TNBGGA: The No Bullshit Guide to Genetic Analysis

The classical definition of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is based on Mendel's Laws of Inheritance. Most genetics textbooks teach Mendelian genetics as a matter of course (“because it's how we've ALWAYS done things, duh!”), but there is an inherent danger in doing so. Mendel's view of genetics is very limiting because of what was known about genetics and biology in his day, and it is not uncommon for students that spend a lot of effort learning Mendel to become trapped into the same limiting world view.

We discuss basic Mendelian genetics here in this chapter for several reasons. First, there is some value in understanding Mendel's analysis because it helps in further understanding meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs). (Chapter 01), an understanding of which is essential for learning all genetics. Second, we use classical Mendelian genetics in a more experimentally practical way as a vehicle to try to wean students off bad habits in learning genetics, including Mendelian notationplugin-autotooltip__default plugin-autotooltip_bigMendelian notation: a method to write genotypes invented by Gregor Mendel. Examples include: Pp, Tt, Ww, etc. We strongly discourage the use of Mendelian notation. and Punnett squaresplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares.. We will deliberately choose Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. for our examples instead of pea plants (as is traditional when learning Mendelian genetics) to learn and use Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. genetic notation (what we refer to as fractional notationplugin-autotooltip__default plugin-autotooltip_bigFractional notation: a style of genotype notation that uses “fractions”, e.g., $\frac{unc\text{-}4}{+}$. We strongly encourage this notational style as it generally is preferred by genetics researchers. in this book), which is generally preferable when discussing more advanced diploidplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. genetics. Third, it is instructive to learn about Mendel's definition of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) to see how ideas about genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) have changed as scientists have learned more about genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-).

Classical Mendelian genetics can be studied using yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02, but there are more powerful tools for analysis of yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 genetics (tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A.) that will be discussed in Chap. 13 and Appendix A. Mendelian genetics is more commonly used for analyzing obligate diploidplugin-autotooltip__default plugin-autotooltip_bigObligate diploid: a species wherein all cells except gametes are diploid. organisms.

Some organisms, such as baker's yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 Saccharomyces cerevisiae introduced in Chap. 02, can exist as either haploidplugin-autotooltip__default plugin-autotooltip_bigHaploid: a term that describes a cell or organism that has only one copy of genetic information. Haploid cells typically arise from meiosis (or mitosis of a haploid mother cell). or diploidplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. cells. But some organisms are obligate diploidsplugin-autotooltip__default plugin-autotooltip_bigObligate diploid: a species wherein all cells except gametes are diploid., meaning that their cells exist only as diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. (except for their gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. and other rare exceptions). Humans and other mammals, for instance, are obligate diploidsplugin-autotooltip__default plugin-autotooltip_bigObligate diploid: a species wherein all cells except gametes are diploid.. For this chapter, we will focus on the fruit fly Drosophila melanogasterplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research., because it is a well characterized model genetic organism (Fig. 1). We can do genetic experiments with Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research., something that is not easily or ethically done with humans. Let's consider the genetics of diploidplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. organisms:

A zygoteplugin-autotooltip__default plugin-autotooltip_bigZygote: a cell formed by the fertilization of an oocyte by a sperm. is a cell that is formed through the fertilization of gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. (sperm and egg cells). The genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. of the zygoteplugin-autotooltip__default plugin-autotooltip_bigZygote: a cell formed by the fertilization of an oocyte by a sperm. will depend on which allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are carried by the gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. that form it. Let's consider a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) “$A$” for which two allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. exist, $A$ and $a$. Two parents, both of which are $\frac{A}{a}$ heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other., mate to form offspring, or progenyplugin-autotooltip__defaultProgeny: a synonym for offspring.:

When heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. mate, their offspring may have different phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.: If $A$ is dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. to $a$, the two possible phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. will be the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of $\frac{a}{a}$ (the recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.) or the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of $\frac{A}{A}$ and $\frac{A}{a}$ (the dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.). See below for notes on how we write genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. similar to mathematical fractions.

