The word genotype was coined c. 1898 by Wilhelm Ludvig Johannsen in reference to Gregor Mendel's work involving pea plants (see below). The word specifically referred to the identity of the alleles of the "factors" (which didn't become genes until 1911) which Mendel used to derive his laws. Thus, the term originally referred to the specific allelic composition at a given locus. Since then, the term has expanded to also mean an organism's entire genetic code. In other words, the genotype is that information, in the form of a nucleic acid, which encodes (nearly) every protein, every ribosomal RNA, every part of the organism. This is in contrast with the phenotype, which is simply the appearance of the organism, or the outward expression of a given locus.

In haploid organisms**, the genotype and the phenotype are the same. Whatever genes the organism has are expressed, whether they are lethal or beneficial. Conversely, in diploid organisms**, the phenotype indicates only the dominant portion of the genotype, even if the recessive allele is beneficial.

During asexual reproduction, the genotype passed from the single parent cell to the two (usually) daughter cells produced is identical. During sexual reproduction, the genotype varies because of the introduction of the second parent. Independent assortment and recombination account for the thousands of possible permutations of even the simplest genome through sexual reproduction.

While the genotype is not directly affected by the environment (with the exception of mutagens and suchlike), through subsequent generations, the prevalence of a given phenotype tends to shift according to the demands of the environment, as a result of the "weeding out" of the less desirable genotype. (See also population genetics, evolution)

It's worth mentioning that most of the earliest genetic tests involved a test cross, which involves mating an organism with a dominant phenotype but unknown genotype at a given locus with an organism of recessive genotype at that locus in order to determine the genotype of the unknown. Gregor Mendel and his followers did a lot of this.

Also worth mentioning is the fact that the "one gene, one feature" concept is a little oversimplified. Genotype can be difficult to uncover (unless you're really into genome sequencing, that is) because of the fact that multiple genes can affect a single feature additively, eg. the multiple genes for skin color, or such that one allele of one gene will mask any allele of other genes (epistasis); or, multiple features may be affected by one gene (pleiotropy); or, there may be multiple alleles of the same gene, such as the ABO blood type gene, which has three alleles (A, B, O), two of which (A and B) are codominant over the third (O). The advent of DNA sequencing and completed genome sequences of several model organisms, however, has allowed a greater understanding of these phenomena and their effects on our perceptions of genotype.


** - the terms haploid and diploid refer to the dominant phase of the life cycle.
Sources:

  • for several dictionary citations that all said the same thing: http://www.online-dictionary.net/
  • for information on the origins of words: http://wjmll.ncl.ac.uk/issue02/west1.htm and http://www.idiotsguides.com/Chapters/0028635868_CIG_Decod_Genes/file.htm

And special thanks to Gritchka and Chris-O for help and encouragement.

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