Text assignment: Chapter 13, Pages 381-393.
Major concepts
Wild-type and mutant alleles: For many of the genetic loci in many of the species used in genetic analysis, one of the alternatives can be identified as the "wild-type" allele based on its frequency of occurrence or its arbitrary designation as "normal". In most, but not all cases, the wild-type allele will be dominant over alternatives that have been generated by mutations resulting in partial or complete loss of function. However, caution must be exercised in attempting to designate alleles as "wild-type" just because they are dominant. This is particularly true in species where substantial natural variation occurs and the mutational history responsible for the variability is not clearly understood. Examples that come to mind easily include human racial characteristics and alternative forms of agricultural species (both plant and animal) with long histories of domestication.
Hyphenation of "wild-type: When it is used as an adjective, as in "wild-type alllele" or "wild-type function, the term "wild-type" is always hyphenated. However, some authors use "wild type" as a noun without hyphenation, whereas others claim that "wild-type phenotype" is implied in such cases and insist on always using the hyphen. We will accept either usage. The authors of our current textbook appear to avoid the issue by never using "wild type" (with or without a hyphen) as a noun.
Genetic notation in Drosophila: The genetic designations used for Drosophila melanogaster are organized around the way that specific mutations or alternative alleles differ from the widely accepted wild-type phenotype. Recessive mutations are named with one or a few lower case letters, and the corresponding wild-type alleles are designated as the + form. Thus, a fly that is heterozygous for the ebony mutation, e, would be designated as e +/e, or simply as +/e. Note that a slash (/) is normally inserted between the two alleles when describing a genotype in Drosophila (and many other species). Dominant alleles that cause a phenotype different from the wild-type when they are heterozygous with wild-type are designated with an upper case letter, often followed by one or more lower case letters. One such example is the lobed-eye locus, L, located on chromosome 2 (for a chromsome map of Drosophila showing the locations of many different genetic loci, see Figure 15.3 on page 448 of the textbook). A heterozygous fly exhibiting the dominant lobed-eye phenotype would be given the genotypic designation L+/L or simply +/L.
Genetic notation in humans: Although a standardized system of genetic notation for humans has been in place somce 1987, ours is the first beginning genetics textbook that I have seen that employs the standard nomenclature. The new system of nomemclature is based on the enzyme or gene product encoded by the gene if it is known, and the phenotype when the gene product has not been identified. For example, the locus whose loss-of-function mutation is responsible for phenylketonuria is called PAH (for phenylalanine hydroxylase). An asterisk separates the name of the locus from a descriptor for the specific mutation that is being designated. Thus, PAH*R408W says that an arginine at position 408 of phenylalanine hydroxylase has been changed by mutation to a tryptophan (see inside front cover of text book for one-letter amino acid code). A number of other examples are given on page 385. I have not previously used this system of nomemclature in this course, so there may be some places where older forms slip past me as I am revising the notes for this year. If you catch any, please let me know and I will correct them. Also, please note that the textbook uses italics for all human genetic notations, whereas OMIM does not. In the interest of getting these notes into useable form quickly, I am not using italics. (I have been told by Dr. Ken Krauter that both forms are acceptable).
OMIM: The easiest place to check for the correct current human genetic nomenclature is the extensive set of web pages provided by the National Center for Biotechnology Information, a branch of the National Library of Medicine, entitled Online Mendelian Inheritance in Man ( OMIM). I have added a direct link to OMIM on our course home page, as well as a link to a new web page describing how to use OMIM.
The nature of alleles:, For our current purposes, a gene can be viewed in molecular terms as the DNA coding unit that specifies the amino acid sequence for one polypeptide chain (or in some cases, the ribonucleotide sequence of an RNA molecule that performs a biological function without being translated into protein). An allele is an alternative form of a gene. Most of the analysis that follows will be restricted to alternatives that are responsible for detectable phenotypic differences.
Causes of phenotypic difference: The differences that distinguish alleles from each other can be either in the coding sequence, ranging from one base changes that cause one amino acid substitutions in the coded proteins to major deletions, insertions or rearrangements of the coding sequence, or they can be in closely linked regulatory sequences that influence how much of the gene product is synthesized. In many cases, there are multiple allleles at the same genetic locus. In such cases, the phenotypic effects that are caused by the various alleles often range from complete loss of function of the coded protein to subtle changes in function of the gene product whose effects are barely detectable.