When we do genetic crosses in breeding experiments, it is important to know the genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. of the parents. But as you can see from the example above, progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. from the cross with the dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. trait could have either $\frac{A}{A}$ or $\frac{A}{a}$ as their genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally.. Without knowledge of what geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $A$ is, we can only make inferences as to an organism's genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. by looking at its phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.. One way to be more certain about genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. is to start with populations that we know to be homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. for a particular geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). One way to do this is to keep inbreeding individuals (that is, breeding siblings or close relatives together for multiple generations) until all crosses among related individuals always produce identical or nearly identical offspring. This generates a true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and. We can assume that individuals from a true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. population are homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. for most genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (or homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. if they are bred for that particular mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.). Laboratory wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. strains are assumed to be homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. for nearly all genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-).

Say we have a true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. lineplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and of mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. fruit flies. These flies are paralyzed compared to wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. flies that have normal mobility. We name this mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. $shibire$ (hiragana: しびれ), which means “numb” in Japanese. We assume there is a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (the $shibire$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), abbreviated $shi$) that is mutated in this strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and, and we assume it has the genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. $\frac{shi^-}{shi^-}$, with the “-” superscript indicating that this is a mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence.. The “+” sign is usually used to indicate a wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence.. Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. and genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are traditionally named after mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism., and Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. scientists can be very creative in naming their mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.¹⁾. For now, we will use these +/- symbols as superscript. Later, we will use a more streamlined set of symbols.

We can use some of the same ideas presented in Chapter 02 to analyze $shibire$. We can first test to see whether the mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. $shi^-$ alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. is dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. or recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. by crossing true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $shi^-$ flies to true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. ($shi^+$) flies. For simplicity, we don't consider the sex of the mating flies (for now):

The offspring from a cross are known as the F1 (this stands for first filial generation). Geneticists often joke that their children are their F1s. In Fig. 2 , the F1 flies are heterozygousplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. and appear like wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms.. Therefore, the $shi^–$ alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. (relative to the wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms.).

Table 1 above shows a genetic cross and analysis of its outcomes using a Punnett squareplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares.. Many beginning students like using the Punnett squareplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares. because it is intuitive, and it is also usually how they learned it in high school or earlier. As you start to learn more advanced genetic concepts, it is important to learn how to write genetic crosses for diploidplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. organisms and their outcomes using “fractional notationplugin-autotooltip__default plugin-autotooltip_bigFractional notation: a style of genotype notation that uses “fractions”, e.g., $\frac{unc\text{-}4}{+}$. We strongly encourage this notational style as it generally is preferred by genetics researchers.”. An example is given in Fig. 2 above. Genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. are written similar to mathematical fractions, with the genetic contributions of each parent written in the “numerator” and “denominator”. The “$\times$” (pronounced “cross”) symbol is used to indicate a cross, or a mating event. Parents are indicated using the “P” symbol (sometimes P0 is used), and subsequent generations of offspring use the symbols F1, F2, etc. At this point it may not be clear why “fractional notationplugin-autotooltip__default plugin-autotooltip_bigFractional notation: a style of genotype notation that uses “fractions”, e.g., $\frac{unc\text{-}4}{+}$. We strongly encourage this notational style as it generally is preferred by genetics researchers.” is better than using a Punnett squareplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares.. You will soon see that Punnett squaresplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares. work very poorly when crosses get more complex, and they also work poorly for thinking about crossing overplugin-autotooltip__default plugin-autotooltip_bigCrossing over: an event where non-sister chromatids exchange material with each other during meiosis I., which we will see in Chapter 05. You can write genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. in fractional notationplugin-autotooltip__default plugin-autotooltip_bigFractional notation: a style of genotype notation that uses “fractions”, e.g., $\frac{unc\text{-}4}{+}$. We strongly encourage this notational style as it generally is preferred by genetics researchers. either vertically as shown in Fig. 2, or you can also write then horizontally (e.g., $shi^-$/$shi^-$) when typing, for instance (although you can also type vertical fractions now with most modern word processing/typesetting software such as Microsoft Word or $\LaTeX$). When writing horizontally, you can include parentheses or brackets to help reduce ambiguity: for example, ($shi^-$)/($shi^-$) or ($shi^-$/$shi^-$). In general, the vertical method is better and usually preferred.

