells are unique. Some of the genotypes are repeated. In this example there are nine distinct types of zygotes. Further, the order of listing of alleles within a locus has no importance, e.g., there is no difference between B1B2 and B2B1. With the information from the Square, it is possible to determine the likelihood or probability of any particular offspring genotype occurring by noting the frequency of the cells that contain that genotype for “simply-inherited” traits (traits affected by only a one or a few pairs of genes) you can also determine the expected proportions of offspring phenotypes.

This would not be the case for more complex polygenic traits. Polygenic traits are controlled by many genes, where no single gene has an overriding influence. In considering issues of likelihood and probability, there are two fundamental rules that must be assumed:

The probability of two independent events occurring together is the product of the probabilities of their individual occurrences. For example if the combination at the “A” locus in the above table, is independent of what is going on at the “B” locus, then if the probability of having an A1A1 genotype is 0.25, and if the probability of having a B2B2 genotype is 0.25 then the probability of having an A1A1B2B2 genotype out of all the possibilities is 0.25 x 0.25 = 0.0625; or we could say 6.25% or 1/16th.
The probability of one or the other of two mutually exclusive events occurring is equal to the sum of the probabilities of their individual occurrences. The probability of tossing a die twice and getting a one or a six each time is equal to the probability of the sum of the single probabilities. That is 1/6 + 1/6 = 2/6 = 1/3.

Randomness – a key to understanding this stuff

There is a significant amount of randomness in what goes on with meat goat, and other livestock, inheritance. Mathematical rules, guidelines, and expectations do exist, but outcomes are often measured in terms of probabilities rather than absolute outcomes. This is partially because of the tremendous genetic variability that exists, and the many genes that influence most traits of economic importance. The randomness of inheritance is critically important from an evolutionary standpoint and you will see that it is also vitally important to the success of artificial selection. Nonetheless it does create problems for breeding improved meat goats because it reduces our ability to control the outcomes of matings. There is no control over the Mendelian sampling of genes which determines the genetic makeup of the offspring. An individual superior offspring or an individual inferior offspring from a particular mating does not mean that worse or better results will occur in the future. Genetics of goat breeding involves chance, and to some degree some luck or good fortune. When you begin to think that you are entirely in control as a breeder, you are in serious danger of overestimating your abilities in biology.

It ain’t all dominance and recessive

Gene action is the term that is used to describe the expression of genes in the phenotype. There are two general categories and several additional specific categories which will be visited briefly. The two general categories are additive and nonadditive gene action. Nonadditive gene action is the expression of most simply-inherited traits — those that are easily observed. Two general categories exist for nonadditive gene action: