How to determine genotype?

How to determine genotype?

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In humans, the ability or inability to roll the tongue is a single gene trait. The allele for tongue rolling (R) is dominant to the allele for not being able to roll the tongue (r). Whether or not an individual can taste PTC is also an single gene trait. The allele for being a taster (T) is dominants to the allele for not being able to taste PTC (t).

Claudia cannot roll her tongue but can taste PTC. Her mom also can taste PTC but her dad is not a taster. Claudia's grandparents were all unable to roll tongues.

1) Based on the Info, what is Claudia's GENOTYPE?

I know she is "rr" because she cannot roll her tongue and it is recessive. However; I do not know the complete genotype for the PTC taster. I know it for sure is a "T," but is it "TT" or "Tt?" How do we know? Do we have enough info to figure it out?

Claudia's dad is not a taster, so he is tt. He passes one allele on to his daughter. Since he is homozygous, he can only pass t. Claudia is a taster, so she must have the dominant allele from her mother, who is also a taster. Thus, Claudia is Tt.

What Do the Letters Mean in a Genotype?

When you were conceived, your parent's sex cells contributed an equal amount of genetic information to describe the physical traits you would display to the world. In biology, these outward physical traits are called a phenotype, and that underlying genetic code is called a genotype. Scientists use certain letters to represent different types of genes, known as alleles, which come together to create the genotype. Each one of these letters and how it is written has a special meaning.

Genetics Vocabulary Overview

Genetics studies the patterns of how traits pass from generation to generation. Inherited traits include hair color, eye color, height and blood type. Different versions of the same gene, such as blue eye color and brown eye color, are called alleles. One version or allele of a gene may be dominant over a different recessive allele, or the two alleles may be equal or codominant.

Alleles usually are represented by the same letter, but the dominant allele is capitalized. For example, brown eye alleles, all other factors being equal, are dominant over blue eye alleles. Blood type alleles are an exception to this standard practice.

How to use chi-squared to test for Hardy-Weinberg equilibrium

This post demonstrates the use of chi-squared to test for Hardy-Weinberg equilibrium. There is a question on a recent (February 2020) AP Biology practice test that required this calculation. The question is a secure item, so the exact question will not be discussed here. There is a previous post on this blog explaining how to test for evolution using the null hypothesis and chi-squared.

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For our examples, we'll use the fictional species featured in many of the evolution simulations. The population demonstrates incomplete dominance for color. There are two alleles red and blue. Heterozygotes have a purple phenotype.

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Chi-squared is a statistical test used to determine if observed data (o) is equivalent to expected data (e). A population is at Hardy-Weinberg equilibrium for a gene if five conditions are met random mating, no mutation, no gene flow, no natural selection, and large population size. Under these circumstances, the allele frequencies for a population are expected to remain consistent (equilibrium) over time. The H-W equations are expected to estimate genotype and allele frequencies for a population that is at equilibrium. The equations may not accurately predict the frequencies if the population is not at equilibrium (for example, if selection is occurring). However, it is possible that, even with the presence of an evolutionary force, a population may still demonstrate the expected H-W data.

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In the case of a trait showing incomplete dominance, the heterozygotes are distinct from the homozygous dominant individuals, which allows the genotype and allele frequencies to be calculated directly (without the H-W equations). This direct calculation can be compared to values based on H-W calculations to determine if the population is at H-W equilibrium.

For the first example, we'll use a simple data set (not generated by a simulation). In this case, there are 50 total individuals in the population 10 are red, 10 are purple, and 30 are blue. These are the observed values for the chi-squared analysis.

How to determine genotype? - Biology


Determining the phenotype of an organism is fairly straight forward . you look at it (since phenotype means physical characteristics).
Determining genotype isn't as cut & dry because you can't see an organism's genes by just looking at it.

Before we dive into the TEST CROSS, let's review our three possible genotypes & the phenotypes they create. For our example let's use guinea pig fur color black being dominant (B) & white being recessive (b).

Homozygous Dominant
(Pure Dominant)
BB Black
Bb Black
Homozygous Recessive
(Pure Recessive)
bb White

So remember,

If I handed you a black guinea pig & asked,"What's its phenotype for fur color?" You would gently hold the guinea pig, look at it and reply, "Black, you dummy . all you gotta do is look at it". And I would say, "Correct, & please don't call me dummy".

If I handed you the same guinea pig & asked, "What's the genotype of this guinea pig with respect to its fur color?" You wouldn't be able to tell me, and I wouldn't be able to tell you either. The reason we don't know is because there are two genotypes that BOTH produce a dominant trait phenotype, homozygous dominant (BB) & heterozygous (Bb), & we can't see the actual alleles (letters) without serious scientific chromosomal-type analysis --- and that's assuming that a Guinea Pig Genome Project has been completed for us to refer to, & I don't think it has.