We can also use complementationplugin-autotooltip__default plugin-autotooltip_bigComplementation: a concept where an additional allele of a gene (usually a wildtype allele) can provide normal function to an organism with a recessive loss of function mutation in that gene. The concept of complementation underlies the complementation test. testing (Chapter 02) to analyze other Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that have similar phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. to ask if those mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. are allelic with other mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. with similar phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.. Say we have isolated a different paralyzed Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that we temporarily call $par$. We start with a true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $par^-$ strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and (i.e., we can assume that its genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. is $\frac{par^-}{par^-}$) that we mate to wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms.. We find that the $par$ mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is not expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. in the F1 heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. (i.e., the F1 heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. are not paralyzed) and therefore is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele..

Since both the $par^-$ and $shi^-$ mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. are recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., we can do a complementation testplugin-autotooltip__default plugin-autotooltip_bigComplementation test: a genetic experiment that answers the question: how many different genes are represented within a collection of mutants? (Figure 3). For this test, we cross a true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $par^–$ strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and to a true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $shi^–$ strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and. Just like we saw in Chapter 02, the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of the F1 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. tells us if $shi$ and $par$ are allelic to each other. The possible outcomes and interpretations are shown in Table 2.

If $par^-$ and $shi^-$ complementplugin-autotooltip__default plugin-autotooltip_bigComplement: used to describe the relationship between two recessive mutants. If a diploid created by mating the two mutants has a wildtype phenotype, we say the two mutants complement each other., this means we can think of the parents in Figure 3 as having the genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. $\frac{par^-}{par^-} \cdot \frac{shi^+}{shi^+}$ and $\frac{par^+}{par^+} \cdot \frac{shi^-}{shi^-}$. On the other hand, if $par^-$ and $shi^-$ do not complementplugin-autotooltip__default plugin-autotooltip_bigComplement: used to describe the relationship between two recessive mutants. If a diploid created by mating the two mutants has a wildtype phenotype, we say the two mutants complement each other., this implies that $par^-$ and $shi^-$ are mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in the same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (i.e., $par = shi$). Since $shibire$ has already been named and $par$ is just a temporary name, we preferably write the outcome of the cross as $\frac{shi^-}{shi^-}$ instead of $\frac{par^-}{shi^-}$.

In the above discussion, we are assuming that the true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $shibire$ lineplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and contains a mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (the $shibire$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)). However, it is entirely possible that there are mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in multiple genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), all of which (either singly or in combination) cause the paralyzed phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. we observe. For instance, it is possible that two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), $shi1$ and $shi2$, are mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in our true-breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $shibire$ lineplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and and it is the combinatorial effect of two mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. that is causing paralysis. In this case we can re-write the cross in Fig. 2 as:  

Provided that the $shi1$ and $shi2$ mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. are recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., the F1 offspring in Figure 4 will have the same non-paralyzed phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. as the F1 offspring in Figure 2. In other words, crossing a paralyzed mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. to wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. (the experiments being done in Figures 2 and 4) tells us that the mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant.(s) is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., but does not (and cannot) tell us how many different mutationsplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. are contributing to the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.. Similarly, the complementation testplugin-autotooltip__default plugin-autotooltip_bigComplementation test: a genetic experiment that answers the question: how many different genes are represented within a collection of mutants? (Figure 3) tells us that “$par$” and $shi$ are different, but it does not (and cannot) tell us whether the paralysis in a $shibire$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. is the result of one mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. or more.

