R

Genes and their alleles may interact with each other in a variety of ways. Sometimes one copy of a gene may predominate. In other cases both copies share influence.

that is, there are four possible genotypes: RR, Rr, rR and rr. The genotypes Rr and rR differ only depending on which of the pair of chromosomes carries r or R (see Fig. 1.09). When two identical alleles are present the organism is said to be homozygous for that gene (either RR or rr), but if two different alleles are present the organism is heterozygous (Rr or rR). Apart from a few exceptional cases there is no phenotypic difference between rR and Rr individuals, as it does not usually matter which of a pair of homologous chromosomes carries the r allele and which carries the R allele.

If both copies of the gene are wild-type, R-alleles (genotype, RR), then the flowers will be red. If both copies are mutant r-alleles (genotype, rr) then the flowers will be white. But what if the flower is heterozygous, with one copy "red" and the other copy "white" (genotype, Rr or rR)? The enzyme model presented above predicts that one copy of the gene produces enzyme and the other does not. Overall, there should be half as much of the enzyme, so red flowers will still be the result. Most of the time this turns out to be true, as many enzymes are present in levels that exceed minimum requirements. [In addition, many genes are regulated by complex feedback mechanisms. These may increase or decrease gene expression so that the same final level of enzyme is made whether there are two functional alleles or only one.]

From the outside, a flower that is Rr will therefore look red, just like the RR version. When two different alleles are present, one may dominate the situation and is then known as the dominant allele. The other one, whose properties are masked (or perhaps just function at a lower level), is the recessive allele. In this case, the R allele is dominant and the r allele recessive. Overall, three of the genotypes, RR (homozy-gous dominant), Rr (heterozygous) and rR (heterozygous), share the same phenotype and have red flowers, while only rr (homozygous recessive) plants have white flowers.

Partial Dominance, Co-Dominance, Penetrance and Modifier Genes

The assumption thus far is that one wild-type allele of the flower color gene will produce sufficient red pigment to give red flowers; in other words, the R-allele is dominant. Although one good copy of a gene is usually sufficient, this is not always the case. For example, the possession of only one functional copy of a gene for red pigment may result in half the normal amount of pigment being produced. The result may then be pale red or pink flowers. The phenotype resulting from Rr is then not the same as that seen with RR. This sort of situation, where a single good copy of a gene gives results that are recognizable but not the same as for two good copies, is known as partial dominance.

dominant allele Allele whose properties are expressed in the phenotype whether present as a single or double copy heterozygous Having two different alleles of the same gene homozygous Having two identical alleles of the same gene partial dominance When a functional allele only partly masks a defective allele recessive allele The allele whose properties are not observed because they are masked by the dominant allele

RR = Rr0.5 = Rr = r0.5 r0.5 = rr0.5 = rr = red red red red pink white flowers flowers flowers flowers flowers flowers

FIGURE 1.10 The Possible Phenotypes from Three Different Alleles

RR = Rr0.5 = Rr = r0.5 r0.5 = rr0.5 = rr = red red red red pink white flowers flowers flowers flowers flowers flowers

FIGURE 1.10 The Possible Phenotypes from Three Different Alleles

There are six possible pairs of three different alleles. Here the r0.5 allele is a partly functional allele that makes only 50% of the normal pigment level. R is wild-type and r is null. The R R, R r0.5, R r and r0.5 r0.5 combinations will all make 100% or more of the wild type level of red pigment and so are red. The r r0.5 combination will make 50% as much pigment and so has pink flowers. The r r combination makes no pigment and so has white flowers.

red red blue blue white purple flowers flowers flowers flowers flowers flowers

FIGURE 1.11 Phenotypes Resulting from Co-dominance

Here the B allele makes an altered, blue, pigment. R is wild-type and r is null. The R R and R r combinations will make red pigment. The B r combination will make only blue pigment and the R B combination makes both red and blue pigments so has purple flowers.

