What is the term that describes an individual that has two identical copies of a gene?

A gene is the basic physical and functional unit of heredity. Genes are made up of DNA. Some genes act as instructions to make molecules called proteins. However, many genes do not code for proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. An international research effort called the Human Genome Project, which worked to determine the sequence of the human genome and identify the genes that it contains, estimated that humans have between 20,000 and 25,000 genes.

Every person has two copies of each gene, one inherited from each parent. Most genes are the same in all people, but a small number of genes (less than 1 percent of the total) are slightly different between people. Alleles are forms of the same gene with small differences in their sequence of DNA bases. These small differences contribute to each person’s unique physical features.

Scientists keep track of genes by giving them unique names. Because gene names can be long, genes are also assigned symbols, which are short combinations of letters (and sometimes numbers) that represent an abbreviated version of the gene name. For example, a gene on chromosome 7 that has been associated with cystic fibrosis is called the cystic fibrosis transmembrane conductance regulator; its symbol is CFTR.

• Since human cells carry two copies of each chromosome they have two versions of each gene. These different versions of a gene are called alleles.
• Alleles can be either dominant or recessive.
• Dominant alleles show their effect even if the individual only has one copy of the allele (also known as being heterozygous). For example, the allele for brown eyes is dominant, therefore you only need one copy of the ‘brown eye’ allele to have brown eyes (although, with two copies you will still have brown eyes).
• If both alleles are dominant, it is called codominance. The resulting characteristic is due to both alleles being expressed equally. An example of this is the blood group AB which is the result of codominance of the A and B dominant alleles.
• Recessive alleles only show their effect if the individual has two copies of the allele (also known as being homozygous). For example, the allele for blue eyes is recessive, therefore to have blue eyes you need to have two copies of the ‘blue eye’ allele.

Illustration to show the inheritance of dominant and recessive alleles for eye colour.
Image credit: Genome Research Limited

What are sex-linked genes?

• Some genes are found on the sex chromosome, X.
• These genes are inherited with the X chromosome (from the mother if it is a boy or from either mother or father if it is a girl).
• Females have two X chromosomes (XX), while males have one X chromosome and one Y chromosome (XY).
• This means females have two alleles for X-linked genes while males only have one.
• Some genetic diseases, are caused by sex linked genes, for example haemophilia.
• The allele for haemophilia is recessive so two copies are needed for a female to have the disease
• However, because males only have one X chromosome, they only need one copy of the haemophilia allele to have the disease.
• This means haemophilia is much more common in males than in females.

For example:

Functioning allele = H

Haemophilia allele = h

XH XH = healthy female

XH Xh = carrier female

Xh Xh = haemophilia female

XH Y = healthy male

Xh Y = haemophilia male

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Any organism is a by-product of both its genetic makeup and the environment. To understand this in detail, we must first appreciate some basic genetic vocabulary and concepts.  Here, we provide definitions for the terms genotype and phenotype, discuss their relationship and take a look at why and how we might choose to study them. 

An individual’s genotype is the combination of alleles that they possess for a specific gene. An individual’s phenotype is the combination of their observable characteristics or traits. While an organism’s genotype is directly inherited from its parents, phenotype is merely influenced by genotype. Environmental factors can also affect phenotype. 

What is the definition of a genotype? 

In biology, a gene is a section of DNA that encodes a trait. The precise arrangement of nucleotides (each composed of a phosphate group, sugar and a base) in a gene can differ between copies of the same gene. Therefore, a gene can exist in different forms across organisms. These different forms are known as alleles. The exact fixed position on the chromosome that contains a particular gene is known as a locus.A diploid organism either inherits two copies of the same allele or one copy of two different alleles from their parents. If an individual inherits two identical alleles, their genotype is said to be homozygous at that locus.However, if they possess two different alleles, their genotype is classed as heterozygous for that locus. Alleles of the same gene are either autosomal dominant or recessive. An autosomal dominant allele will always be preferentially expressed over a recessive allele.

The subsequent combination of alleles that an individual possesses for a specific gene is their genotype.  

Genotype examples

• A gene encodes eye color.
• In this example, the allele is either brown, or blue, with one inherited from the mother, and the other inherited from the father.
• The brown allele is dominant (B), and the blue allele is recessive (b). If the child inherits two different alleles (heterozygous) then they will have brown eyes. For the child to have blue eyes, they must be homozygous for the blue eye allele. 
   

Figure 1: Inheritance chart detailing how an individual may inherit blue or brown eyes depending on the alleles carried by their parents, with the brown eye color allele being dominant and the blue eye color allele being recessive. Other examples of  genotype include:

• Hair color
• Height
• Shoe size

The sum of an organism’s observable characteristics is their phenotype. A key difference between phenotype and genotype is that, whilst genotype is inherited from an organism’s parents, the phenotype is not.

Whilst a phenotype is influenced the genotype, genotype does not equal phenotype. The phenotype is influenced by the genotype and factors including:

• Epigenetic modifications
• Environmental and lifestyle factors 

Figure 2: Flamingos are naturally white in color, it is only the pigments in the organisms that they eat that cause them to turn vibrantly pink.

Environmental factors that may influence the phenotype include nutrition, temperature, humidity and stress. Flamingos are a classic example of how the environment influences the phenotype. Whilst renowned for being vibrantly pink, their natural color is white – the pink color is caused by pigments in the organisms in their diet. A second example is an individual's skin color. Our genes control the amount and type of melanin that we produce, however, exposure to UV light in sunny climates causes the darkening of existing melanin and encourages increased melanogenesis and thus darker skin. Observing the phenotype is simple – we take a look at an organism’s outward features and characteristics, and form conclusions about them. Observing the genotype, however, is a little more complex. Genotyping is the process by which differences in the genotype of an individual are analyzed using biological assays. The data obtained can then be compared against either a second individual’s sequence, or a database of sequences.

Previously, genotyping would enable only partial sequences to be obtained. Now, thanks to major technological advances in recent years, state-of-the-art whole genome sequencing.

Figure 3: A workflow depicting the various steps of whole genome sequencing (WGS).

(WGS) allows entire sequences to be obtained. An efficient process that is increasingly affordable, WGS involves using high-throughput sequencing techniques such as single-molecule real-time (SMRT) sequencing to identify the raw sequence of nucleotides constituting an organism’s DNA. 

WGS is not the only way to analyze an organism’s genome - a variety of methods are available.

Understanding the relationship between a genotype and phenotype can be extremely useful in a variety of research areas.

A particularly interesting area is pharmacogenomics. Genetic variations can occur in liver enzymes required for drug metabolism, such as CYP450. Therefore, an individual’s phenotype, i.e. their ability to metabolize a specific drug, may vary depending on which form of the enzyme-encoding gene they possess. For pharmaceutical companies and physicians, this knowledge is key for determining recommended drug dosages across populations.

Making use of genotyping and phenotyping techniques in tandem appear to be better than using genotype tests alone. In a comparative clinical pharmacogenomics study, a multiplexing approach identified greater differences in drug metabolism capacity than was predicted by genotyping alone. This has important implications for personalized medicine and highlights the need to be cautious when exclusively relying on genotyping.

Using animal models such as mice, scientists can genetically modify an organism so that it no longer expresses a specific gene – known as knockout mice. By comparing the phenotype of this animal to the wild type phenotype (i.e. the phenotype that exists when the gene has not been removed), we can study the role of certain genes in delivering certain phenotypes.

The Mouse Genome Informatics (MGI) initiative has compiled a database of thousands of phenotypes that can be created and studied, and the genes that must be knocked out to produce each specific phenotype.