To answer the question of whether the paralysis phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of a $shibire$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. is caused by a single mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. or not, we need to do a different experiment involving the F2 generation. From Figure 2 above, we can take the heterozygoteplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. F1s and perform a sibling crossplugin-autotooltip__default plugin-autotooltip_bigSib cross: a genetic cross wherein males and females from the same brood (i.e., brothers and sisters) are mated to each other. Similar to a self cross. (or sib crossplugin-autotooltip__default plugin-autotooltip_bigSib cross: a genetic cross wherein males and females from the same brood (i.e., brothers and sisters) are mated to each other. Similar to a self cross.). Look more carefully at how allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. will segregate in a cross between heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other.:

What is the probability of a paralyzed fly in the next (F2) generation? The probability is calculated as:

$$ p(a)=\frac{n_a}N $$

where $n_a$ = number of outcomes that satisfy condition $a$, and $N$ = total number of possible outcomes (of equal probability). Probability problems can be solved by accounting for every outcome, but usually it is easier to combine probabilities.

We have not yet discussed linkageplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. (Chapters 4 and 5), but Mendel's original findings showed that each parent contributes one of two allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. from each geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) to the zygoteplugin-autotooltip__default plugin-autotooltip_bigZygote: a cell formed by the fertilization of an oocyte by a sperm.. For our purposes here we can use the product ruleplugin-autotooltip__default plugin-autotooltip_bigProduct rule: in probability theory, the probability of two independent events both occurring (i.e., rolling snake eyes on a pair of dice) is the product of the probability of the individual events (i.e., $\frac{1}{6}\times\frac{1}{6}=\frac{1}{36}$)., which lets us calculate the probability $p$ of events $a$ and $b$ both happening:

Note the product ruleplugin-autotooltip__default plugin-autotooltip_bigProduct rule: in probability theory, the probability of two independent events both occurring (i.e., rolling snake eyes on a pair of dice) is the product of the probability of the individual events (i.e., $\frac{1}{6}\times\frac{1}{6}=\frac{1}{36}$). only applies if events $a$ and $b$ are independent of each other, which is the case here since the alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. from mother does not affect the alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. from the father.

There are only two possible outcomes from our cross; either the progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. are paralyzed, or they are not paralyzed (wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms.). Since all possible probabilities must add up to 1, we can easily calculate the probability of obtaining progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. that are not paralyzed as follows:

Each individual Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. mating event can produce several hundred offspring. With large numbers of progenyplugin-autotooltip__defaultProgeny: a synonym for offspring., the ratio of phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. will mirror the probabilities of the outcomes. Thus, in the F2 generation the phenotypicplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. ratio for not paralyzed: paralyzed = $\frac{3}{4}$: $\frac{1}{4}$ = 3:1. The genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. are:

A 3:1 phenotypicplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. ratio among the F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. in a breeding experiment shows that allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are segregating. Any result other than 3:1 tells us that something other than a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is segregating.

This actually constitutes our second definition of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-): genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are units of inheritance that follow Mendel's Laws. A phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is determined by a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) if it displays a 3:1 dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. to recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. ratio in a monohybrid crossplugin-autotooltip__default plugin-autotooltip_bigMonohybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's First Law. See Chapter 03.. Historically, this was the first and original definition of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) developed by Gregor Mendel in the 1860s. Mendel was able to detect geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) segregation of single genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in pea plants because he looked at simple traits and started with true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. strains. That genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) with two allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. segregate in this way is often described as Mendel's First Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's First Law: also called Mendel's Law of Segregation. It states that during gamete formation, the two alleles at a gene locus segregate from each toher; each gamete has an equal opportunity of containing either allele..

Now let’s look at the properties of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) segregation when two different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are involved. Here we introduce a new Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. called $vestigial$ ($vg$ for short). $vg$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. flies have misshapen wings compared to wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. (Figure 6); the vg mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. we are talking about is also recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele..

