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Genetic Improvement and Crossbreeding in Meat Goats Lessons in Animal Breeding for Goats Bred and Raised for Meat Will R. Getz Fort Valley State University Appendix B. Fundamental Genetics for Understanding Breeding Stock Change Genes, Chromosomes, Alleles, Nucleus, DNA Appendix Contents • • Introduction o Genotype o Expected outcomes in the formation of new offspring o Randomness – a key to understanding this stuff o It ain’t all dominance and recessive The Concept of Gene Frequency o Factors that change it and implications for meat goat breeders o Role of selection o Simply-inherited versus polygenic traits o Threshold traits Introduction 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 1 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. B B (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 2 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 the 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 oversimplification 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 3 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. Example No. 1 Female gametes (eggs) A1 B1 A1 B2 A2 B1 A2 B2 Male gametes A1 B1 A1A1 B1B1 A1A1 B1B2 A1A2 B1B1 A1A2 B1B2 A1 B2 A1A1 B1B2 A1A1 B2B2 A1A2 B1B2 A1A2 B2B2 A2 B1 A1A2 B1B1 A1A2 B1B2 A2A2 B1B1 A2A2 B1B2 A2 B2 A1A2 B1B2 A1A2 B2B2 A2A2 B1B2 A2A2 B2B2 B B B B B B B B B B B B B B B B 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. B B 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. B • B 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 4 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: • Dominance – defined as an interaction between genes at a single locus. There are four degrees of dominance. o Complete dominance – defined as when the expression of the heterozygote is identical to the expression of the homozygous dominant genotype. The mode of gene expression at the “height” locus in Mendel’s experiments was complete dominance. It was the only type of gene action he observed. o Partial dominance occurs when the expression of the heterozygote is intermediate to the expressions of the homozygous genotypes and more closely resembles the expression of the homozygous dominant genotype. An actual, if not meat goat, example is the condition in horses, particularly show and pleasure horses, known as HYPP (hyperkalemic periodic paralysis) where in there are episodes of muscle tremors ranging from shaking to complete collapse. It is also an example of a trait that could be easily eliminated because the condition is expressed in both the homozygous dominant and heterozygous individuals, i.e. it is visible. However because these individuals are often show winners, members of the show horse fraternity often lack the will to do so. o No dominance exists if the expression of the heterozygote is exactly midway between the expressions of the homozygous genotypes. Both alleles appear to have equal expression. A hypothetical example might exist when a homozygous individual carrying two resistant genes would survive 100% of the time when exposed to a communicable pathogen; the homozygous individual carrying two susceptible genes would survive only 40% of the time, and the heterozygous population would survive 70% of the time. 5 o • Overdominance is the most extreme form of dominance. The expression of the heterozygote is outside the range defined by the expressions of the homozygous genotypes and most closely resembles the expression of the homozygous dominant genotype. Overdominance is often characterized as having an extreme genotype. An instructive example involves survivability in wild rats in regard to the anticoagulant poison warfarin. In places where warfarin is used, rats without the resistance gene die from warfarin poisoning, rats homozygous for the resistance gene suffer from vitamin K deficiency because the poison increases the need for vitamin K, and the heterozygote rats remain healthy. The heterozygote rats are healthier than either of the two homozygous populations. Epistasis – another form of nonadditive gene action in which there is interaction among genes at different loci such that the expression of genes at one locus depends on the alleles present at one or more other loci. Color or color pattern in several species is governed by epistasis, especially in regard to dilution genes. Illustration of types of dominance on a line of comparative results at the “A” locus No dominance = ________AA________________Aa________________aa______ Partial dominance = _______ AA________Aa________________________aa______ Complete dominance = _______AA__________________________________aa______ Aa Overdominance = _Aa_ _AA_ _____________________________ aa_____ Additive or independent gene action generally occurs when traits are influenced by many pairs of genes (polygenic) and each gene has small but additive effects that accumulate. Years of breeding research has indicated that most of the performance traits of economic importance are governed by additive gene action. This is related to breeding value. The Concept of Gene Frequency Factors that change it and implications for meat goat breeders Mendelian principles again explain genetic mechanisms operating in individual goats. However the charge to meat goat breeders is not to change individuals, but populations of individuals (herds or breeds). In describing an individual for some simply-inherited trait, reference might be made to the specific genes which that individual possesses or the one-locus or two locus genotype might be described. To describe populations genetically the answer is to use gene and genotypic frequencies. A gene frequency or allelic frequency is the relative frequency of a particular allele in a population. It is a measure of how common that allele is relative to other alleles that occur at that locus. Relative frequencies range from zero to one. If an allele does not exist in a population then its gene frequency is zero. As an example in a herd of black Angus cattle, if there are no “red” alleles, the 6 gene frequency for red is zero. Likewise in that same herd the gene frequency for the “black” allele is one. In a black Angus herd in which an occasional red calf is born, the frequency of the