Genetics of Organisms

The genetics* of organisms deals with the physical expression of gene at the organismal level and the organization and transfer of genetic material as it passes from generation to generation during reproduction.

Alleles, Genotype and Phenotype

Genetics is the study of the organization, expression and transfer of heritable information. The ability for information to pass from generation to generation requires a mechanism. Living organisms use DNA. DNA is a chain, or polymer, of nucleic acids. Individual polymers of DNA can contain hundreds of millions of individual nucleic acids molecules. These long DNA strands are called chromosomes. Information is contained in the order of the individual nucleic acids that make up the DNA polymer. The use of DNA as the information molecule is a universal property of all life on Earth. Genetic information is read by our cellular machinery and allows our bodies to synthesize the many enzymes and proteins required for life.



Genetic information is carried in discrete units called genes. Each gene contains the information required to synthesize individual components of an organism’s cellular machinery. The coordinated expression of many different genes is responsible for an organism’s growth and activity. Within an individual species, genes occur in set locations on chromosomes. This allows their locations to be mapped. The position of a specific gene on a chromosome is called its locus.

Variation in the order of nucleic acids in a DNA molecule allow genes to encode enough information to synthesize the huge diversity of different proteins and enzymes needed for life. In addition to differences between genes, the arrangement of nucleic acids can differ between copies of the same gene. This results in different forms of individual genes. Different forms of a gene are called alleles.

Organisms that reproduce sexually receive one complete copy of their genetic material from each parent. This is referred to as being diploid.  Matching chromosomes from each parent are called homologous chromosomes. Diploid organisms have two copies of every gene. Matching genes from each parent occur at the same location on homologous chromosomes.

A diploid organism can either have two copies of the same allele or one copy each of two different alleles. Individuals who have two copies of the same allele are said to be homozygous at that locus. Individuals who receive different alleles from each parent are said to be heterozygous at that locus. The alleles an individual has at a locus is called a genotype. The genotype of an organism is often expressed using letters. The visible expression of the genotype is called an organism’s phenotype.

Alleles are not created equal. Some alleles mask the presence others. Alleles that are masked by others are called recessive alleles. Recessive alleles are only expressed when an organism is homozygous at that locus. Alleles that are expressed regardless of the presence of other alleles are called dominant.

If one allele completely masks the presence of another at the same locus, that allele is said to exhibit complete dominance. However, dominance is not always complete. In cases of incomplete dominance, intermediate phenotypes are possible.

The illustration explores the relationship between the presence of different alleles at a specific locus and an organism's genotype and phenotype. The organism in the model is a plant. It is diploid and the trait is flower color. Below there is also a youtube video demonstrating the use of the illustration and a problem set you can use to test your understanding of these concepts.

Demonstration video:

Gene interactions can be quite complicated. The example above demonstrates a simple situation in which a single gene corresponds to an individual trait. In more complicated cases, multiple genes can influence  individual traits. This is called polygenic inheritance. In these situations the relationship between specific alleles and characteristics is not as straightforward.

In his famous pea plant studies, Mendel studied seven traits that have the characteristics needed to allow the observation of inheritance of discrete traits. The traits he studied were seed shape, seed color, flower color, seed pod shaped, seed pod color, flower position and plant stature.

Among the major contributions of Mendel's work was the understanding that information was passed from one generation to the next in discrete units rather than through blending.

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Punnett Square

During sexual reproduction, a parent is equally likely to pass on to its offspring either of the two alleles it has at each genetic locus. This makes it possible to list and estimate the probability of specific genotypes being produced from the pairing of two individuals. Given two allele from each parent, four allele combinations are possible. These combinations and their probabilities can be readily visualized using a Punnett square.

To set up a single locus Punnett Square, the genotype of each parent is placed on the sides of a four chambered box. One parent’s alleles are placed across the top. The alleles of the other parent are placed down one side. The alleles on the edges guide how the central squares are filled in. Once complete, a Punnett square shows the genotypes possible from crossing two individuals. Each of the four boxes in the square contains one of the four possible genotypes. The genotype in each box has a 25% probability of occurring every time the two individuals are crossed. If two boxes contain the same genotype, the probability of that genotype occurring doubles to 50%.

Punnett squares are most commonly used to examine genotype probabilities from one genetic locus at a time. They can be used to look at more than one locus at time, but some find the resulting diagrams complicated and difficult to interpret.

The model below illustrates the use of a Punnett Square to determine the possible genotypes that can arise from mating two individuals with known genotypes. The organism in the model is a plant. The plant is diploid. The trait is flower color. Below the illustration is a youtube video demonstrating its use. There is also a problem set you can use to test your understanding of these concepts.



Video Demonstration
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Genotype and Phenotype Probabilities

Patterns of genetic inheritance obey the laws of probability. In a monohybrid cross, where the allele*s present in both parents are known, each genotype* shown in a Punnett Square* is equally likely to occur. Since there are four boxes in the square, every offspring produced has a one in four, or 25%, chance of having one of the genotypes shown.



Like flipping a coin, previous matings do not influence the results of subsequent matings. Because of random variation, the actual number of each genotype produced over a series of matings (or crosses) between two individuals will differ slightly from the expected 25% per box.

The illustration above explores how the probabilities predicted by a monohybrid Punnett Square relate to the actual pattern of genotypes and phenotype*s produced from repeatedly crossing two individuals.