We cross true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain. $shi$ and $vg$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. together to see what happens:

As before, we ignore the sex of the parents for now. A few notes about how we wrote the cross above:

• The $\frac{+}{+}$ in the genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. of the first parent indicates that it is homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. for $vg^+$.
• The $\frac{+}{+}$ in the genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. of the second parent indicates that it is homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. for $shi^+$.
• Since Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. are obligate diploidsplugin-autotooltip__default plugin-autotooltip_bigObligate diploid: a species wherein all cells except gametes are diploid., $shi$ implies $\frac{shi}{shi}$. A really lazy geneticist will just write: $shi \times vg$. This means exactly the same thing as what is written in Figure 7, but we will try to write as clearly as we can in this book without being too lazy.

Since both the parents are true breedingplugin-autotooltip__default plugin-autotooltip_bigTrue breeding: a true breeding strain is one that has been inbred for multiple generations. We assume that the vast majority of loci are homozygous in a true breeding strain., the gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. from the first parent will all be ($shi$ $\cdot$ +) and from the second parent (+ $\cdot$ $vg$). These gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. will then give an F1 generation whose genotypeplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. are all $\frac{shi}{+} \cdot \frac{+}{vg}$. It's also OK to write this as $\frac{shi}{+} \cdot \frac{vg}{+}$, although it's customary to write the gameteplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. contributions from each parent on the “numerator” and “denominator” in a consistent way.

Mendel discovered that allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) segregate independently of each other (he did not know about the exception, which is when genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes.; see Chapter 05). If $shi$ and $vg$ segregate independently of each other the same way as Mendel observed, we can calculate the probabilities of all possible F2 phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. resulting between a sib crossplugin-autotooltip__default plugin-autotooltip_bigSib cross: a genetic cross wherein males and females from the same brood (i.e., brothers and sisters) are mated to each other. Similar to a self cross. between F1 individuals. Mendel called this kind of cross a dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03..

The possible F2 outcomes are given in Table 3.3 and can be calculated also using the product ruleplugin-autotooltip__default plugin-autotooltip_bigProduct rule: in probability theory, the probability of two independent events both occurring (i.e., rolling snake eyes on a pair of dice) is the product of the probability of the individual events (i.e., $\frac{1}{6}\times\frac{1}{6}=\frac{1}{36}$)., since our assumption is that $shi$ and $vg$ segregate independently of each other:

The ratio of the four different possible F2 phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. shown in Table 3 is $\frac{9}{16}:\frac{3}{16}:\frac{3}{16}:\frac{1}{16}$, or 9:3:3:1. Beginning geneticists will often solve the problem above by figuring out all the genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. first using a 4×4 Punnett squareplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares. (which also assumes independent assortment). You are strongly discouraged from continuing to use Punnett squaresplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares. (although since there are 16 different possible genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally., a 4×4 Punnett squareplugin-autotooltip__default plugin-autotooltip_bigPunnett square: a $n \times n$ grid used to determine the genotypes of a cross involving $n$ different genes. WE strongly discourage the use of Punnett squares. can be helpful in figuring those out).

Calculating the probabilities (and determining all 16 possible genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally.) for the outcomes of a dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03. is not difficult, but it is complex. A more convenient way to look at segregation of two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is by a test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03. of the F1 heterozygoteplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. to a homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. testerplugin-autotooltip__default plugin-autotooltip_bigTester: a strain that is homozygous mutant at $n$ different loci that is used in a test cross. See Chapter 03. individual (assuming such a thing exists in your lab):

The four possible gameteplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. genotypesplugin-autotooltip__default plugin-autotooltip_bigGenotype: the combination of alleles within an organism or strain. When used as a verb, it means to determine the genotype experimentally. from the F1 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. will be ($shi \cdot +$), ($+ \cdot vg$), ($shi \cdot vg$), and ($+ \cdot +$), and the probability of obtaining any one of those is $\frac{1}{4}$. However, the homozygousplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other. recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele. testerplugin-autotooltip__default plugin-autotooltip_bigTester: a strain that is homozygous mutant at $n$ different loci that is used in a test cross. See Chapter 03. can only produce ($shi \cdot vg$) gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes.. In other words, the probability $p$ of the testerplugin-autotooltip__default plugin-autotooltip_bigTester: a strain that is homozygous mutant at $n$ different loci that is used in a test cross. See Chapter 03. producing a ($shi \cdot vg$) gameteplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. is $p=1$. Thus, the possible F2 outcomes for this cross are:

