Introduction to Genetics Reading: Freeman, Chapter 13 (read twice, do all the questions at the back of the chapter), also Chapter 12 (to review meiosis, mostly) Information Genetics is, quite simply, the study of the process by which information is transmitted from one generation of living things to the next. Every living thing is organized via coded information, called its genetic material. Reproduction involves duplication and transmission of an organisms genetic material. WHAT IS A GENE? A gene is an information entity. It is a sequence of DNA that codes for a single genetic instruction. Usually, this instruction is the sequence of a protein, but a gene may also serve to activate or deactivate other genes, in a cell, or in neighboring cells. Every aspect of our species is constructed based on information encoded in genes. The genes themselves do very little, they are information storage molecules. It is the cytological machinery of our cells, passed from one generation to the next, that translate these instructions into a living organism. The effects of every gene depend both upon other genes, and upon the environment. What is an allele? • An allele is ONE variant of a gene. Many genes have two, several, or many different variants of the same basic genetic information. • Some alleles are minor differences that to not significantly affect the organism, others cause profound changes. Example: • Nucleotide substitutions in the third codon position often produces no change at all, because they code for the same transfer RNA and thus the same protein is produced. • In humans…CCU CCA does not cause a change, both triplets code for proline. • Other substitutions may produce profound effects, sickle cell anemia is caused by a single nucleotide substitution: GAG GUG changes normal hemoglobin to hemoglobin that “sickles” under low oxygen concentrations. Prokaryotes, which include the archaea and bacteria, are the simplest, oldest, and most common organisms on the planet. A typical prokaryote has a much smaller genome than a typical eukaryote. Nearly always, it is in the form of a simple loop of DNA (with associated proteins). This loop is attached to the cell membrane. Even though the structure simple, there is a lot of DNA in a single bacterium. .… Stretched out, the DNA in an E. coli would be 500 times longer than the cell itself. Prokaryotes do not have sexual reproduction, though they have several forms of gene exchange. These include swapping plasmids • The various genes, about 1200 in a typical bacterium, are arranged along the length of the chromosome, like beads on a string. – There is no particular functional grouping to their order, it is mostly evolutionary chance that determines their location • In prokaryotes, the DNA loop replicates before fission, with both loops still attached to the cell membrane • During fission, as the cell membrane splits in two, one loop of DNA ends up in each new “daughter cell” Thanks to/stolen from fig.cox.miami.edu Most eukaryotes have several orders of magnitude more DNA than a typical prokaryote. Like prokaryotes, eukaryote genes are arranged along the length of a chromosome like beads on a string. There is no particular functional reason for their location, either within a chromosome, or with respect to what chromosome they are on, it is mostly an evolutionary accident. Eukaryote DNA (except plastid DNA, which is very similar to bacterial DNA because of its evolutionary origin) is usually linear, not circular. These strands are long, and extended (thus, invisible to microscopes) during the normal life of the cell. These linear strands of DNA are called chromosomes and packed into a nucleus (or nuclei, in some cases). In multicellular eukarotes, every cell has the same DNA, though in any given cell, only a fraction of the genes are active, others are permanently “turned off” The increased amount of DNA necessitates a means of condensing these long strands into compact structures that can be sorted into separate daughter cells during cell division. Histones are important and very evolutionarily conservative proteins. Loops of DNA are wrapped around one histone (like thread around a spool), and locked in by a second, forming a structure called a nucleosome. These structures further supercoil into a condensed configuration, to form the familiar shapes that scientists have viewed under light microscopes. Thank you/stolen from www.geneticengineering.org Mitosis • Mitosis, the duplication of the genetic material within a eukaryote cell, is worth mentioning here because of what it IS and what it IS NOT. – A cell gives rise to two, smaller but genetically identical copies of itself. – It IS a duplication of the genetic complement of a eukaryote cell. Since it is usually followed by cell division, it can lead to growth, in a multicellular organism, or asexual reproduction, in a single-celled organism. – It IS NOT a means of producing gametes. In sexual organisms, mitosis is peripheral to sexual reproduction, it serves to give rise to cell types which ultimately “kill themselves off” by splitting and splitting again, into four, very different, cells. Do not bother to memorize the phases of mitosis/meiosis, I do not care Sexual Reproduction • Sexual reproduction is a particular type of reproduction, a sharing of genetic material, to form an individual with equal contributions from two separate parents. • This involves: – The formation of haploid sex cells, called gametes, from a diploid cell, a process called Meiosis. – Syngamy (or, fertilization), a combination of genetic information from two separate cells to form a diploid cell, called a zygote. • Gametes usually, but not always, come from separate parents: female produces an egg and male