Now, I must tell you that in your life, as an exceptional biology student, you will most likely NEVER actually PERFORM a test cross. What you need to understand are the possible results of a test cross & what they mean. Our black guinea pig is either BB or Bb, which one is it?
To perform an actual test cross with this guinea pig, we would need a guinea pig (of the opposite sex) that is homozygous recessive ("bb"). In other words, we would need a white guinea pig to mate with our black guinea pig. We would give them a little privacy, hope that the female becomes pregnant, wait for however long the gestation period of a guinea pig is, & THEN we would look at the offspring.

In our scenario, if we see any white baby guinea piglets, our black parent pig is "Bb". If all the baby piglets are black, the black parent is "BB".

I should mention that the reliability of a test cross increases with the number of offspring produced. So ideally (in our example) we would want a large litter of guinea pigs to look at. If a small litter is produced (like only 4 or 5 or 6), we would probably have those same parent guinea pigs "do it" again & make more offspring so that our conclusion is more reliable.

That's the bottom-line on a test cross, that stuff in the table. But you don't want to settle for just the bottom line. You want to understand the concept in a little more detail, don't you? Yes, believe me, you do.

In our guinea pig example, our mystery black pig is either BB or Bb. Allow me to use "B?" for the mystery genotype. Thanks.
The white guinea pig is "bb" because white is the recessive trait & the only way a recessive trait appears is if the genotype is homozygous recessive. Let's put this info in a series of Punnett Squares.

For the offspring in that bottom row, their phenotype depends on what that second ("?") allele is in our black guinea pig parent.

As you can see, if our mystery genotype pig has a "B" in the "?" spot, all of the offspring from the test cross will be heterozygous (Bb) & have the dominant phenotype --- black fur.

There is NO WAY white guinea pigs can be produced because to be white the offspring need to inherit one little "b" from each parent, and in this scenario the black parent doesn't have ANY little "b's" to pass on.

On the other hand, if the mystery allele "?" = "b", then we can predict that half (2 of 4 boxes) of the offspring from the test cross are going to have the recessive phenotype i.e. have white fur.

The only way to get white guinea pig piglets is if both parent guinea pigs have at least one "b". We KNOW the white parent has got 'em (the only way to be white is to be "bb"), and we KNOW the black parent has one big "B" (has to in order to be black), so if we get white offspring, that second allele in the black parent is "b".

Our test cross = mystery black genotype x recessive white genotype = B__ x bb

Any white offspring must be "bb".
One "b" came from the white parent, the other must be in that "blank", making the mystery genotype "Bb".


1. In African-violet plants, purple flowers are dominant to white flowers. You purchase an African-violet plant with white flowers. It's genotype could be represented as :

Like I stated ealier, it is highly unlikely that you will be asked to actually perform a test cross --- like really mate two organisms & then analyze their offspring. If you do, consider yourself lucky & more power to ya. Perhaps you'll be fortunate enough to run some computer simulations or something in lab. Anyway, the concepts behind a TEST CROSS are important. So study-up, do your best.

biotopics page

click here


1. In African-violet plants, purple flowers are dominant to white flowers. You purchase an African-violet plant with white flowers. It's genotype could be represented as :


Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their parents. [1] Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.

Current methods of genotyping include restriction fragment length polymorphism identification (RFLPI) of genomic DNA, random amplified polymorphic detection (RAPD) of genomic DNA, amplified fragment length polymorphism detection (AFLPD), polymerase chain reaction (PCR), DNA sequencing, allele specific oligonucleotide (ASO) probes, and hybridization to DNA microarrays or beads. Genotyping is important in research of genes and gene variants associated with disease. Due to current technological limitations, almost all genotyping is partial. That is, only a small fraction of an individual’s genotype is determined, such as with (epi)GBS (Genotyping by sequencing) or RADseq. New [2] mass-sequencing technologies promise to provide whole-genome genotyping (or whole genome sequencing) in the future.

Genotyping applies to a broad range of individuals, including microorganisms. For example, viruses and bacteria can be genotyped. Genotyping in this context may help in controlling the spreading of pathogens, by tracing the origin of outbreaks. This area is often referred to as molecular epidemiology or forensic microbiology.

Humans can also be genotyped. For example, when testing fatherhood or motherhood, scientists typically only need to examine 10 or 20 genomic regions (like single-nucleotide polymorphism (SNPs)), which represent a tiny fraction of the human genome.