Note that the frequency of the different F2 phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. from the test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03. is exactly the same as the frequency of the different gametesplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. that can form from the F1 heterozygoteplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other.. This makes interpreting test crosses easier than a dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03., especially when doing a real-life experiment. In this case we can easily observe that each F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. receives either the $shi$ or + alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. and receives either the $vg$ or + alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence.. The test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03. clearly shows geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) segregation for each geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Also note that in a test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03., you will get two kinds of outcomes: parental types, which resemble the original parents; and recombinantplugin-autotooltip__default plugin-autotooltip_bigRecombinant: (adj.) Describing something that has undergone recombination, e.g., recombinant DNA or recombinant offspring. “Non-parental” is a synonym when referring to organisms. (n.) Something that has undergone recombination, e.g., “This fly is a recombinant.” types, which do not resemble the parents (Figure 7). This becomes very convenient when we look at mappingplugin-autotooltip__default plugin-autotooltip_bigGenetic mapping: a term describing a variety of different experimental approaches used to determine the physical locations of genes on chromosomes. in Chapter 05.

No matter if we do a dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03. between F1 heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. (and get a 9:3:3:1 ratio) or if we do a test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03. with F1 heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. (and get a 1:1:1:1 ratio), either outcome shows that the two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) $shi$ and $vg$ segregate independently of each other. That is, the segregation of allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. for one geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) does not affect that of another geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Mendel called this independent assortment, and this phenomenon is often referred to as Mendel's Second Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's Second Law: also called the Law of Independent Assortment. It states that alleles from each genetic loci segregate independently of each other. This “law” actually only applies to unlinked genes..

For now, it seems like regardless of whether you look at it from a 9:3:3:1 “dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03.” perspective or a 1:1:1:1 “test crossplugin-autotooltip__default plugin-autotooltip_bigTest cross: a genetic cross devised by Gregor Mendel that allows a researcher to easily determine the genotype of an individual that appears wildtype but has an unknown genotype. This assumes you have a tester strain readily available. See Chapter 03.” perspective, Mendel's Second Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's Second Law: also called the Law of Independent Assortment. It states that alleles from each genetic loci segregate independently of each other. This “law” actually only applies to unlinked genes. is not as useful as Mendel's First Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's First Law: also called Mendel's Law of Segregation. It states that during gamete formation, the two alleles at a gene locus segregate from each toher; each gamete has an equal opportunity of containing either allele.. The First Law gives you information about whether a mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is caused by mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) – this seems to be useful. The Second Law appears to describe a phenomenon (allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. for different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) segregate independently of each other) but doesn't seem to give useful information about the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) themselves. In Chapters 04 and 05, you will see that the ideas underlying the Second Law set the stage for understanding linkageplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes., which provide a new definition of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) based on position.

Historically, Mendel's First and Second Laws also set the stage for chromosome theoryplugin-autotooltip__default plugin-autotooltip_bigChromosome theory: the theory that genes, the basic unit of inheritance, are located on chromosomes. First demonstrated by Thomas Hunt Morgan in 1911 using Drosophila and sex-linked mutants., which we discuss in Chapter 04. Chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. behave in meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs). the same way that Mendel showed genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) to behave. This is now a good time to review Chapter 01. Each gameteplugin-autotooltip__default plugin-autotooltip_bigGamete: a specialized (usually haploid) cell used for sexual reproduction. Eggs (oocytes) and sperm are gametes. receives only one of the two homologous chromosomesplugin-autotooltip__default plugin-autotooltip_bigHomologous chromosomes: highly similar but non-identical chromosomes that are the same size and contain the same genes. from its mother cellplugin-autotooltip__default plugin-autotooltip_bigMother/daughter cells: in cell division, a mother cell divides to form two daughter cells., a behavior that is analogous to segregation of allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (Mendel's First Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's First Law: also called Mendel's Law of Segregation. It states that during gamete formation, the two alleles at a gene locus segregate from each toher; each gamete has an equal opportunity of containing either allele.). Furthermore, the relative orientation of different homologous chromosomeplugin-autotooltip__default plugin-autotooltip_bigHomologous chromosomes: highly similar but non-identical chromosomes that are the same size and contain the same genes. pairs (tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I.) at the first meiotic cell division is random, which is analogous to independent assortment of two different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (Mendel's Second Lawplugin-autotooltip__default plugin-autotooltip_bigMendel's Second Law: also called the Law of Independent Assortment. It states that alleles from each genetic loci segregate independently of each other. This “law” actually only applies to unlinked genes.). To scientists in the early 20th century when chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. were just recently discovered and Mendel was just being re-discovered, this correlation strongly suggested that genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are physically located on chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.. In Chapter 04, we will see the experimental evidence that supported this idea.