As indicated above, there may be more than two alleles. In addition to the wildtype and null alleles, there may be alleles with partial function. Assume that a single gene dosage of enzyme is sufficient to make enough red pigment to give red flowers. Suppose there is an allele that is 50% functional, or "r0.5." Any combination of alleles that gives a total of 100% (= one gene dosage) or greater will yield red flowers. If there are three alleles, R = wild-type, r = null and r0.5 = 50% active, then the following genotypes and resulting phenotypes are possible (Fig. 1.10). In such a scenario, there are three different phenotypes resulting from six possible allele combinations.

Another possibility is alleles with altered function. For example, there may be a mutant allele that gives rise to an altered protein that still makes pigment but which carries out a slightly altered biochemical reaction. Instead of making red pigment, the altered protein could produce a pigment whose altered chemical structure results in a different color, say blue. Let's name this allele "B." Both R and B are able to make pigment and so both are dominant over r (absence of pigment). The combination of R with B gives both red and blue pigment in the same flower, which will look purple, and so they are said to be co-dominant. There are six possible genotypes and four possible phenotypes (colors, in this case) of flowers, as shown in Fig. 1.11.

As the above example shows, mutant alleles need not be recessive. There are even cases where the wild-type is recessive to a dominant mutation. Note also that a characteristic that is due to a dominant allele in one organism may be due, in another organism, to an allele that is recessive. For example, the allele for black fur is dominant in guinea pigs, but recessive in sheep. Note that a dominant allele receives a capital letter, even if it is a mutant rather than a wild-type allele. Sometimes a "+" is used for the wild-type allele, irrespective of whether the wild-type allele is dominant or recessive. A "-" is frequently used to designate a defective or mutant allele.

Does any particular allele always behave the same in each individual that carries it? Usually it does, but not always. Certain alleles show major effects in some individuals and only minor or undetectable effects in others. The term penetrance refers to the co-dominance When two different alleles both contribute to the observed properties penetrance Variability in the phenotypic expression of an allele

A comlex and largely unresolved issue is that different versions of certain genes may behave differently in different individuals. Such individualized responses, especially to medication, have become a hot research topic.

Genes from Both Parents Are Mixed by Sexual Reproduction 11

Genes from Both Parents Are Mixed by Sexual Reproduction 11

FIGURE 1.12 Polydactyly

A dominant mutation may cause the appearance of extra fingers and/or toes.

FIGURE 1.12 Polydactyly

A dominant mutation may cause the appearance of extra fingers and/or toes.

relative extent to which an allele affects the phenotypic in a particular individual. Pen-etrance effects are often due to variation in other genes in the population under study.

In humans, there is a dominant mutation (allele = P) that causes polydactyly, a condition in which extra fingers and toes appear on the hands and feet (Fig. 1.12).This may well be the oldest human genetic defect to be noticed as the Bible mentions Philistine warriors with six fingers on each hand and six toes on each foot (II Samuel, Chapter 21, verse 20). About 1 in 500 newborn American babies shows this trait, although nowadays the extra fingers or toes are usually removed surgically,leaving little trace. Detailed investigation has shown that heterozygotes (Pp or P+) carrying this dominant allele do not always show the trait. Furthermore, the extra digits may be fully formed or only partially developed. The P allele is thus said to have variable penetrance.

Such variation in the expression of one gene is often due to its interaction with other genes. For example, the presence of white spots on the coat of mice is due to a recessive mutation, and in this case, the homozygote with two such recessive alleles is expected to show white spots. However, the size of the spots varies enormously, depending on the state of several other genes. These are consequently termed modifier genes. Variation in the modifier genes among different individuals will result in variation in expression of the major gene for a particular character. Environmental effects may also affect penetrance. In the fruit fly, alterations in temperature may change the penetrance of many alleles from 100% down to as low as 0%.

To geneticists, sex is merely a mechanism for reshuffling genes to promote evolution. From the gene's perspective, an organism is just a machine for making more copies of the gene.

Genes from Both Parents Are Mixed by Sexual Reproduction

How are alleles distributed at mating? If both copies of both parents' genes were passed on to all their descendants, the offspring would have four copies of each gene, two from their mother and two from their father. The next generation would end up with eight copies and so on. Clearly, a mechanism is needed to ensure that the number of copies of each gene remains stable from generation to generation!