When genotyping transgenic organisms, a single genomic region may be all that needs to be examined to determine the genotype. A single PCR assay is typically enough to genotype a transgenic mouse the mouse is the mammalian model of choice for much of medical research today.

How to determine genotype? - Biology

Definitions: phenotype is the constellation of observable traits genotype is the genetic endowment of the individual. Phenotype = genotype + development (in a given environment). To consider these in the context of evolutionary biology, we want to know how these two are related. In a narrow "genetic" sense, the genotype defines the phenotype. But how, in and evolutionary sense, does the phenotype "determine" the genotype? Selection acts on phenotypes because differential reproduction and survivorship depend on phenotype. If the phenotype affecting reproduction or survivorship is genetically based, then selection can winnow out genotypes indirectly by winnowing out phenotypes.

How do we get from genotype to phenotype? Central dogma : DNA via transcription to RNA via translation to protein proteins can act to alter the patterns and timing of gene expression which can lead to cytodifferentiation where cells take on different states cell communication can lead to pattern formation and morphogenesis and eventually we have an adult!

Genotype is also used to refer to the pair of alleles present at a single locus . With alleles 'A' and 'a' there are three possible genotypes AA, Aa and aa. With three alleles 1, 2, 3 there are six possible genotypes: 11, 12, 13, 22, 23, 33. First we must appreciate that genes do not act in isolation. The genome in which a genotype is found can affect the expression of that genotype, and the environment can affect the phenotype.

Not all pairs of alleles will have the same phenotype: dominance when AA = Aa in phenotype, A is dominant, a is recessive . An allele can be dominant over one allele but recessive to another allele. Model of dominance from enzyme activity: no copies produce no phenotype, one copy produces x amount of product and two copies produces 2x then the alleles are additive and there is no dominance (intermediate inheritance). If one copy of the allele produces as much product (or has as high a rate of flux) as a homozygote then there is dominance . There are cases where the heterozygote is greater in phenotypic value than either homozygote: called overdominance

Single genes do not always work as simply as indicated by a dominance and recessive relationship. Other genes can affect the phenotypic expression of a given gene. One example is epistasis ("standing on") where one locus can mask the expression of another. Classic example is a synthetic pathway of a pigment. Mutations at loci controlling the early steps in the pathway (gene 1) can be epistatic on the expression of genes later in the pathway (gene 3) by failing to produce pigment precursors (e.g. albinos) A-> gene 1 -> B -> gene 2 -> C gene 3 -> Pigment

Genes can also be pleitropic when they affect more than one trait. The single base pair mutation that lead to sickle cell anemia is a classic example. The altered hemoglobin sequence is not the only effect: lower oxygen affinity=anemia clogged capillaries=circulatory problems in heterozygote state=malarial resistance. Mutations in cartilage are another example since cartilage makes up many different structures the effects of the mutation are evident in many different phenotypic characters.

Polygenic inheritance can be explained by additive effects of many loci: if each "capital" allele contributes one increment to the phenotype. With one locus and additive effects we have three phenotypic classes: AA, Aa and aa. With two loci and two alleles in a strictly additive model (i.e., no epistasis or other modifying effects) we can have five phenotypic classes aabb<Aabb=aaBb<AaBb=AAbb=aaBB<AABb=AaBB<AABB and the intermediate phenotypic values can be produced in more ways, so should be more frequent. The more loci affecting the trait, the greater number of phenotypic classes.

Evolution by Natural Selection rests on the following principles:

1. there is variation in natural populations

2. the variation is heritable has a genetic basis

3. more offspring are produced than will survive each generation: struggle for existence

4. if heritable variation affects survival/reproduction, there will be differential reproduction=selection

Without genetic variation there will be no evolution. Thus, characterizing the genetic variation in natural populations is fundamental to the study of evolution. (see The Genetic Basis of Evolutionary Change by Lewontin , 1974)

What kinds of variation are there? Discrete polymorphisms (e.g., Biston betularia ) easily noticed, but not frequent or representative of the variation in natural populations (eye color in humans also quasi discrete). Continuously varying traits can be described by the mean x = ( X i )/n and variance V = 1/n S (X i -x) 2 . Examples: the carrots in the Burpee Catologue human height. Continuously varying traits will have both a genetic and environmental components.

How much genetic variation is there? Historical debate: Classical school held that there was very little genetic variation, most individuals were homozygous for a "wild-type" allele. Rare heterozygous loci due to recurrent mutation natural selection purges populations of their "load" of mutations. Balance school held that many loci will be heterozygous in natural populations and heterozygotes maintained by "balancing selection" (heterozygote advantage). Selection thus plays a role in maintaining variation.