You might also be wondering at this point: what if two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) happen to be on the same chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.? We address this later in Chapters 04 and 05. Mendel got lucky - the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) he chose to study were all unlinkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. to each other. If he had chosen genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that were linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. to each other (closely positioned on the same chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.) he may not have been able to draw the same conclusions that he did regarding his Second Law.

Let's step outside the box a little and see how Mendel's Laws can be applied to a very interesting problem in the evolution of domestic corn (maize). Domestic corn is derived from its wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. progenitor, a plant called teosinte (Figure 10). Native Americans in what is now Mexico likely started to domesticate teosinte around 6000 years ago.

There is no historical record of how the breeding was done to produce maize, but there is a genetic record of the differences between teosinte and maize recorded in the genomicplugin-autotooltip__default plugin-autotooltip_bigGenome: a dataset that contains all DNA information of an organism. Most of the time, this also includes annotation and curation of that information, e.g., the names, locations, and functions of genes within the genome. As an adjective (“genomic”), this usually is used in the context of differences between these two species. Maize and teosinte can be crossed to give viable progenyplugin-autotooltip__defaultProgeny: a synonym for offspring., which can then be self-crossed. Because plants are hermaphroditic, a self-cross is basically the same thing as a sib crossplugin-autotooltip__default plugin-autotooltip_bigSib cross: a genetic cross wherein males and females from the same brood (i.e., brothers and sisters) are mated to each other. Similar to a self cross.:

Of the 50,000 F2 plants that are produced, around 100 (or 1 in 500) look like teosinte and around 100 (also 1 in 500) look like maize. The remaining F2 plants look like neither maize nor teosinte. How many genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) contribute to the differences between the two kinds of plants? Let’s designate the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that differ as $A, B, C, D$ … etc.

For each geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) let's imagine there are two allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence.: the alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. present in teosinte and the alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. present in maize. For the $A$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) we will designate these allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. $A_T$ and $A_M$ respectively. For the $B$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) there will be allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. $B_T$ and $B_M$, and so on, for all the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that are different.

Let’s follow the $A$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) through the cross between maize and teosinte:

Because the F1 don't look like either parent, let's assume that the allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are codominantplugin-autotooltip__default plugin-autotooltip_bigCodominant: refers to two alleles of the same gene that, when both present, will express the phenotypes of both alleles. An example is the $A$ and $B$ alleles for human bloodtype; some humans have $AB$ bloodtype because the $A$ and $B$ alleles are codominant, whereas the $O$ allele is recessive to both $A$ and $B$.. That is to say, the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. is different than either homozygoteplugin-autotooltip__default plugin-autotooltip_bigHomozygous: a state for a diploid organism wherein the two alleles for a gene are identical to each other.. This is not the only possible explanation, but for now let's just keep it simple.