produces sperm. (In some organisms, the haploid phase of the life cycle is multicellular, and haploid individuals simply grow together during the process of syngamy.) • Both gametes are haploid, the resulting zygote is diploid. • Sex probably evolved as a means of producing variable offspring in the face of an uncertain future, though its evolutionary origins are obscure. • It is virtually ubiquitous among eukaryotes, though many can produce sexually or asexually. • It has the potential to produce enormously variable sets of genetic information, something that can be crucial to the survival of a species. Diploidy • Diploidy is the state of having two copies of every single gene-like pairs of shoes, pairs of gloves, pairs of stereo speakers. – Humans, and many of the organisms with which we are familiar (flies, zebras, potatoes), are diploid. – We have two copies of every gene in our bodies. – For many genes, these copies are identical matches (they are homozygous). – For others, there are subtle differences between the two copies (they are heterozygous). • Not all organisms are diploid as adults, some are haploid. – For sexual reproduction to occur, there must be both a diploid and a haploid phase of the life cycle. Meiosis • Meiosis is that process by which a single diploid cell gives rise to four, genetically different, haploid cells. • It works like this (forget the phases): – The diploid progenitor duplicates its genetic material…thus, every chromosome is composed of two, identical, chromatids, joined at the centromere (this happens before meiosis starts) – Each chromosome finds its match, to form “matching pairs” of homologous chromosomes. This process, which occurs during the first of the two meiotic divisions, is unique to meiosis, it does not occur during mitosis. – Four strands (two homologous chromosomes, composed of two identical strands each) cluster in structures sometimes called tetrads, along a plane in the center of the dividing cell. A process called “crossing over” may occur at this time. • First division, homologous chromosomes separate. – Spindle fibers drag them to opposite poles of the cell. The cell then divides. Which chromosome ends up where is completely random and is not influenced by the fate of the other chromosomes around it. The cell then divides. • Second division, chromatids separate. - Spindle fibers drag them to opposite poles of the cell. The cell then divides. • This gives you four, genetically different, daughter cells from a single parent. www.biologycorner.com Meiosis results in 4 daughter cells Daughter cells are haploid Daughter cells have unique combinations of chromosomes Daughter cells do not have homologous pairs Meiosis creates gametes (sperm and eggs) Meiosis ensures variability in offspring The ancestral sexual species Probably had a life cycle similar To that pictured above. Errors in Meiosis • Errors in meiosis have the potential to produce unusual phenotypes in the offspring. • The most common meiotic error is nondisjunction, where an entire homologous pair of chromosomes migrates to the pole of a cell, without splitting. • If this happens to a single pair, it causes either a trisomy, or a monosomy, in the resulting offspring. • If it happens to the entire genome, it can produce triploid or even tetraploid offspring. • The human condition of Down’s syndrome results from a trisomy at chromosome 21, a trisomy at chromosome 18, 13, or the sex chromosomes (23), is also survivable. In humans, trisomies for other chromosomes are not usually viable. • In other organisms, triploids and tetraploids may be viable. How Meiosis, and Sex, Produce Variation • Meiosis starts with a single diploid cell with two redundant sets of DNA, and produces four haploid cells, each with a single set of DNA. • These four cells all have DIFFERENT sets of alleles, although they have the same genes (one copy of each, not two). • Meiosis produces variation in two ways. – By randomly selecting one, or the other, chromosome from a diploid set, to form a haploid set, an enormous number of potential gametes arise. In an organism with 23 pairs of chromosomes, for instance, 223 potential gametes can be formed this way. This phenomenon is called assortment. • By the process of recombination, which is a result of crossing over, new combinations of alleles on chromosomes may arise. • Crossing over is a cytological phenomenon that occurs during the first of the two meiotic divisions. – Two strands of DNA from complimentary chromosomes cross over each other, and a break forms. – The break is quickly repaired, switching stretches of DNA among the two compliments to create two new chromosomes. – A pair of chromosomes can cross over once, several times, or not at all. The farther apart two genes are on a chromosome, the more likely it is that crossing over will create recombination between the two of them. • Crossing over creates new combinations of alleles on chromosomes, and permits favorable alleles to combine together on the same chromosome. • The genetic result is called recombination. •When geneticists speak about genes, they prefer to use the word locus. The two are virtual synonyms, but locus means location, and it refers to the place where variation can occur. Using the word gene emphasizes its information content. •Thus, as you might be able to intuit from the diagram to the left, the more distant the loci (plural), the more likely it is for a particular recombination event to switch them between chromosomes. The Patterns Inherent in Mendelian Genetics Result from the Nature of the Eukaryote Genome, and the Events of Meiosis • • • • The preceding information explains the cytological and evolutionary reasons why genetics works the way it does in