How do we measure variation? To show that there is a genetic basis to a continuously varying character one can study 1) resemblance among relatives : look at the offspring of individuals from parents in different parts of the distribution can estimate heritability (more later). 2) artificial selection : pigeons and dogs show that there is variation present does not tell how much variation

Protein electrophoresis : phenotype = gene product of specific locus (loci). Took off in mid 60's (Lewontin and Hubby, 1966 Harris, 1966) still used. Grind up organism in buffer, apply homogenate to gel (starch, acrylamide), apply electric field, proteins migrate in gel according to charge, stain gel with histochemical stain for enzyme activity, bands reveal variation. Do this for many loci and can estimate: proportion of loci polymorphic per population (10-60%, depending on organism) proportion of loci heterozygous per individual (3-20% depending on organism). The technique provides a minimum estimate because different amino acid sequences may migrate at the same rate in the gel.

DNA variation. Measure the genetic material directly sequencing is the most precise but the most laborious restriction enzyme analysis faster but has less information. These techniques have revealed that there is even more genetic variation that what was revealed by protein electrophoresis. Hence the debate between the Classical and Balance schools of genetic variation has evolved into a debate about the forces maintaining genetic variation: the Neutralist-Selectionist controversy (or debate). Some loci are neutral others under selection (more in lecture on Molecular Evolution). The debate is not over.

How is variation apportioned within and among populations? Hierarchy in patterns of variation: are populations either melanistic or normal or do populations contain some of both if so what are the frequencies in different populations? Is the variation within or among populations ?

Spatial Patterns of Variation

Geographical isolates: discontinuous or disjunct distribution. Is there differentiation?Are there continuous distributions, clinal variation , abrupt discontinuities ("step" cline).

How to determine genotype? - Biology

Department of Genetics and Cell Biology
Washington State University
P. O. Box 644234
Pullman, WA 99164-4234
Voice: (509) 335-5591
Fax: (509) 335-1907


Most students, whether non-science majors or life-sciences majors, have difficulty in using what they learn of basic Mendelian genetics to deduce the underlying genetic rules from the results of crosses. This is especially true for organisms that have relatively few offspring and thus the result of any one cross does not often result in the predicted ratios of phenotypes. Being able to predict ratios of genotypes and phenotypes of a cross from known parental genotypes is but a first step in understanding Mendelian genetics. The true utility of Mendelian genetics is to be able to deduce the underlying genetics from a pedigree. I have devised a simple coin toss game that allows students to get a grasp on how Mendelian genetics works. This hands-on activity requires very little preparation or materials but provides a clear and meaningful way to demonstrate the fundamentals of Mendelian genetics. This exercise is only appropriate for simple Mendelian traits, that is, those traits determined by a single nuclear gene in a simple dominance or recessive relationship. It is not suitable for cytoplasmic/mitochondrial inheritance, nor for the complexity of varying penetrance. This exercise is most useful after the students have been introduced to Mendelian genetics and Punnett square. This simple exercise can be fun and challenging not only for non-science majors but for biology majors as well.

A Macintosh computer program written in Director 5.0 which uses the genetics of parakeet is available for downloading.


The main materials for this exercise are sets of pedigree charts.
We also use a coin and a marker pen which students can provide. The pedigree charts already have the circles and squares connected by lines. Each group of 3-5 students is provided with pedigree charts one "genotype" chart and several blank "phenotype" charts. The genotype chart has the genotype of select individuals noted (Fig. 1a and Fig. 3) and whether the trait to be simulated is dominant, recessive, or sex-linked recessive. The phenotype charts have the same number and orientation of squares and circles connected by lines but are otherwise blank. The exercise involves filling in the genotype chart by tossing a coin to determine which of the two alleles is inherited by an offspring. Thus the exercise simulates nature each offspring is a result of random choice of one of the two copies of the gene in each parent.

Instructors can make their own pedigree charts. One can make a blank pedigree chart using as a guide the pedigree charts on Figure 3 and adding and/or deleting individuals or generations. Alternatively one can use one's own or other families' pedigrees. Then decide upon the type of trait, dominant, recessive, or sex-linked recessive. Then keeping in mind the type of trait, pick the genotype for select individuals. It is easiest to indicate the genotype of the oldest (top) part of the pedigree and new individuals that marry into the pedigree.


1) First note the genotype for select individuals on the genotype chart. In the example given in Figure 1a, the father is heterozygous and mother is homozygous recessive.

2) Next decide which copy of the gene corresponds to heads and tails, for example, heads = A and tails = a . Once decided, keep it the same throughout.