Nature of dominance: A fully dominant allele typically codes for the production of enough functional gene product so that no obvious phenotypic difference is seen when it is paired with a non-functional recessive allele. However, with the exception of a few specialized genetic loci that code for critically important proteins whose levels of expression are carefully regulated, the amount of a gene product that is produced is usually rather directly related to the number of functional alleles that are present. In extreme cases, such as the red, pink, and white flowers discussed below under incomplete dominance, the reduced level of gene product in the heterozygote is reflected in its phenotype. However, even when there is no immediately obvious phenotypic difference, the level of the gene product is likely to be substantially reduced at the biochemical level.
Mutations affecting dominance and recessiveness: In most cases, dominance and recessiveness are determined by the amount of the gene product that is generated and by its biological activity. The most common recessive is due to complete loss of function or loss of production of the gene product. However, as discussed later in this lecture, so-called "leaky" mutants may cause partial expression of the dominant phenotype due to reduced specific activity of the gene product (e.g. a less efficient enzyme protein) or reduced levels of expression of the gene product. The most straightforward mechanism for a mutation that is dominant relative to wild type is "gain of function", due to regulatory changes that result in a higher level of expression of the gene product (or the synthesis of a gene product that has a greater specific activity). In cases where more than one subunit must combine to form an active enzyme, it is possible to obtain dominant loss-of-function mutations. In this case, protein subunits are synthesized that are not functional, but are still able to combine with normal subunits in a heterozygous individual, blocking their function (figure 13.3). Another possibility, which is not discussed in our textbook, is haploinsufficiency. In this case, two copies of the wild type gene are needed to support a normal phenotype. Individuals who are heterozygous for a loss-of-function mutation will show an altered phenotype, which by definition makes the mutation "dominant".
Deviations from Mendelian ratios: In the previous lectures on Mendelian inheritance, we have focused primarily on situations where the expected 3:1 and 9:3:3:1 F2 phenotypic ratios are obtained. In the remainder of this lecture, and in the next lecture, we will examine various mechanisms that cause the expected Mendelian ratios to be altered for a variety of reasons. This lecture concentrates on effects that involve only a single genetic locus. In the next lecture we will examine interactions among genes at two or more loci, as well as variable levels of phenotypic expression. Future lectures will also examine altered phenotypic ratios that are observed in the inheritance of genes carried on the sex chromosomes.
Incomplete dominance: In the lectures on Mendelian patterns of inheritance, we focused primarily on situations where one allele at a genetic locus was completely dominant over the alternative allele in terms of overt phenotypic expression. We now turn to situations where dominance is only partial. In such cases, the phenotype is determined by the gene dosage, with the heterozygote exhibiting an intermediate phenotype. There is apparent blending in the F1 generation, and a 1:2:1 ratio of the first parental phenotype, the intermediate phenotype, and the second parental phenotype in the F2 generation. In such cases, the F2 phenotypic distribution directly reflects the F2 genotypic ratios. An example is pink flowers on the F1 hybrid of true-breeding red-flowered and white-flowered snapdragons (Figure 13.1).
Tay-Sachs disease: There have been reports that Tay-Sachs disease (OMIM 272800) is an example of incomplete dominance at the biochemical level that is not readily evident at the phenotyopic level. Individuals who are homozygous for this recessive human biochemical disorder are severely affected with a lipid storage disease that is fatal within the first three years of life. The underlying biochemical defect is virtual absence of an enzyme, hexosaminidase-A, which is needed to prevent the abnormal lipid accumulation. Individuals who are heterozygous for this defect have about one-half of the normal level of hemoxaminadase, but this amount is enough to keep them symptom-free and healthy (for more information, see pages 81-82 of Klug and Cummings, Concepts of Genetics, 5th Edition, Norlin Reserve). In fact, some individuals with enzyme levels as low as 12 -20% of the usual level appear to be clinically normal. Cases such as this severely blur the distinction between full and partial dominance, particularly at the more sensitive biochemical level.