eukaryotes. Meiosis does not produce new genes, or new alleles The genetics that follow have their cytological underpinnings in the events of meiosis. It does, however, create new combinations of chromosomes, and new combinations of alleles on chromosomes • For example: – Segregation is the process by which a gamete comes to have only one of the two alleles its parent possesses, for every gene. It is random, and it occurs because of the separation of homologous chromosomes during the first meiotic division. – Assortment accounts for the fact that most eukaryotes possess many pairs of chromosomes, it is segregation at two or many loci simultaneously. Assortment is responsible for the variation in gametes created by the random selection of chromosome from each pair into gametes.. • Example: via assortment alone a human with 23 pairs of chromosomes can produce 223 potential gametes, far more than every person who has ever lived. • When genes are on separate chromosomes, it is said that they assort independently. When they are on the same chromosome, they tend to get passed on as a unit, which can only be broken up by recombination, this is called linkage. Variation is ubiquitous, all organisms exhibit SOME variation • Look around the classroom and you will immediately notice a great deal of variation among members of this class. • Some of this variation is morphological: hair color, height, eye color, etc.. • Some is behavioral: preference for certain foods, knowledge of languages, choice of clothing, etc.. – Other organisms; crayfish, salamanders, scorpions, exhibit similar amounts of variation (though we are not as sensitive to it at first glance). • For centuries, biologists have sought an explanation for this variation. • Much of this variation has its basis in our genes, a fact that is of tremendous biological significance. Variation within the White-cheeked Rosella The White-cheeked Rosella is made up of four varieties, each with its own distinct color combination and markings. The diagram shows where these varieties are found. Stolen from-www.environment.gov.au Question-Based upon this information alone, can you Tell whether the variation is genetic, environmental, or both? Types of Variation • Attributes, or qualitative variables, can be scored, but not fall into a continuum. – Examples: human eye color, political party, blood type, gender, etc.. • Quantitative, or measurable, variables fall along a measurable axis, and can be measured to observe their place relative to others. • Discontinuous measurable variables: fall into discrete intervals. Examples: shoe size, number of mates, number of arrests for drunk driving, etc.. • Continuous measurable variables do not fall into discrete intervals, they exist along a continuum. Examples: height, weight, age, etc.. Distributions of Values • A group of individuals has a distribution of values for every quantitative variable. This reflects the number of individuals possessing each value for the trait. • The group of individuals in question is the statistical population, the population has a distribution of values for the variable. • These distributions are frequently expressed as a histogram: the range of values for the category is broken into intervals, and the number of individuals within that interval is expressed as the height of a bar. A Histogram Types of Distributions • Populations of actual organisms exhibit a great variety of distributions for different measurable variables. • Some common distributions are: – Normal – Bimodal – Multimodal • Distributions may also be skewed, or exhibit kurtosis. Normal Distribution A Skewed Distribution Bimodal Distribution Mean, Median, Variance, etc. • The distribution of numerical values can be described by several statistics: • (Arithmetic) Mean: the average: x=Sx/N • Median: The value with the same number of observations preceding it, and following it • Variance: s2 =the variability of values in the data set, their tendency to depart from the mean s2=(S(x-x) 2 /N-1 ) • Standard Deviation: s=the square root of the variance. Dominance • As you remember, diploid organisms have two sets of redundant genetic information-two copies of every gene. – An individual is homozygous at a locus if they have two alleles for a gene, and heterozygous at that locus if they have different copies. • Dominant alleles mask the effect of a recessive allele at that locus, they are expressed in the homozygous or the heterozygous state. • Recessive alleles are only expressed in the homozygous state. By convention, we usually use a capital letter to designate the dominant allele, and the lower case of the same letter to designate the recessive allele. • Example: Alleles for albino coloration in many animals result from recessive alleles. – It is usually a defective protein that inhibits the metabolic pathway associated with the production of a protein, or (more often), inhibits its placement in the target tissue. – In most cases, even one copy of a nondefective gene at this locus restores the pathway. • Thus, for albino coat color in mice, Individuals with either one or two copies A (dominant) allele have brown fur. • Therefore AA and Aa have brown fur. Note that Aa individuals can pass on the a allele, even though they do not express it themselves, they are carriers. • Individuals with two copies of the albino allele, aa, have white fur. media.ebaumsworld.com/.. Some Alleles of Medical Interest • Because, when rare, recessive alleles are usually in the heterozygous state, and not subject to natural selection, human populations harbor quite a few harmful, recessive alleles at low frequencies. – For instance, a rare, autosomal recessive allele on chromosome 7 disrupts the normal migration of neurons, leading