How does nature ensure that the correct copy number of genes is transferred? When diploid organisms such as animals or plants reproduce sexually, the parents both make sex cells, or gametes. These are specialized cells that pass on genetic information gametes Cells specialized for sexual reproduction that are haploid (have one set of genes) modifier gene Gene that modifies the expression of another gene

FIGURE 1.13 Principle

Meiosis—the

Diploid organisms distribute their chromosomes among their gametes by the process of meiosis. The principle is illustrated, but the detailed mechanism of meiosis is not shown. Chromosome reduction means that the gametes formed contain only half of the genetic material of the diploid parental cell (i.e. each gamete has one complete haploid set of genes). Each chromosome of a pair has a 50% chance of appearing in any one gamete, a phenomenon known as random segregation. While only sperm are shown here, the same process occurs during the production of ova.

to the next generation of organisms, as opposed to the somatic cells, which make up the body. Female gametes are known as eggs or ova (singular = ovum) and male gametes as sperm. When a male gamete combines with a female gamete at fertilization, they form a zygote, the first cell of a new individual (Fig 1.13). Although the somatic cells are diploid, the egg and sperm cells only have a single copy of each gene and are haploid. During the formation of the gametes, the diploid set of chromosomes must be halved to give only a single set of chromosomes. Reduction of chromosome number is achieved by a process known as meiosis. Figure 1.13 bypasses the technical details of meiosis and just illustrates its genetic consequences. In addition to reducing the number of chromosomes to one of each kind, meiosis randomly distributes the members of each pair. Thus, different gametes from the same parent contain different assortments of chromosomes.

Because egg and sperm cells only have a single copy of each chromosome, each parent passes on a single allele of each gene to any particular descendent. Which of the original pair of alleles gets passed to any particular descendant is purely a matter of chance. For example, when crossing an RR parent with an rr parent, each offspring gets a single R-allele from the first parent and a single r-allele from the second parent. The offspring will therefore all be Rr (Fig.1.14).Thus,by crossing a plant that has red flowers with a plant that has white flowers, the result is offspring that all have red flowers. Note that the offspring, while phenotypically similar, are not genetically identical to either parent; they are heterozygous. The parents are regarded as generation zero and the offspring are the first, or F1, generation. Successive generations of descendants are labeled F1, F2, F3, etc.; this stands for first filial generation, second filial generation, etc.

Extending the ideas presented above, Figure 1.16 shows the result of a cross between two Rr plants. Each parent randomly contributes one copy of the gene, which may be an R or an r allele, to its gametes. Sexual reproduction ensures that the offspring get one copy from each parent. The relative numbers of each type of progeny as depicted in Fig. 1.16 are often referred to as Mendelian ratios. The Mendelian ratio in the F2 generation is 3 red : 1 white. Note that white flowers have reappeared after skipping a generation. This is because the parents were both heterozygous for the r allele which is recessive and so was masked by the R allele.

A similar situation exists with human eye color. In this case the allele for blue eyes (b) is recessive to brown (B). This explains how two heterozygous parents (Bb) who both have brown eyes can produce a child who has blue eyes (bb, homozygous reces-sive).The same scenario also explains why inherited diseases do not afflict all members of a family and often skip a generation.

filial generations Successive generations of descendants from a genetic cross which are numbered F1, F2, F3, etc., to keep track of them meiosis Formation of haploid gametes from diploid parent cells

Mendelian ratios Whole number ratios of inherited characters found as the result of a genetic cross somatic cell Cell making up the body, as opposed to the germline zygote Cell formed by union of sperm and egg which develops into a new individual

Sex Determination and Sex-Linked Characteristics 13

Red flowers (homozygous)

Parent RR

Red flowers (homozygous)

White flowers (homozygous)

FIGURE 1.14 Cross between Homozygous Dominant and Recessive for Red Flower Color

When individuals with the genotypes RR and rr are crossed, all the progeny of the cross, known as the F1 generation, are red.

Parent RR

Gametes R

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