Codominance: In certain cases, different alleles at the same locus result in production of detectably different gene products, with no clear pattern of dominance of one over the other. In such cases, the heterozygote will exhibit both phenotypic properties in a codominant manner. One classically cited example is the blood type antigens M and N, which are different forms of a glycoprotein found on the surface of red blood cells. Homozygous individuals have type M or type N antigens on their red blood cells. Heterozygotes exhibit both antigens on their red blood cells and are designated type MN. However, the molecular genetics and biochemistry underlying this particular set of phenotypes remains murky. Because of this, the A and B alleles of the ABO blood group, discussed below, are a more informative example. For codominant genes in general, a cross between homozgotes results in coexpression in F1 and a 1:2:1 ratio in F2.
Multiple alleles: Mendel dealt with either/or choices, with just 2 alleles at each genetic locus. Whenever a genetic locus is extensively studied, multiple alleles, often with intermediate phenotypic effects, can be found. These usually reflect amino acid substitutions in enzymes (or other proteins) that reduce their effectiveness, but do not totally destroy their functionality. Wild populations often contain natural distributions of 3 or more alleles, with no obvious functional advantage of one over the others.
For small numbers of alleles this can easily be verified by writing out all possibilities. Thus, if n = 4 alleles, the possible combinations are
The same result can also be obtained by using the formula:
ABO blood types: Human ABO blood types are determined by three alleles at a single locus: ABO*A, ABO*B, and ABO*O. The A and B alleles each code for variants of an enzyme that cause mutually exclusive changes to a glycolipid called H substance on the surface of red blood cells. Specifically, the enzyme coded by the A allele adds an acetylgalactosamine residue in an exposed terminal position, whereas the B allele codes for an altered enzymatic activity that adds a galactose residue in the same position, as shown in Figure 13.4 in the textbook. This results in the generation of two different types of antigenic properties, which are recognized by appropriate antibodies as type A and type B, respectively.
Type O: The ABO*O allele does not code for a functional enzyme. As descried in boxed example 13.1, this is due to a frameshift mutation in a coding sequence that is otherwise identical to that of the A allele. Thus, type A and type B are both dominant over type O, and exhibit codominance to each other. There are six possible genotypes: AA, AB, BB, AO, BO, OO. Genotypes AA and AO are type A; genotypes BB and BO are type B; genotype AB is type AB; and genotype OO is type O. Human blood contains antibodies against all A/B antigens except those on its own red cells. These antibodies cause a severe reaction to transfused blood containing the target antigens. Type type O is a universal donor (but other classes of blood antigens must match) and type AB is a universal recipient.
Inheritance of ABO blood types: Although three different alleles are involved in the inheritance of ABO blood types, any one individual can carry only two of them. This results in a substantial number of subtly different patterns of inheritance of these blood types. Perhaps the most unusual is a cross between heterozygous A/O and heterozygous B/O, which can give rise to four different phenotypes, A, B, AB, and O, in a 1:1:1:1 ratio.
Bombay phenotype: The textbook describes an additional genetic locus that has been found to affect the ABO phenotype. A woman was identified in Bombay who was phenotypically type O, despite the fact that pedigree analysis showed clearly that she carried the ABO*B allele, which she received from her type AB father and passed on to two of her children. A detailed analysis revealed that she had a recessive mutation at a different locus, now designated FUT1*O for alpha-(1,2)-fucosyltransferase (deficient). The enzyme coded at that locus is required for the addition of a fucose residue to H substance, which must be present before the acetylgalactosamine or galactose residues can be added to generate type A or type B antigens (see figures 13.6 and 13.5). The recessive allele responsible for the Bombay phenotype is very rare, but it does make it possible for some individuals who are phenotypically type O to be carriers of the alleles for type A or type B. Although the H antigen is not normally detected as a blood type, there are tests that can determine whether or not it is present.