to an abnormally thick and smooth cerebral cortex, and reduced cerebellum, hippocampus, and brainstem causing a condition called lissencephaly. – It is typical of these conditions for an affected individual to be born to normal parents. • Dominant alleles, by contrast, are generally manifested in the parents. • For instance, ectrodactly, a condition where the affected individual has severely deformed digits, is caused by a dominant allele. • It runs in families, conspicuously, and was passed from the famous circus performer, Grady Stiles Junior, to one of his offspring. Typical manifestation of lissencephaly Grady Stiles Junior, as a young man Codominance • Codominance (sometimes called incomplete dominance) is the allelic interaction where, in the heterozygous state, both alleles are expressed (for attributes), or the heterozygote is in between the phenotypes of the homozygous individuals for those alleles (in the case of measurable characters). – Thus, the heterozygote has a unique phenotype. • For example, in chickens, black feather color is codominant with white feather color. Heterozygous chickens have black and white feathers in a checkered pattern. • FBFB is black, FWFW is white, and FWFB is checkered. Note that the notation uses superscripts, which makes it clear that neither allele is dominant. Human Blood Type • The human ABO locus has three loci, which exhibit both dominance and codominance. • Human blood types are encoded by a single locus with three alleles: IA, IB, and i0. • IA and IB code for two different proteins, cell surface antigen A, or antigen B. i0 codes for the lack of that particular protein. • Since we are diploid, we have a blood type, a phenotype, that depends upon the proteins on the surface of our blood cells. • IA IA and IA i0 are A, IBIB and IB i0 are B, i0i0 is O. • IA and IB are therefore CODOMINANT with respect to each other, and both are DOMINANT with respect to i0. • Most traits are not coded by a single gene…the Rh+/Rh- status of an individual is coded by at least two loci, RhD and RhCE.. • Having a dominant allele at either of these loci makes a person Rh+, having recessive alleles at all the Rh loci makes a person Rhce d/ce d Negative CE D/ce d Positive CE d/CE d Positive ce D/ce d Positive CE d/CE D Positive CE D/CE D Positive Phenotype vs. Genotype • An organism’s PHENOTYPE is its observable characteristics. • An organism’s GENOTYPE is its genetic composition of alleles. • Thus, an organism heterozygous for a recessive allele, such as albinism, would exhibit the dominant trait, yet would possess the heterozygous genotype. How Many Loci are There? – Bacteria have about 1,200 genes – Yeast have about 5,000, – Drosophila melanogaster have about 10,000 – Human beings have approximately 29,000. • Do all loci have multiple alleles? – No, only a small percentage of loci have multiple alleles, perhaps 1-5% or less, depending upon the species. Genes Interact with the Environment to Produce a Phenotype • A gene does not act alone, it gives instructions to other aspects of the developing organism, or it produces a protein that is put to use in various metabolic pathways and processes. – Nearly every gene interacts with the environment to some extent. Sometimes the contribution of the environment is small, sometimes it is very significant. • This is no mere nature vs. nurture dichotomy, it is a complicated interaction and interplay. Geographic Variation in Yarrow-A Norm of Reaction • The norm of reaction describes the pattern of phenotypic expression of a particular genotype across different environments. • For example, in yarrow, tall plants grow at low elevation roadsides, and much shorter plants grow in the mountains. • A naive researcher might conclude that the mountain plants simply had genes for growing short, or that the cold conditions in the mountain dwarfed them. • Grown under identical conditions, at low elevations, the mountain plants grow a little taller, but not nearly as tall as low-elevation plants. • Grown under identical conditions, in the mountains, the lowelevation plants grow VERY small, or die. In fact, the mountain plants have a variety of alleles at different loci coding for aspects of dealing with cold winters and short summers, but the cost of these alleles is reduced growth under friendlier conditions. Differently adapted local varieties of a species are called ecotypes. An ecotype that performs well in one situation might perform very poorly in another environment. Genetics Problem • A chicken with black feathers is mated to a chicken with white feathers. – (by convention, this generation is called the P1) • This cross produces 9 offspring, all of which have checkered, black and white feathers. – (by convention, this generation is called the F1) • Two of these offspring (the F1) are allowed to mate and produce offspring of their own. • Diagram the cross, including the – – – – – genotypes of the parents the genotypes of the GAMETES each parent produces the genotypes of the F1 offspring and the gametes the F1 can produce and the genotypes of the various F2 offspring. • Predict the phenotypic composition of this next generation, the F2. • Answer. • Start by listing the genotypes of the P1s, this is part of the answer, and you will get nowhere if you skip right to a Punnet square. – The P1s are FwFw and Fb Fb • The white parent can produce one type of gamete, Fw, the black parent can produce one type of gamete, Fb. Note, gametes are always haploid. • The F1 are all FwFb, this is the only possible genotype, given the two parents. Note, adults are always diploid. • These F1 can produce two types of gametes, Fw and Fb. • To produce an F2, these two gametes can unite in four possible ways. • The male F1 parent can