red allele will be something greater than zero. The sum of the frequencies of the various alleles (two or multiple) at a single locus in a population must equal one. Not all alleles are of equal merit or desirability. Role of selection From a population genetics standpoint, the effect of selection is to increase the gene frequency of favorable alleles. When replacement does are chosen the owner is attempting to retain those animals with the best sets of genes and reject those with poorer sets of genes. As a result, offspring in the next generation should have, on average, better sets of genes than the current generation. Another way of saying better sets of genes is to say better breeding values. Gene frequencies, average breeding values, and mean (average) performance are really tied together. Although selection is not the only force that can change gene frequencies in a population, it is the most powerful one available to most meat goat breeders. Simply-inherited versus polygenic traits Simply-inherited traits are affected by only a few genes. Only a single locus or at most, a few loci are involved in their expression. There are two common secondary characteristics of simplyinherited traits: • • They tend to be “either / or” or categorical in nature. They are typically affected very little by environmental factors. Polygenic traits are affected by many genes, and no single gene is thought to have an overriding influence. Examples include growth rate, feed efficiency, and ribeye area of the carcass. • • • • Phenotypes for polygenic traits are usually described by numbers, e.g. 0.45 pounds per day in gain, 40 pound weaning weight, 1.89 square inch ribeye. Phenotypes for polygenic traits are typically quantitative or continuous in their expression rather than either / or. Most, although not all, polygenic traits are also quantitative traits. Polygenic traits are clearly affected by environmental factors to varying degrees. Be aware that there can be some crossover between the secondary characteristics of simplyinherited and polygenic traits. Size is an example wherein mature size is clearly polygenic but some dwarf body types are simply-inherited and controlled by a major gene as well. Threshold traits There is a special category of traits which are polygenic in control but in which the phenotypes are expressed in discrete categories, not different from simply-inherited traits. Two such traits that come to mind are dystocia and fertility, as reflected in conception rate (pregnant versus not pregnant). 7 These threshold traits present special challenges for the breeder. Fertility is believed to be influenced by many genes and is therefore polygenic. But the trait may be measured in only two phenotypes; pregnant or nonpregnant. Dystocia is measured in only three to five categories although there is evidence that it is polygenic. Threshold traits are no different from quantitative polygenic traits in regard to genotype. How do we deal with this? Well think of a threshold trait as having a continuous but unobservable underlying scale of expression; a liability scale. Think of an animal’s liability for a threshold trait as the sum of its genetic values for the trait. On the liability scale there is a point above which animals exhibit one phenotype, and below which they exhibit another. Simply-inherited and polygenic traits have a great deal in common as noted below: • • • Genes affecting both kinds of traits are subject to the same Mendelian mechanisms. Mendel’s laws of segregation and independent assortment apply equally. Dominance and epistasis affect gene expression for both kinds of traits. The basic tools of goat breeding, selection and mating, are the same for both types of traits. Selection focuses on increasing the frequencies of favorable alleles. However, different approaches to genetic improvement are taken between the two types of traits. This different approach is primarily a function of the number of genes involved. The more genes affecting a trait, the more difficult it is to observe the effects of individual genes, and therefore the less specific information we have about those genes. The amount of available information affects the way we characterize genotypes and therefore determines the breeding technology to be used. To add to this difficulty, consider the fact that relatively few studies have been made on the specific genetics of meat goats. There is somewhat more for dairy goats, but even so not abundant amounts. Test matings may be advisable in some cases to more clearly identify or describe the genotype. Polygenic traits are affected by so many genes that it is extremely difficult to observe the effects of specific loci and specific alleles at those loci. It is impossible then to explicitly identify an individual’s many – locus genotype for a polygenic trait. The logical alternative is to characterize the net effect of the individual genes influencing the trait. That is, to quantify the individual performance and breeding value for a trait. This requires statistical tools including concepts such as heritability and accuracy. The terminology will change from A1A2 or Bb used for simplyinherited traits, to the terminology of polygenic traits, e.g. EBV’s, EPD’s, ACC’s and the like. ________________________________________________________________________________________________________ Information contained in this document is part of a web-based training and certification program for meat goat producers (http://www2.luresext.edu/goats/training/qa.html) that was developed with funding received by Langston University from USDA/FSIS/OPHS project #FSIS-C-10-2004 entitled "Development of a Web-based Training and Certification Program for Meat Goat Producers." Collaborating institutions/organizations include Alcorn State University, American Boer Goat Association, American Kiko Goat Association, American Meat Goat Association, Florida A&M University, Fort Valley State University, Kentucky State University, Langston University, Prairie View A&M University, Southern University, Tennessee Goat Producers Association, Tennessee State University, Tuskegee University, United States Boer Goat Association, University of Arkansas Pine Bluff, and Virginia State University. 8