The genotype is the genetic composition of an organism, or the combination of all of an individual organism’s alleles. Alleles are the potential variants of a particular gene.
For example, if a gene controls whether a plant will have blue flowers or white flowers, the genetic variants that lead to those different possibilities that might be inherited by offspring are called alleles.
An organism’s genotype is one of several factors that influences its phenotype, which is the observable expression of its genetic characteristics. The other two factors that influence phenotype are epigenetics and environmental factors.
You can think of genotype as the genetic makeup or the genetic blueprint of an organism. In much the same way that the code behind a software program contains the information the program needs to run, a genotype contains the particular genes necessary to “run” the organism.
TL;DR (Too Long; Didn't Read)
A genotype is the genetic makeup of an organism. For each individual, it describes the specific combination of alleles that the organism inherited from its parents. A phenotype is the genotype's outward expression in the environment. Mutations can change the genotype, and therefore, the phenotype.
Mutations Alter the Genotype
The genotype may be altered due to random changes, or mutations, in the genes that offspring inherit from the parents’ DNA. The vast majority are not passed on to offspring because:
- They occur in non-reproductive cells called somatic cells whose DNA is not passed on to offspring.
- They cause dysfunction in the cell, causing the cell to self-destruct.
An organism's genotype does not include mutations that are acquired during an individual’s lifetime because these are not inherited. Mutations caused by excess sun radiation, for example, no more describe an individual’s genetic potential than a scar on a tree trunk where it was pierced by a woodpecker’s beak.
Where Genotype Ends and Phenotype Begins
The genotype-phenotype relationship is inextricable. The genotype is one of the primary influences for the expression of the phenotype. It can be unclear in many situations where the first ends and the second begins.
For instance, very rarely, when a heritable mutation occurs and is passed on to an offspring, the mutation better equips the offspring for survival and reproduction in that environment. It is therefore selected for as the individuals with the mutation thrive, and it spreads in the organism’s population. Over generations, these once-rare mutations may become part of the species’ genome.
But are the pressures of the environment selecting for traits in the organism's genotype or phenotype? Some scientists argue that the environment is influencing the phenotype, since it is only allowing the most fit individuals (in terms of observable traits) to pass on their genes, which influences the genotype.
Allele Dominance and Phenotype
When you inherit a trait such as hair color, you are expressing your phenotype. You inherited one allele from each parent for every gene in your genome. There are usually several possible inherited alleles for any gene. The full genotype is impossible to determine from observing traits in the phenotype.
Dominant alleles paired with recessive alleles cause the phenotypic expression of the dominant allele’s trait. This is also true when dominant alleles are paired together. The only way for recessive alleles’ traits to be expressed is when they are paired together without dominant alleles.
Co-dominance occurs when different alleles are paired together and are both expressed simultaneously. For example, if a flower has co-dominant alleles for red color and white color, the resulting offspring might have pink petals.
Many inherited traits (the majority of human traits, in fact) involve the alleles of more than one gene.
For example, it might seem simple to predict the eye color of two parents’ offspring based on the eye color of the parents. However, a number of genes determine eye color, so the probabilities are more complex. Still, since blue eyes are a recessive trait that cannot be masking another hidden genotype, the odds are very high that if both parents have blue eyes, the baby will too.
Why Look at Genotype When We Have Phenotype?
When an individual expresses a recessive phenotype, such as a cleft chin in humans, it is clear that her genotype is a combination of two recessive cleft chin alleles. But when a human has no cleft chin, this could be because he has two dominant no-cleft alleles, or a combination of one dominant no-cleft allele with a recessive cleft allele.
The only way to know is to look at the genotype using modern scientific techniques that map an individual’s DNA.
Engaging in this genetic analysis might not seem worth it for chins, but separating phenotype from genotype has much more important real-world applications. The science is being used in agriculture, industrial manufacturing and many other fields, but the most immediate and helpful application has to do with human disease.
For example, some people are carriers of serious inherited diseases, which means that the disease is not part of their phenotype – they could appear to be completely healthy – but it is part of their genotype. Without examining the genotype by using an analysis of the chromosomes, the disease could be passed down and show up in the phenotype in their offspring.