produce a Fw or a Fb • The female F1 parent can produce a Fw or a Fb • This gives: – – – – Fw from the male parent x Fw from the female-white chicken Fb from the male parent x Fb from the female-black chicken Fw from the male parent x Fb from the female-checkered Fb from the male parent and Fw from the female-checkered • The colors in the offspring are ¼ black, ¼ white, ½ checkered. – If you answered ¼ to ¾, you should consider that this is a codominant system. Much of what we know about genes was first discovered by Gregor Mendel • Gregor Mendel was one of those rare historical geniuses who seems to exist in a vacuum (he didn’t he lived at a monestery with a tradition of science). His work was not well known until after his death. • He conducted experiments on the garden pea, Pisum sativum, a species that exhibits variation for several interesting characters: pod color, seed color, flower color, height, etc.. These differ because of alleles at a single locus. • Garden peas also produce a large number of offspring, a key to Mendel’s success. • Mendel was among the first scientists to think in quantitative, rather than strictly qualitative terms. Mendel’s Laws • Through experiments, Mendel deduced some basic patterns. • Inheritance is particulate: “particles” called genes carry the information that makes parents tend to resemble their offspring. – This was a huge departure from the previous scientific paradigm, believed for centuries, that inheritance was somehow carried in the blood and blended together every generation. • These “particles” segregate, so that individuals with two particles produce gametes with only one particle, the law of segregation. • The “particles” for each gene segregate independently of each other, the law of independent assortment. – This law is, of course,not universal. It applies only to the special case where genes are on separate chromosomes. It was not until decades later that the relationship between chromosomes, and Mendel’s particles, was discovered. A Classic Mendelian Experiment • Two lines of garden peas have been grown separately for a long time, they are called “true breeding” lines because the parents always resemble the offspring. One line has purple flowers and one line has white flowers. A parent is chosen from each line. These are called the P1. • When they are artificially crossed (garden peas normally self-fertilize), the resulting offspring (called F1) are all purple. • Two individuals from the F1 are crossed. • The resulting offspring (the F2) are 75% purple-flowered and 25% white flowered. WHY? • DIAGRAM THIS CROSS in a similar way to the way you diagrammed the last one. Questions: • 1. What is the probability that any given pollen grain from the white flowered line contains an allele for white flowers? • 2. How about a pollen grain from the F1? • 3. What about a pollen grain from a white individual taken from the F2? Answers: • 1. 1.0 • 2. .50 • 3. 1.0 Another Experiment • One of F1 from the cross above is mated to an individual from the whiteflowered line. • DIAGRAM THIS CROSS – What would be the phenotypic composition of the resulting offspring? – What would be the genotypic composition of the resulting offspring? Independent Assortment • The segregation of alleles into gametes follows the laws of probability: therefore an Aa individual would produce 50% A gametes and 50% a gametes. • If you consider two loci, with independent assortment, the chance of a particular allelic genotype is a product of the probabilities of the alleles at each locus. – Ie., an AaBb individual would produce 25% AB gametes, .50 is the probability of a A in the gamete, and .50 is the probability of B in the gamete, .5 x .5 is .25 – An AaBbCc individual would produce 1/8 ABc gametes, for analogous reasons. • If genes are on different chromosomes, alleles assort independently of each other. This is called independent assortment. The chance of an allele at one locus being in a particular gamete is independent for each locus. • The number of potential, different, gametes a parent can produce is equal to 2N, where N is the number of loci assorting (do not count homozygous loci). • Thus, a heterozygote for three loci: Aa Bb Cc could form EIGHT different gametes: • ABC, ABc, AbC, aBC, Abc, aBc, abC, abc – By contrast, AA BB Cc can form only two different gametes, ABc and ABC, because only one locus is assorting • For N independently assorting loci, there are 2N different gametes that can be created. If they are truly assorting independently, they will be present in equal numbers. – Departures from independent assortment are most often caused by LINKAGE, when two loci are close to each other on the same chromosome. • Linkage causes certain combinations of alleles to be over-represented in the gametes. Sample Problem • Albinism is a condition that results from the lack of normal pigmentation. In humans, individuals with two recessive alleles at the ALBINO locus are albino, • therefore AA=pigmented • Aa=pigmented • aa=albino • Attached earlobes result from two recessive alleles at the EARLOBE locus. • therefore EE=non-attached earlobes • Ee=non-attached earlobes • ee=attached earlobes • Imagine an albino man with non-attached earlobes marries a pigmented woman with attached earlobes. • They have 23 children, none of them twins. • All of their children are pigmented with non-attached earlobes. • QUESTIONS; • What is the most likely genotype of the man? • What is the most likely genotype of the woman? • What alleles for pigmentation will HIS gametes carry? • What alleles for pigmentation will HER gametes carry? • What alleles for earlobes will HIS gametes carry? • What alleles for earlobes will HER gametes carry? • What are the possible GENOTYPES of their