Test your understanding of genotype and phenotype probabilities

Video Overview

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X-Linked Inheritance

Chromosome*s that both males and females possess in matched sets are called autosome*s. The X and Y-chromosomes that determine the sex of an individual are called allosome*s. Males have one X and one Y-chromosome while females have two X-chromosomes. Due to the differences between the X and Y-chromosomes, the number and type of genes inherited by an individual depends on its sex. The genes present on the X and Y-chromosomes are called sex-linked genes. Sex-linked genes and their related traits are further distinguished as either X-linked or Y-linked depending on which chromosome they are located.

With both an X and a Y-chromosome, males inherit both X and Y-linked traits, while females only inherit X-linked traits. Since males have only one copy of each sex chromosome, they are hemizygous for all sex-linked genes and they always express the phenotype* of the allele* they get. In other words, their phenotypes always match their genotype*s. Females get two copies of X-linked genes, so they demonstrate the more typical dominant-recessive expression patterns of non-sex linked traits. These distinctions cause expression patterns of sex-linked traits to differ between male and female offspring.

Since the X-chromosome is bigger and contains more genes than the Y-chromosome, most sex-linked traits are X-linked traits.

Wild-type fruit flies have dark red eyes, but there are recessive alleles of this eye color gene (called the white gene) that cause individuals to have white eyes. As recessive trait, the white eye phenotype is masked by the presence of a wild-type (red encoding) allele. If the white gene were on an autosome, it would exhibit classical Mendelian inheritance patterns . However, the gene is on the X-chromosome, making it an excellent illustration of sex-linked inheritance patterns.


Select one male and one female individual for the P1 generation and click 'begin' to explore eye color inheritance patterns in fruit flies:


Since control of eye color is encoded by a gene on the X-chromosome, females (XX) carry two copies and males (XY) only carry one. In females, the presence of a dominant red encoding allele (XW) will produce red eyes even if the individual in heterozygous for the white allele. Females can be

  • Homozygous dominant for the red encoding allele - genotype: XWXW; phenotype: red eyes.
  • Heterozygous - genotype XWXw; phenotype: red eyes.
  • Homozygous recessive with two white encoding alleles - genotype XwXw; phenotype white eyes.

With only one copy of the X-chromosome, all males are hemizygous for this gene. They have only two options:

  • Hemizygous dominant - genotype: XWY; phenotype: red eyes
  • Hemizygous recessive - genotype: XwY; phenotype: white eyes.

The difference between sex-linked inheritance patterns and classic Mendelian patterns can be shown by observing the ratio of male and female red and white-eyed individuals produced with reciprocal cross*es. Reciprocal crosses involve crossing true breeding red and white-eyed individuals.

Two reciprocal crosses can be performed: a true breeding red-eyed female with a white-eyed male and a true breeding white-eyed female with a red-eyed male.

Performing the first reciprocal cross: a true breeding red-eyed female (homozygous dominant) with a true breeding white-eyed male (hemizygous recessive) results in an F1 generation comprised entirely of red-eyed individuals. 100% red-eyed individuals is consistent what would be predicted based on Mendelian inheritance of a recessive allele. However, with an X-linked gene, the reason for red eyes differs between males and females.

All of the female offspring are heterozygous receiving an X-chromosome with a red allele from their mother and an X-chromosome with the white allele from their father. The presence of the red allele masks the presence of the white allele. Male offsprings only have one X-chromosome which they received from their female parent. In this reciprocal cross that allele has encode for red eyes. So, females are red-eyed because the presence of the recessive copy is masked. Males are red-eyed because they only have one copy of the gene and that copy is for the red allele.

The females’ phenotype and genotype are consistent with the patterns discovered by Mendel, but the males, as hemizygotes, are not. The differences between the sexes become more apparent when the red-eyed F1 male and red-eyed F1 females are crossed. The results of this cross produce a 3:1 ratio of red-eyed to white-eyed individuals, but all of the white-eyed individuals are male. No females have white eyes because they received one of their X-chromosomes from their hemizygous dominant, red-eyed father. The male offspring all received their single X-chromosome from the heterozygous female parent, so half received a red allele, and half received a white allele.

Inheritance patterns with the other reciprocal cross (hemizygous dominant male with homozygous recessive female) diverge from the Mendelian pattern more quickly. The F1 generation contains an equal proportion of white and red-eyed individuals, but all males have white eyes and all females have red eyes. Crossing these F1’s again results in 1:1 ratio of red and white-eyed individuals, but in the F2, half the females offspring and half the male offspring have red eyes.

In both of these reciprocal crosses, patterns in inheritance beyond the F2 generation vary depending on which F2 individuals are chosen for the cross.

The fact that males are hemizygous for sex-linked alleles is the reason X-linked recessive phenotypes are more commonly observed in males. Females can be heterozygous for a trait and therefore carry the recessive allele without expressing it. These carrier females have a 50% chance of passing the recessive alleles to their male offspring. These male offspring can not be carriers. If they receive the recessive allele, they will express the recessive trait.

Females expressing detrimental recessive traits like Hemophilia are particularly rare because the only way for a female to be more than a carrier is for a female carrier to produce a daughter with an affected male. The extreme case of an affected female mating with an affected male produces 100% affected offspring.

Test your understanding of the patterns discussed above with the x-linked gene fill in the blank and multiple choice questions

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