3) Now determine the genotype of an offspring by tossing a coin. Toss the coin for the father. This determines which copy of the gene the father contributes to his offspring. By tossing a coin, we have 50:50 chance of getting heads, that is A or getting tails, that is a . In the example on Figure 1, the chance of getting a from the mother is 100%, or 1.0, and chance of getting A or a from the father is 50% or 0.5. Thus there is 1.0 times 0.5 equals 0.5, that is 50% chance of offspring with genotype Aa and 50% chance of offspring with genotype aa . However, with the small number of offspring, the coin toss may result in all Aa or all aa offspring or any combination in-between.

Similarly, the sex is determined by the sex chromosomes. In mammals, females have two X chromosomes and males have an X and a Y. The probability of the father contributing an X is 50% and Y is 50%, so on average, the offspring should be roughly 50% female and 50% male. In Figure 2, I have indicated vertical lines to indicate offspring but there are no squares or circles below the lines to indicate their gender.
Try tossing the coin, with X as heads and Y as tails to determine the sex ratio of the ten offspring. If everyone in the class did it, the overall ratio of male to female offspring will be close to 50% but many individual pedigree charts will have ratios different from 50:50.

In Figure 1, if the mother was also heterozygous, Aa , then the probability of an offspring with genotype aa is the probability of father contributing an a , 50%, and the mother contributing an a , 50%, that is 0.5 times 0.5 which is 0.25 or 25%. The same calculation will apply for an offspring of genotype AA . In calculating the probability for an offspring with genotype Aa , since either the mother or the father can contribute A and then the mother or the father can contribute a , the probability of genotype Aa is 2 times 0.5 times 0.5 which is 0.5 or 50%. This is the probability that one derives from using the Punnett square. However, the results from coin toss for the small number of offspring in any of the pedigrees may not match these expectations. This is what makes this exercise a challenge.

Note: You need not toss a coin for any homozygous parent. For example, in the example given here, you need not toss the coin for the mother since she can only contribute a . You also need not toss the coin for a father in the case of a sex-linked trait since the sex of the offspring requires that either the X or the Y chromosome is contributed by the father.

4) Continue for each individual that does not have the genotype written. Faithfully note the result of each coin toss. Even if the expected ratio of offspring genotypes is 1 Aa : 1 aa like in this example, if each time you tossed the coin for the father you came up with heads, that is A , write Aa for each offspring.

5) As you determine the genotype or after completing the genotype pedigree chart, fill in the phenotype pedigree chart appropriate for the trait noted on your genotype chart. For example, if your genotype chart looked like Figure 1b, and the trait was dominant, the phenotype charts would look like Figure 1c. On the other hand, if the trait was recessive, the phenotype chart would look like Figure 1d. 6) Produce a phenotype chart for your group, one for the instructor, and for each of the other groups in the class. Of course, all the phenotype charts from one group should be identical.

7) Keep the genotype chart and a copy of the phenotype chart for your group and distribute phenotype chart to each of the other groups


I instruct each group to look at their own phenotype chart and discuss within their group whether one can unambiguously decide whether the trait was a dominant, recessive, or sex-linked recessive. The challenge for the instructor is to provide genotype charts that result in unambiguous phenotype charts most of the time. One way to ensure that particular genotypes arise is to indicate the genotype for key individuals or have a cross to an individual with a particular genotype. Some examples of genotype charts I have used in class are given in Figure 3.
It is useful to have a variety of genotype charts, some with many offspring, others with more generations, and others with combinations of these. One may choose to have a genotype chart that often results in ambiguous phenotype chart, since it is important that students recognize that pedigrees can be ambiguous. In those cases in which the resulting pedigree is ambiguous, I instruct the students to write the genotypes consistent with the alternative.

Once the group has finished analyzing their own phenotype chart, they can then discuss the phenotype charts of other groups. The challenge here is to determine the genetic rules by which such a phenotype chart can result. Depending on the number of groups, I allow greater time for group discussion. This group discussion time among students is valuable for learning and should not be hastened.

While students are doing this, I reproduce each of the phenotype charts on an overhead transparency that I have prepared before class of each blank phenotype chart. This is also the time for the instructor to check on the phenotype chart, first to ensure that it can result from the assigned genotype, and second to determine whether the phenotype chart unambiguously indicates one type of trait.

