The concepts of genotype and phenotype are so intricately connected that they can be difficult to distinguish from each other. The complex relationship between all organisms’ genotypes and phenotypes was a mystery to scientists until the past 150 years. The first research to accurately reveal how the two factors interact – in other words, how heredity works – contributed to some of the most significant breakthroughs in the history of biology, paving the way for discoveries about evolution, DNA, inherited disease, medicine, species taxonomy, genetic engineering and countless others branches of science. At the time of the early research, there were not yet words for genotype or phenotype, although each finding brought scientists closer to developing a universal vocabulary for describing the principals of heredity they were consistently observing.
TL;DR (Too Long; Didn't Read)
The word genotype refers to the genetic code contained in almost all living organisms, like a blueprint. The word phenotype refers to the observable traits that manifest from the organism’s genetic code, whether it’s on a microscopic, metabolic level, or a visible or behavioral level.
The Meaning of Genotype and Phenotype
The word genotype, in its most common usage, refers to the genetic code contained in almost all living organisms, which is unique for each individual, with the exception of identical offspring or siblings. Sometimes genotype is used differently: Instead it can refer to a smaller portion of an organism’s genetic code. Usually this usage has to do with the portion relevant to a certain trait in the organism. For example, when talking about the chromosomes responsible for determining sex in humans, the genotype scientists reference is the twenty-third chromosome pair, instead of the entire human genome. Generally males inherit the X and Y chromosomes, and females inherit two X chromosomes.
The word phenotype refers to the observable traits that manifest from the organism’s genetic blueprint, whether it’s on a microscopic, metabolic level, or a visible or behavioral level. It refers to the organism’s morphology, whether it’s observable by the naked eye (and other four senses) or requires special equipment to see. For example, phenotype can refer to something as small as the arrangement and composition of phospholipids in cell membranes, or the ornamented plumage in an individual male Indian peacock’s train. The words themselves were coined by a Danish biologist named Wilhelm Johannsen in 1909, along with the word “gene,” although he and many other men were celebrated for a great number of theoretical advances in the preceding decades before the words "genotype" and "phenotype" were ever uttered.
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Darwin and Others' Discoveries
These biological discoveries were taking place during the mid-1800s to early 1900s, and at the time, most scientists worked alone or in small collaborative groups, with very limited knowledge of the scientific progress happening concurrently with their peers. When the concepts of genotype and phenotype became known to science, they gave credence to theories about whether there existed some type of particulate matter in organisms’ cells that was being passed on to offspring (this indeed later proved to be DNA). The world’s increasing understanding of genotype and phenotype was indivisible from the increasing conception about the nature of heredity and evolution. Before this time, there was little or no knowledge of how heritable material was passed on from one generation to the past, or why some traits were passed on and some were not.
Scientists’ important discoveries about genotype and phenotype were all, in some way or another, about the particular rules about which traits were passed on from one generation of an organism to the next. Specifically, researchers were curious about why some of organism’s traits were transferred to its offspring while some were not, and others still did get passed on but seemed to require environmental factors to push the offspring into expressing the given trait that had been readily expressed in the parent. Many similar breakthroughs happened at similar times, overlapping in their insights and moving forward incrementally toward massive changes in thinking about the nature of the world. This slow, halting type of progress no longer happens since the advent of modern transportation and communication. Much of the great cascade of independent discoveries was set in motion by Darwin’s treatise on natural selection.
In 1859, Charles Darwin published his revolutionary book, “On the Origin of Species.” This book posited a theory of natural selection, or “descent with modification,” to explain how humans and all other species came to exist. He proposed that all species were descended from a common ancestor; migration and environmental forces influencing certain traits in offspring gave rise to different species over periods of time. His ideas gave rise to the field of evolutionary biology and are now universally accepted in scientific and medical fields (for more information about Darwinism, see the Resources section). His scientific work required great intuitive leaps since at the time, technology was limited, and scientists were not yet aware of what went on inside of a cell. They did not yet know about genetics, DNA or chromosomes. His work was derived entirely from what he could observe in the field; in other words, the phenotypes of the finches, turtles and other species he spent so much time with in their natural habitats.
Competing Theories of Inheritance
At the same time that Darwin was sharing his ideas about evolution with the world, an obscure monk in Central Europe named Gregor Mendel was one of many scientists working in obscurity across the globe to determine exactly how heredity worked. Part of his and other’s interest stemmed from humanity’s growing knowledge base and improving technology – such as microscopes – and part stemmed from a desire to improve selective breeding of livestock and plants. Standing out from the numerous hypotheses put forth to explain heredity, Mendel’s was the most accurate. He published his findings in 1866, shortly after publication of “On the Origin of Species,” but he did not receive widespread recognition for his breakthrough ideas until 1900. Mendel died well before that, in 1884, after spending the latter part of his life focused on his duties as the abbot of his monastery instead of scientific research. Mendel is considered the father of genetics.