Leaky recessive alleles: The white eyed locus in Drosophila is one of the more extreme examples of multiple alleles. Wild-type Drosophila have a characteristic deep red pigmentation in their eyes. The original white-eyed mutation had a complete absence of eye pigmentation. Since the original discovery of white, many other eye color mutations have been discovered and mapped to the same locus. The text claims that there are now over 100 subtly different alleles at this locus, ranging from total loss of eye pigmentation to a variety of altered shades that involve reduced levels of pigmentation. Our textbook uses the apricot (wa) locus as an example of a leaky mutation (figure 13.7).
Compound heterozygotes and dominance series: In cases where there are multiple alleles that support differing levels of gene function at a single genetic locus, it is often possible to generate a dominance hierarchy. The textbook describes a series of coat color alleles in rabbits, in which more intense color is in each case dominant over less intense color. There are some errors in figure 13.9. In particular, the agouti phenotype is seen in a heterozygote of agouti and chinchilla. Also, the albino should be "cc".
Peppered moth: The British peppered moth, Biston betularia, provides another example of a dominance series. It has 3 pigmentation alleles: M is dominant over the other two; M' is recessive to M, but dominant over m; m is recessive to the other two. This results in three phenotypes: dark (MM, MM', and Mm); intermediate (M'M', M'm); and light (mm). Recent industrialization has resulted in a sharp increase in the dark form, which is less visible on the bark of soot-covered trees (described on pages 591-592 and illustrated in Figure 19.7 on page 591).
Homozygous lethal alleles: Yet another disturbance of expected phenotypic ratios occurs when one of the homozygous phenotypes is lethal. One example (which is not described in our textbook) is the Manx cat, which has no tail. The lack of a tail behaves dominantly, but there are no true-breeding lines of Manx cats. One third of the progeny of a cross between two tail-less cats have tails. It turns out that the dominant gene is a developmental defect that is lethal when homozygous and causes failure of the tail to develop when present in a single copy. Thus,
M/M is an early embryonic lethal, such that no M/M kittens are ever born. Thus the dominance of the absence of a tail that is observed in this case is apparently due to haploinsufficiency. One copy of the wild type allele does not support sufficiently rapid spinal development for it to extend into the tail. An interesting alternative interpretation of the same data is that wild type is partially dominant over the severe recessive developmental defect, such that in the heterozygote, only the tail fails to develop.
Yellow mouse: At the classic dominant yellow locus in mice, a yellow coat color (Figure 13.10 in the textbook) is dominant. However, the Y allele is lethal when homozygous.
Y/Y is an embryonic lethal. Thus, no true breeding dominant yellow mice are ever obtained. Although widely cited in textbooks as a simple dominant lethal, this is actually a more complex situation, as described below.
Deletion and gene fusion: The dominant yellow lethal allele in mice results from a deletion that includes part of the agouti (A) locus, whose normal function is to cause the formation of yellow bands in hair shafts (figure 13.8). The deletion removes the promoter for the agouti gene and nearly all of an upstream gene in the same orientation, designated Merc, that is essential for normal embryonic development. The Merc promoter is left linked to the agouti gene, causing major overexpression, both in amount and location (figure 13.11). This results in a dominant yellow phenotype, and also has pleiotropic effects, including obesity, increased size, elevated blood sugar, and increased susceptibility to cancer. The early lethal effect (before implantation) in homozygous mutant embryos is due to the complete absence of the Merc protein, and has nothing directly to do with the yellow color. There are, in fact, other dominant yellows in which agouti is overexpressed without loss of Merc (also called Raly in some publications).
Pleiotropy: The term pleiotropy refers to the ability of a gene to affect more than one phenotypic characteristic. Our textbook cites two examples. The purple flower allele in peas also causesi purple rings around leaf axils and purple sead coats (figure 13.12). The second is sickle-cell anemia, in which a single amino acid change in beta globin (pages 161-163) causes many different types of pathology in many different organ systems (Figure 13.13). Yet another example from last year's textbook is human phenylketonuria, in which loss of an enzyme involved in the breakdown of excess phenylalanine causes pleiotropic effects that include elevated phenylalanine levels in the blood plasma, urinary excretion of intermediate products of phenylalanine breakdown, severely reduced IQ, changes in hair color, and changes in head size. Under close scrutiny, many genes have some degree of pleiotropic effect. This is easily understandable, since enzymes and other gene products are often expressed in many different cell types within a multicellular organism.