After students have had adequate time to analyze the phenotype charts, I lead a class discussion of each phenotype chart. A good starting point is to ask the group producing the phenotype chart whether they feel that the rules of inheritance for the trait can be decided unambiguously. If the group decided that the chart is ambiguous, the rest of the class can go through the exercise of what the genotypes of individuals must be if it is recessive, dominant, or sex-linked. In this process, sometimes it may be determined that the group was wrong and that the trait can only be due to one or another type of inheritance. In any case, it is valuable for the instructor to lead the discussion assuming that the group producing the phenotype chart has reached the correct conclusion. Inevitably, the group discussion will reveal the error and why it is erroneous. If the group producing the phenotype chart decided that the chart is unambiguous, it is the job of the rest of the class to decide which type of trait it is. This can be quite lively with students providing the reason for suggesting one or another type of trait and another student saying "well but what about that individual." By this process, students truly grasp the meaning of dominant, recessive and sex-linked inheritance. Also in this process, students learn the importance of having multiple generations and more offspring in determining the rules of inheritance for a particular trait.


After this exercise, students are better able to appreciate pedigrees in textbooks and historical pedigrees such as that of hemophilia in Queen Victoria's large family found in variety of human genetics textbooks reprinted from McKusick (1969).

A good follow-up homework assignment is to have students research their own family pedigree. It may be helpful to provide a list of Mendelian human traits, those traits determined by single nuclear genes found in many genetic texts, though many emphasize disease traits. A handy list of non-disease physical traits can be found in Winchester & Wejksnora (1996). A good resource for human genetic disease is the Online Mendelian Inheritance in Man, OMIM (TM).which lists over 5,000 human genetics diseases.

One pedigree that most students can construct uses the ABO blood type which is actually a co-dominant trait. An example of a genotype and phenotype chart for blood type is given in Figure 4. In this case of codominance, O is recessive to A and B, but A and B are codominant, that is, both forms are expressed. So if an individual has A blood type, their genotype can be either AA or AO. Similarly, B blood type can be due to either BB or BO. The genotype of AB, however, can only be AB.


Understanding the fundamentals of Mendelian genetics is important for biological sciences majors as well as the general public. This coin toss game graphically illustrates simple Mendelian inheritance and the difficulty in determining the genetics of traits by just looking at the pedigree. The exercise is useful for a wide range of student backgrounds. By having students actually "do" crosses, key features of basic Mendelian inheritance is vividly grasped by the students.

McKusick, V.A. (1969) Human genetics, 2nds edition. Prentice-Hall, Inc. Englewood N.J.

Online Mendelian Inheritance in Man, OMIM (TM). Center for Medical Genetics, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 1996.

Genetics jargon: Grade 9 Understanding for IGCSE Biology 3.20

The science of genetics looks at how inherited characteristics are passed from one generation to the next. The father of genetics was the Moravian monk, Gregor Mendel, who showed with his breeding experiments in peas that individual, discrete “particles” are passed from one generation to the next. We now know that these “particles” are actually small sections of a DNA molecule called genes.

Mendel worked out that there were always two such “particles” in any cell which acted together to determine the feature described. But he knew that gametes (sex cells such as pollen grains and egg cells) only contained one “particle” for each feature. You should understand why this is.

The discrete particles that are passed from generation to generation are genes: these are sections of a DNA molecule and are located on chromosomes. Chromosomes in most organisms are found in pairs within the nucleus of a cell. The word for a cell that contains pairs of homologous chromosomes is a diploid. The gametes do not have pairs of chromosomes: they are haploid cells that contain one member of each pair. This ensures that at fertilisation when two gametes fuse, a diploid zygote is produced.

iGCSE candidates can find genetics a difficult topic and one reason is that there is lots of jargon. Have a look at my definitions for these jargon words and ensure that you understand what they mean. Genetics is not a topic in which rote learning and memorisation are helpful – the very top candidates at iGCSE will understand what is going on, and can then answer all possible questions with ease.

Gene: ” a section of a DNA molecule that codes for a single protein”

Allele: “an alternative version of a gene found at the same gene locus”

Gene locus: “the place on a chromosome where a particular gene is found”

Phenotype: “the appearance of an organism, e.g tall, short, blue eyes etc.”

Genotype: “the combination of alleles at a single gene locus that an organism possesses – e.g TT, Tt”

Homozygous: “a gene locus where the two alleles are identical is said to be homozygous – e.g. TT, tt”

Heterozygous: “a gene locus where the two alleles are different is heterozygous – e.g. Tt”

Dominant allele: “a dominant allele is the one that determines the phenotype in a heterozygous individual”

Recessive allele: ” a recessive allele can only determine the phenotype in a homozygous individual”

Codominance: “two alleles are codominant if they both contribute to the phenotype in a heterozygous individual”

What is a Test Cross: Why is it used (Biology)

If I handed you a black guinea pig & asked, “What’s its phenotype for fur color?” You would gently hold the guinea pig, look at it and reply, “Black, you dummy … all you gotta do is look at it”. And I would say, “Correct, & please don’t call me dummy”.