With regard to the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. conferred by the $A$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), $\frac{1}{4}$ of the F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. will look like maize, $\frac{1}{4}$ will look like teosinte, and $\frac{2}{4}$ will look like neither (see Exercise 2 at the end of the chapter). By a similar logic, with regard to the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. conferred by the $B$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), $\frac{1}{4}$ of the F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. will look like maize, $\frac{1}{4}$ will look like teosinte, and $\frac{2}{4}$ will look like neither. Using the product ruleplugin-autotooltip__default plugin-autotooltip_bigProduct rule: in probability theory, the probability of two independent events both occurring (i.e., rolling snake eyes on a pair of dice) is the product of the probability of the individual events (i.e., $\frac{1}{6}\times\frac{1}{6}=\frac{1}{36}$)., we can calculate what proportion of F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. will phenotypically be maize-like with regards to two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), i.e., the A and B genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-):

Similarly, for three genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) the probability will be $\frac{1}{64}$ ($\frac{1}{4} \times \frac{1}{4} \times \frac{1}{4}$ or $4^{-3}$). For four genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) it will be $\frac{1}{256}$ (or $4^{-4}$), and for five genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) it will be $\frac{1}{1024}$ (or $4^{-5}$). Since around $\frac{1}{500}$ of the F2 progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. look like maize, the conclusion is that approximately 4 to 5 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) differ between wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. corn (teosinte) and domestic corn (maize). Using modern molecular genetics, it has been confirmed that there are about five genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) with significantly different allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. between maize and teosinte. Several of these genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) have been located using mappingplugin-autotooltip__default plugin-autotooltip_bigGenetic mapping: a term describing a variety of different experimental approaches used to determine the physical locations of genes on chromosomes. methods.

If you revisit Chapter 01 at this time, you will see that both Mendel's First and Second Laws relate directly to meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs).. The patterns of alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. segregation as described by Mendel match nearly perfectly with the patterns of chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. segregation in meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs).. It is very important for students of genetics to know that Mendel's view of genetics helps us understand the relationship between segregation patterns of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs).. However, it is equally important for students to realize that Mendel made these discoveries in the 1860s, and in many ways Mendel's Laws are very outdated both in terms of their conclusions and how they are described. In fact, continuing to call his discoveries “Laws” is a misnomer reflecting a great deal of European cultural bias; his view of heredity is much too simplistic, and there are many exceptions to Mendel's Laws as he described them, such as linkageplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes., codominanceplugin-autotooltip__default plugin-autotooltip_bigCodominant: refers to two alleles of the same gene that, when both present, will express the phenotypes of both alleles. An example is the $A$ and $B$ alleles for human bloodtype; some humans have $AB$ bloodtype because the $A$ and $B$ alleles are codominant, whereas the $O$ allele is recessive to both $A$ and $B$., epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway., epigenetic inheritance, allelic series, etc., most of which we don't cover in detail in this book (many of these concepts make more sense once you stop thinking like Mendel and start thinking about genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) from a molecular perspective anyway). Once you reach Chapter 06, it's important to relate everything you learn about genetics to the physical definition of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins., rather than view Mendel as dogma. View Mendel as a beginner’s learning tool instead.

Exercise 1: See Figure 3 above. What would the F2 outcomes be from an F1 dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03. if $shi$ and $par$ were allelic? What if they were not allelic? Remember that the $shi$ and $par$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. have identical phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.!

Exercise 2: This question relates to the teosinte experiment. In the F2 generation arising from self-crossing the F1, the ratio for the $A_M$ and $A_T$ allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. segregating is $\frac{A_M}{A_M}∶\frac{A_M}{A_T}∶\frac{A_T}{A_T} = 1:2:1$. Using what you have learned about how a single geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) should segregate in a dihybrid crossplugin-autotooltip__default plugin-autotooltip_bigDihybrid cross: a cross, developed by Gregor Mendel, that illustrates Mendel's Second Law. See Chapter 03., write out the cross in fractional notationplugin-autotooltip__default plugin-autotooltip_bigFractional notation: a style of genotype notation that uses “fractions”, e.g., $\frac{unc\text{-}4}{+}$. We strongly encourage this notational style as it generally is preferred by genetics researchers. and show how this ratio is derived using probability calculations.