Mendel primarily used pea plants in his research to study heredity, but his findings of the mechanisms how traits are passed on have been generalized to much of life on Earth. Like Darwin, Mendel was only knowingly working with the phenotype of his pea plants and not their genotypes, even if he did not have the terms for either concept; that is, he was only able to study their visible and tangible traits because he lacked the technology to observe their cells and DNA, and did not, in fact, know that DNA existed. Using only his awareness of his pea plants’ gross morphology, Mendel observed that there were seven traits in all of the plants that manifested as one of only two possible forms. For example, one of the seven traits was flower color, and the pea plants’ flower color would always be either white or purple. Another one of the seven traits was seed shape, which would always be either round or wrinkled.
The predominant thinking of the time was that heredity involved the blending of traits between parents when passed on to offspring. For instance, according to the blending theory, if a very large lion and a small lioness mated, their offspring might be medium in size. Another theory about heredity was posited by Darwin that he dubbed “pangenesis.” According to the theory of pangenesis, certain particles in the body were changed – or not changed – by environmental factors during the course of life, and then these particles passed through the bloodstream to the body’s reproductive cells, where they could be passed to offspring during sexual reproduction. Darwin’s theory, although more specific in its description of particles and blood transmission, was similar to the theories of Jean-Baptiste Lamarck, who erroneously believed that traits acquired during life were inherited by one’s offspring. For example, Lamarckian evolution postulated that giraffe’s necks grew progressively longer each generation because giraffes stretched their necks to reach the leaves, and their offspring were born with longer necks as a result.
Mendel's Intuition About Genotype
Mendel noted that the pea plants’ seven traits were always either one of the two forms, and never something in between. Mendel bred two pea plants with, for example, white flowers on one and purple flowers on the other. Their offspring all had purple flowers. He was interested to discover that when the purple-flowered offspring generation was crossbred with itself, the next generation was 75 percent purple-flowered and 25 percent white-flowered. The white flowers had somehow lain dormant through the entirely purple generation, to emerge again. These findings effectively disproved the blending theory, as well as Darwin’s pangenesis theory and Lamarck’s theory of inheritance, since all of these require the existence of gradually changing traits to arise in offspring. Even without understanding the nature of chromosomes, Mendel intuited the existence of a genotype.
He theorized that there were two “factors” operating for each trait within the pea plants, and that some were dominant, and some recessive. Dominance was what caused the purple flowers to take over the first generation of offspring, and 75 percent of the next generation. He developed the principle of segregation, in which each allele of a chromosome pair is separated during sexual reproduction, and only one is transmitted by each parent. Secondly, he developed the principle of independent assortment, in which the allele that is transmitted is chosen by chance. In this way, using only his observation and manipulations of phenotype, Mendel developed the most comprehensive understanding of genotype yet known to humanity, more than four decades before there would even be a word for either concept.
At the turn of the 20th century, various scientists, building on Darwin, Mendel and others' work, developed an understanding and vocabulary for chromosomes and their role in the inheritance of traits. This was the final major step in the scientific community’s concrete understanding of genotype and phenotype, and in 1909, the biologist Wilhelm Johanssen used those terms to describe the instructions encoded in chromosomes, and the physical and behavioral traits outwardly manifested. In the following century and a half, the microscope’s magnification and resolution improved drastically. In addition, the science of heredity and genetics was improved upon with new types of technology for seeing into tiny spaces without disturbing them, such as X-ray crystallography.
Theories about mutations shaping the evolution of species were posited, as well as of various forces that affected the direction of natural selection, such as sexual preference or extreme environmental conditions. In 1953, James Watson and Francis Crick, building on the work of Rosalind Franklin, presented a model for a double helix structure of DNA that won the two men the Nobel Prize and opened up an entire field of scientific study. Like scientists more than a century ago, modern-day scientists often begin with phenotype and make inferences about genotype before exploring further. Unlike scientists from the 1800s, however, modern-day scientists can now make predictions about individuals’ genotypes based on phenotypes and then use technology to analyze the genotypes.
Some of this research is medical in nature, focused on humans with heritable disease. There are many diseases that run in families, and research studies will often use saliva or blood samples to find the portion of the genotype that is relevant to the disease in order to find the faulty gene. Sometimes the hope is early intervention or cure, and sometimes knowing sooner will prevent afflicted individuals from passing the genes on to offspring. For example, this kind of research was responsible for the discovery of the BRCA1 gene. Females with mutations of this gene have a very high risk of developing breast and ovarian cancer, and all people with the mutation have higher risks of other kinds of cancer. Because it is part of the genotype, a family tree with the mutated BRCA1 genotype is likely to have a phenotype of many women afflicted with cancer, and when individuals are tested, the genotype will be discovered and preventative strategies can be discussed.