If I handed you the same guinea pig & asked, “What’s the genotype of this guinea pig with respect to its fur color?” You wouldn’t be able to tell me, and I wouldn’t be able to tell you either.

The reason we don’t know is that there are two genotypes that BOTH produce a dominant trait phenotype, homozygous dominant (BB) & heterozygous (Bb), & we can’t see the actual alleles (letters) without serious scientific chromosomal-type analysis — and that’s assuming that a Guinea Pig Genome Project has been completed for us to refer to, & I don’t think it has.

So how do we figure it out? We perform a TEST CROSS !

Test cross = the cross of an organism with an unknown dominant genotype with an organism that is homozygous recessive for that trait

What does it do?

A test cross can determine whether the individual being tested is homozygous dominant (pure bred) or heterozygous dominant (hybrid).

To perform an actual test cross with our black guinea pig, we would need a guinea pig (of the opposite sex) that is homozygous recessive (“bb”). In other words, we would need a white guinea pig to mate with our black guinea pig.

We would give them a little privacy, hope that the female becomes pregnant, wait for however long the gestation period of a guinea pig is, & THEN we would look at the offspring .

If any of the offspring from a test cross have the recessive trait, the genotype of the parent with the dominant trait must be heterozygous The reliability of a test cross increases with the number of offspring produced.

“Key Points” to remember about a TEST CROSS :

1. the organism with the dominant trait is always crossed with an organism with the recessive trait

2. if ANY offspring show the recessive trait, the unknown genotype is heterozygous

3. if ALL the offspring have the dominant trait, the unknown genotype is homozygous dominant

Gene-Gene Interactions: An Essential Component to Modeling Complexity for Precision Medicine

Historical Perspectives on Analysis and Interpretation of Gene–Gene Interactions

The analysis of gene-gene interactions long predated the elucidation of the structure of DNA. After the rediscovery of Mendel’s pioneering experiments of pea crosses that spawned the field of genetics, an explosive period of genetic discovery, driven by experiments in model systems and mathematical analysis at the population level, dominated the first two decades of the twentieth century ( Sturtevant, 2001 ). It was during this gilded age of genetics that pioneering analysis of model systems extended and refined Mendel’s laws into a cohesive theory of genetics that formed the basis of our modern understanding. During this period, epistasis was discovered by William Bateson, the biologist who coined the term “genetics” to name the nascent field of the study of heritable variation ( Bateson, 1909 ).

Bateson used the term “epistasis” to describe a cross between two strains in which the phenotypic distribution of the resulting offspring departs from the ratios expected by Mendel’s laws ( Cordell, 2002 ). Specifically, Bateson used the term epistasis to describe one mutation blocking or masking the effects of another, hence the use of term “epistasis” which may be translated as “resting upon.” Bateson’s usage of the term epistasis described an interaction between two genetic variants in which one variant negates the effects of another ( Phillips, 2008 ). This type of genetic interaction, sometimes called modification, was the first form of gene-gene interactions to be observed in experimental crosses. Working together with Reginald Punnett, Bateson developed a two-locus Punnett square to describe the phenotypic ratios of F 2 progeny from crosses of two strains of the flowering sweet pea Lathyrus odoratus which displayed a flower coloration trait only when two separate dominant alleles were present at separate loci ( Sturtevant, 2001 ). This two-locus epistasis model extended Mendel’s original postulations of a two-locus model to incorporate an interaction between genetic variants, without which the phenotypic ratios of Bateson’s and Punnett’s sweet peas did not conform to Mendel’s laws.