offspring? SOLUTION: • Since all their offspring are pigmented with non-attached earlobes: • The man is almost certainly aaEE • The woman is almost certainly AAee • (otherwise, at least one of the children would have been albino, had attached earlobes, or both ) • Their offspring are all AaEe. • The man’s gametes carry a SINGLE a allele for pigmentation, and a single E allele for earlobes. • The woman’s gametes carry a SINGLE A allele for pigmentation and a single e allele for earlobes. • (Based on their phenotypes, you cannot distinguish parental phenotypes aaEe from aaEE, or AAee from Aaee, but since none of their children exhibited the recessive phenotype, it is a pretty good bet the parents were both homozygous at both loci). Now, imagine two of their children interbred and had a child. • How many types of gametes can their children produce? • What would be the possible GENOTYPES and PHENOTYPES of their offspring? • Assuming independent assortment, what is the probability that their first child will be an ALBINO with ATTACHED EARLOBES? SOLUTION: • Their children, the F1generation, are HETEROZYGOUS at TWO loci. • They can produce FOUR different gametes: • AE aE Ae ae • Since the children have interbred with each other, their are SIXTEEN possible combinations of male and female gametes: Punnet Square: • • • • • female gametes • AE aE Ae ae AE AAEE AaEE AAEe AaEe male gametes aE Ae aAEE AAeE aaEE AaeE AaEe AAee aaEe Aaee ae AaEe aaeE aAee aaee • Note that there are only NINE different genotypes and FOUR different phenotypes for the offspring, because several combinations of male and female gametes give the same genotype, and several genotypes give the same phenotype. • The chance their first child will be albino with attached earlobes is 1/16, since only one of sixteen combinations, ae vs. ae, gives the aaee genotype which results in the albino attached phenotype. QUESTION • The mother from the cross goes on the Jerry Springer show for having an illicit affair with her first born son. She claims to have given birth to ANOTHER child, this one is normally pigmented with attached earlobes. What are the potential genotypes, and phenotypes, of that child? • Assuming independent assortment, what is the chance that a child from this type of union will be albino with non-attached earlobes? • Is that child her husband’s, or her son’s? • • • • • • • • ANSWER: Remember, the F1 male (her son) can produce four gametes: AE, Ae, aE, ae She can produce one gamete, Ae therefore: male gametes AE aE Ae ae female gametes Ae AAEe AaEe AAee aAee Note that there are four potential genotypes, and TWO potential phenotypes, pigmented with attached earlobes and pigmented with non-attached earlobes, 50% chance of each. • The child could be her son’s, but it couldn’t be her husband’s. Testing Independent Assortment • A TEST CROSS is used to determine whether two loci are linked. • Cross two true-breeding parental lines, such as Sepia vs. Black Drosophila melanogaster: • se se BK BK x SE SE bk bk • to create a heterozygous F1: • SE se BK bk • Now, INSTEAD of crossing the F1 to ITSELF, cross it to a line which is HOMOZYGOUS for RECESSIVE alleles at BOTH LOCI Test Cross • SE se BK bk x • • • • • female gametes • se se bk bk male gametes se bk SE BK SEse BKbk se BK sese BKbk SE bk SEse bkbk se bk sese bkbk • Note that this cross yields FOUR different Genotypes, each with a distinctive PHENOTYPE, they should be in equal numbers. Test Cross Ratios • • • • • Eyes Red Sepia Red Sepia Body Expected Ratio Normal 1/4 Normal 1/4 Black 1/4 Black 1/4 • If the two alleles are linked, the PARENTAL phenotypes will be OVER-REPRESENTED. The Chi-Square Test: • The Chi-Square test is a good statistical tool to test a hypothesis with distinct OBSERVED and EXPECTED values. • Imagine we did the cross above and counted 400 offspring. We observed the following numbers. • Eyes Body Number Observed • Red Normal 101 • Sepia Normal 99 • Red Black 106 • Sepia Black 94 This is how we would do a Chi-Square test: • if the expected ratio is 1/4:1/4:1/4:1/4, we expect 100 flies with each phenotype. • Eyes Body Number Observed Number Expected • Red Normal 101 100 • Sepia Normal 99 100 • Red Black 106 100 • Sepia Black 94 100 • The Chi-Square (Written c2) =S(O-E)2/E, is in index of how far your observed numbers are from your expected numbers. • QUESTION; What is the Chi-Square value from the cross above? Answer: • Eyes Body • • • • • Red Normal Sepia Normal Red Black Sepia Black # Observed # Expected O-E (O-E)2/E 101 99 106 94 100 100 100 100 1 .01 1 .01 6 .36 6 .36 S(O-E)2/E=.74 What the #@!?? Does this Number Mean? • The c2 value for any given test represents the extent to which the observed values depart from the expected values. • The c2 distribution lists the probability of any given set of observed values departing from the expected values by chance, given the degrees of freedom-degrees of freedom=N-1 where N=the number of comparisons • QUESTION: How many degrees of freedom were there for the cross we just did? • ANSWER: N-1=3 degrees of freedom. • QUESTION: What is the probability that the observed values from the cross above would depart from the expected values to the extent that they did? (see your lab manual, page 93) • ANSWER: With three degrees of freedom, the probability of departure is >.70. In other words, MOST data sets will depart by that much, or more, even if the hypothesis that generated the expected values is perfectly correct. • Why? • Because a certain amount of departure by random chance is part of the essential, probabilistic nature of genetics. • Why >.70? • The table on page 93 gives a few rough benchmarks. For example, at 3 degrees of freedom, 50% of data sets depart to the extent that the c2 value is 2.37 or more (P<.50). 5% depart to the extent that the c2 value is 7.81 or more (P<.05). Most scientists use an arbitrary criterion to determine whether the departure of observed and expected values was due to chance, or due to a flaw in the hypothesis that generated the expected values to begin with. • The arbitrary cutoff is P<.05. If there is less than a 5% chance that the observed and expected values would depart to the extent that they did by chance alone, than we say that the hypothesis is falsified we reject it. • Otherwise, we accept it (this does not mean we have proven it, however, because an infinite number of hypotheses can be concocted to generate the same data). • QUESTION: For the cross above, do we accept, or reject the hypothesis? • What does this mean? • ANSWER: Accept the hypothesis. • The hypothesis that we used to generate the expected values was independent assortment. • Since we cannot reject independent assortment, this means that the genes are not linked. Linkage • Linkage is the result of two loci being located close together on the same chromosome. It causes a departure from independent assortment (thus, Mendel’s second law is incorrect, but he didn’t know about chromosomes). • In crosses involving two loci, linkage causes certain combinations of alleles to be over-represented in an individual’s gametes. Example of Linkage • In Drosophila melanogaster, the recessive allele for the sepia locus causes flies to have very dark colored eyes. The recessive allele at the ebony locus causes the fly to have very dark body color. • A male from a true breeding line of sepia eyed-ebony bodied flies is crossed to a female from a true breeding line of red eyed, tan-bodied flies (the “wild type”). • se se eb eb x SE SE EB EB • to create a heterozygous F1: SE se EB eb • Now, cross a female F1 to a male from the sepia-eyed, ebony bodied, line. • QUESTIONS: What is the phenotype of the F1? • With no linkage, what is the expected proportion of sepiaeyed, ebony-bodied flies? Answer: • The F1 are “Wild Type” • With no linkage, the expected proportion of sepia-eyed, ebony bodied flies is 25%. Now, imagine we got this data • • • • • Eyes Red Sepia Sepia Red Body Normal Normal Ebony Ebony Number Observed 123 77 119 81 Are the loci linked? • Eyes Body • • • • • Red Normal Sepia Normal Sepia Ebony Red Ebony # Observed # Expected O-E (O-E)2/E 123 77 119 81 100 100 100 100 23 ? 23 ? 19 ? 19 ? S(O-E)2/E=?? • Eyes Body • • • • • Red Normal Sepia Normal Sepia Ebony Red Ebony # Observed # Expected O-E (O-E)2/E 123 77 119 81 100 100 100 100 23 5.29 23 5.29 19 3.61 19 3.61 S(O-E)2/E=17.8 • The loci are linked. • QUESTION: Why are there fewer SEPIA NORMAL and RED EBONY? • Answer: Linkage causes the GRANDPARENTAL phenotypes to be over-represented in the progeny from a test cross. • MOM DAD • Egg SE EB SE EB se eb se eb se eb SE EB • sperm F1 SE EB se eb • gametes (without recombination) SE EB • gametes (with recombination) se eb EB se SE BE eb Linkage Mapping • You can tell how far apart loci are by the proportion of the F2 from a test cross that are recombinants. Simply take the number of recombinants and divide by the total, and that gives you r-the proportion of recombinants. – For instance, for the cross we just did, the recombinants were Red Ebony and Sepia Normal. – Thus, r= (81+77)/400=.40 • Hint-the recombinants are the F2 that do not resemble the grandparents. • From r, you can get the distance between loci. Simply multiply r by 100 and you get the distance in map units (Morgans). • Thus .40x 100=40 map units. • Note that the more recombinants, the higher r, and the farther they are away in map units. • Loci that are very close together are said to be tightly linked, and produce few recombinants. This is a linkage map of sorgum, which was a work in progress when I wrote this slide. The linkage groups almost always turn out to be chromosomes the genetic markers are loci that have been placed in order by a comparison of their relative distances (this is from the icrisat website) An Interesting System, Heterostyly in Primrose • In Primula sp., an interesting genetic system maintains two distinct phenotypes in the population, and ensures the virtual absence of intermediate phenotypes. • It is called heterostyly, because each type of flower is well adapted to cross with its opposite, but unable to cross with itself. • This system encourages outcrossing, which can potentially maintain genetic diversity. • The dominant, G allele codes for short style (the female part of the flower), which reaches to the middle of the corolla tube, the recessive, g allele codes for a longer style, which reaches to the lip of the corolla. • The dominant, A allele codes for long anthers (the male part of the flower), which reaches to the edge of the corolla tube, the recessive, a allele codes for short anthers, which reach to the middle of the corolla tube. • The dominant P, allele codes for “thrum” pollen, the recessive, p allele codes for “pin” pollen, which is much smaller. • The three loci are very closely linked-so that crossing over rarely occurs Thrum-left, pin-right • In normal populations, only two genotypes are present, GgAaPp, and ggaapp • The genotype ggaapp gives rise to the “pin” phenotype, which has long styles, short anthers, and pin pollen. • The genotype GgAaPp gives rise to the “thrum” phenotype, which has short styles, long anthers, and thrum pollen. • Even though other genotypes are theoretically possible, a combination of tight linkage, and the mechanical impossibility of thrum x thrum crosses keeps them from becoming common. • Thrum x thrum crosses are impossible, because thrum pollen cannot grow down a short style. • Pin x pin crosses are possible, but very rare. Primula