Bateson and Punnett’s description of epistasis is the result of crosses between self-fertilizing strains of plants, which are essentially controlled for genetic background, allowing the analysis of the effects of one or a small number of genetic variants on visible phenotypes such as morphological traits. Natural populations of organisms, including humans and wild populations of other organisms which are used as model systems in experimental genetics, contain genetic variation across the genome, eliminating the ability to analyze the effects of one or a small number of genetic variants against a controlled background ( Moore and Williams, 2005 ). The statistical geneticist R. A. Fisher extended the description of epistasis to populations which are not controlled for genomic background by defining “epistasy” as deviations from additivity in a linear model ( Fisher, 1919 ). This definition of gene-gene interactions allows for the statistical detection of epistasis in a population which contains a large number of polymorphic sites in the genome by defining epistasis as a statistical deviation from additivity, a definition which incorporates the mean effect of two or more genetic variants in a given population of organisms ( Doust et al., 2014. ). Importantly, Bateson’s definition of epistasis involved organisms which share almost all of their genome (inbred strains) and Fisher’s definition involved organisms which contain polymorphisms across the genome (wild populations). Modern scientists have synthesized these concepts into biological and statistical epistasis ( Moore and Williams, 2005 ). Biological epistasis refers to experimental crosses in which the distribution of phenotypes in offspring deviate from Mendelian ratios (as described by Bateson and Punnett), and statistical epistasis indicates genetic effects which deviate significantly from additivity in highly polymorphic populations (as described by Fisher). As a hypothetical example to demonstrate statistical epistasis consider two loci: LocusA and LocusB. If the relationship between the two loci is additive, we would expect the combined effect of the two on a phenotype to be the addition of the main effect of LocusA and the main effect of LocusB. For example, if there is a 2-fold and 3-fold risk associated with the risk alleles for LocusA and LocusB, respectively, the additive result from both loci is a 5-fold increase risk. If the relationship is epistatic, however, the effect of the two loci together will significantly differ from the combined main effects of the two loci. In the scenario described, the presence of both risk alleles under an epistatic relationship could be a 15-fold risk increase alternately, risk could decrease to 1.1-fold. In other words, when statistical epistasis occurs, there is a non-linear relationship between the effects of two or more loci when combined. While these two forms of epistasis are experimentally distinct, the underlying theory is identical: epistasis, defined broadly, is the interaction between distinct genetic variants ( Phillips, 1998, 2008 ). This definition encompasses both statistical epistasis which might be detectable in population-scale studies and biological epistasis which might be observable in controlled crosses.

Epistasis research has continued to play a central role in genetics since the early work of Bateson, Punnett, Fisher, and others at the dawn of the twentieth century. An important application of epistasis to biological discovery came in the form of pathway ordering, in which multiple strains of a model organism are crossed together and phenotypes observed such that the ordering of a biological pathway becomes evident ( Avery and Wasserman, 1992 ). This important genetic tool can be used to discover which gene products are upstream or downstream of other gene products, providing evidence of gene product function without molecular or biochemical analysis. This can be achieved by crossing together separate mutant strains of a model organism which display different phenotypes ( Beadle, 1945 ). If a double mutant displays the same phenotype as one of the mutants does individually, one mutation likely occurs in a gene whose product functions downstream in a biochemical pathway. While this is certainly not always the case, epistasis as a tool for pathway ordering elucidated the ordering of mutations (and thereby their gene products, even if the molecular functions were only later established) in the biological pathways which control cell cycle in yeast, sex determination in C. elegans, embryonic development in D. melanogaster, and other pathways ( Phillips, 2008 ).

As described by Moore (2003) , epistasis is thought to be ubiquitous in biology ( Moore, 2003 Templeton, 2000 ). Examples of epistasis have been observed in many model organisms ( Mackay, 2014 ), including yeast ( Wagner, 2000 Boone et al., 2007 Tong et al., 2004 Szappanos et al., 2011 Moore, 2005 Baryshnikova et al., 2013 ), C. elegans ( Lehner et al., 2006 Gaertner et al., 2012 Byrne et al., 2007 ), D. melanogaster ( Horn et al., 2011 Huang et al., 2012 Lloyd et al., 1998 ), M. musculus ( Cheng et al., 2011 Hanlon et al., 2006 Gale et al., 2009 ), and A. thaliana ( Rowe et al., 2008 Kroymann and Mitchell-Olds, 2005 ). While examples of epistasis have accrued in model organisms over the years, epistasis is not confined to Mendelian traits, for which a small set of highly penetrant mutations explain much of the variance in observed phenotypes. Epistatic interactions between genetic loci have been discovered in human traits ranging from blood types and eye coloration to complex, polygenic, and multifactorial traits such as disease susceptibility ( Moore, 2005 ). Nelson et al. (2001) identified interactions between ApoB and ApoE in females as well as between the low-density lipoprotein receptor and the ApoAI/CIII/AIV complex in males for triglyceride levels ( Nelson et al., 2001 ). Interactions between SNPs in three estrogen metabolism genes, COMT, CYP1B1, and CYP1A1, were identified by Ritchie et al. (2001) that were predictive of sporadic breast cancer ( Ritchie et al., 2001 ). Further, a study by Hemani et al. (2014) identified and replicated a large number of genetic interactions involved in gene expression regulation ( Hemani et al., 2014 ).

Epistasis research was spawned shortly after the rediscovery of Mendel’s foundational work that gave rise to the field of genetics and has found application in the understanding of how genetic variants interact to determine phenotypic outcomes. While genetic interactions have provided insight into traits which cannot be adequately explained by additive models or Mendelian ratios, epistasis research remains an active application of genetics in the modern scientific research enterprise. Particularly, detection of epistasis in studies of complex traits in humans presents methodological and computational challenges that remain an active area of development.

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