veris. Thrum is on the left, pin is on the right • Each form is adapted to transfer pollen to a different part of the potential pollinator, thrums transfer pollen to the waist, which can be received by the styles of a pin flower. • pins transfer it to the insects head….which can be received by the style of a thrum flower. • Rare crossing over events, in thrum flowers, produce intermediate phenotypes, but these do not do not produce many offspring of their own, at least via animal pollinators. Sex-Linkage • Sex linkage is not really linkage. • Sex linkage is the term for a locus being located on a sex chromosome, such as the X chromosome in humans or Drosophila. • Sex linkage causes a unique combination of inheritance. • For instance, in humans, males receive only ONE allele from each sex linked locus (from their mom). • Recessive alleles are therefore automatically expressed in the male, a state referred to as the hemizygous condition. • Homogametic sex: that sex containing two like sex chromosomes. In most animal species these are females (XX). – Butterflies and Birds, ZZ males. • Heterogametic sex: that sex containing two different sex chromosomes In most animal species these are XY males. – Butterflies and birds, ZW females. – Grasshopers have XO males. • In ants, bees, and wasps, males are haploid, in effect, every locus is sex-linked. • Examples of Sex-Linked Traits in Humans: – Hemophilia – Duchenne’s Muscular Dystrophy – Red-Green Color Blindness • The above are all recessive, exhibiting a characteristic pattern of inheritance: – A female can be a heterozygous “carrier” but a man cannot. – Males, since they always exhibit the trait, are much more commonly affected by it, though the allele occurs in equal frequencies in females. A Genetic Cross With Sex Linkage • Red/white eye color in Drosophila: • The white locus is on the sex chromosome, the white allele is recessive, therefore: • W = red, w= white; • In females: • WW, Ww, = red-eye female • w w = white-eyed females • In males: • W= red-eye male • w= white-eyed male • One key indicator of sex-linkage is that reciprocal crosses give different results: • Cross (purebreeding) red-eyed females to whiteeyed males • F1: All males and all females have red eyes • Reciprocal cross: white females crossed to red males • F1: All males are white, all females red • WHY? • What would the F2 look like in each case? X inactivation • In each female cell in mammals , one X is picked at random and inactivated. Epistasis • Epistasis occurs when a gene at one locus alters the expression of a gene at another locus. Coat Color in Mice • In Mice, Black coat color (allele B) is dominant to brown coat color (allele b). Therefore, bb individuals normally have brown coats, BB and Bb normally have black coats. • A SECOND locus controls the way the pigment is distributed: • Normal distribution (C) is dominant to inhibited distribution (c) . CC and Cc individuals therefore normally have black coats or brown coats (depending upon their alleles at the color locus), and cc individuals are WHITE no matter what they have at the other locus. This is because, if pigment is not deposited, the animal has a white coat, regardless of the potential coat color of the animal. Question: A BROWN mouse is mated to a WHITE mouse. All of the resulting offspring are BLACK. What is the genotype of the offspring? What types of gametes can they produce? Answer: • The parents are bbCC (brown) and BBcc (white). We know the parents are homozygous because ALL the offspring had the dominant trait at each locus (if they were heterozygous, we would see a mixture among the offspring). • Their offspring are BbCc (black). • The F1 can produce four different gametes for these two loci: BC, bC, Bc, bc. Question: • If these F1 mated with each other to produce an F2, what proportion of the offspring would be expected to be BLACK?. What proportion would be expected to be WHITE? Answer. • 9/16 black, and 4/16 white. Pleiotropy: • Most genes exhibit pleiotropy, they have multiple affects. • The best examples come from genetic diseases in humans, such as Marfan’s syndrome. • Individuals with Marfan’s syndrome (a dominant allele, actually a deletion that behaves as a dominant allele) have the potential for: very tall stature, elongated fingers, curved spine, problems with their retina, heart valve problems. • All these effects result from an allele that affects the distribution of the fibrillin molecule. Fibrillin fibers surround the important areas of connective tissue in the body, thus, alleles that modify fibrillin cause MANY changes in the growth of the human body. Penetrance and Expressivity • When researchers perform genetic crosses, they take pains to make sure their strains are all genetically uniform EXCEPT for the alleles in question, and that the environment is identical from one generation to the next. – In the real world, alleles do not act alone, they act in concert with other genes and against a variable environmental background. – Having a particular genotype does not necessarily mean the individual will manifest it. Also, it is possible to manifest a trait to various degrees. • Penetrance describes the probability that, given a genotype, the individual in question will manifest it. – For example, Huntington’s disease is caused by a dominant allele. 95% of persons with this allele manifest the disease, 5% do not. It has 95% penetrance. • Expressivity is the extent to which a trait is manifest, given that it is manifest in an individual. Many traits have variable expressivity. – For example, Marfan Syndrome, caused by a dominant allele, has highly variable expressivity. Some people develop a tall build and long fingers, others develop life-threatening conditions.