Genome Mapping Reveals That Individual Genomes Show Extensive Variation
 
KEY CONCEPTS
- Genomes are mapped by sequencing their DNA and identifying functional genes.
- Polymorphism can be detected at the phenotypic level when a sequence affects gene function, at the restriction fragment level when it affects a restriction enzyme target site, and at the sequence level by direct analysis of DNA.
- The alleles of a gene show extensive polymorphism at the sequence level, but many sequence changes do not affect function.
Defining the contents of a genome essentially means mapping and sequencing the genetic loci found on the organism’s chromosome(s). Prior to the modern technological ease and low cost of DNA sequencing, there were several low-resolution genome mapping techniques. A linkage map shows the distance between loci in units based on recombination frequencies; it is limited by its dependence on the observation of recombination between variable markers that are either directly visible (e.g., phenotypic traits) or that can otherwise be visualized (e.g., by electrophoresis). A restriction map is constructed by cutting DNA into fragments with restriction enzymes and measuring the physical distances, in terms of the length of DNA in base pairs (determined by migration on an electrophoretic gel) between the cut sites.
Today, a genomic map is constructed by sequencing the DNA of the genome. From the sequence, we can identify genes and the distances between them. By analyzing the protein-coding potential of a sequence of the DNA, we can hypothesize about its function.
The basic assumption is that natural selection prevents the accumulation of deleterious mutations in sequences that encode functional products. Reversing the argument, we can assume that an intact coding sequence with accompanying transcription signals is likely to produce a functional polypeptide.
By comparing a wild-type DNA sequence with that of a mutant allele, researchers can determine the nature of a mutation and its exact location in the sequence. This provides a way to determine the relationship between the linkage map (based entirely on variable sites) and the physical map (based on, or even comprising, the sequence of DNA).
Researchers use similar techniques to identify and sequence genes and to map the genome, although there is, of course, a difference of scale. In each case, the approach is to characterize a series of overlapping fragments of DNA that can be connected into a continuous map. The crucial feature is that each segment is identified as adjacent to the next segment on the map by the overlap between them, so that we can be sure no segments are missing. This principle is applied both at the level of assemblinglarge fragments  into a map and in connecting the sequences that make up the fragments.
The original Mendelian view of the genome classified alleles as either wild type or mutant. Subsequently, the existence of multiple alleles for a gene in a population has been recognized, each with a different effect on the phenotype. In some cases, it might not even be appropriate to define any one allele as wild type.
The coexistence of multiple alleles at a locus in a population is called genetic polymorphism. Any site at which multiple alleles exist as stable components of the population is by definition
polymorphic. A locus is usually defined as polymorphic if two or more alleles are present at a frequency of more than 1% in the population. Human eye color is a good example of phenotypic polymorphism resulting from underlying genetic polymorphism.
There is no single “normal” eye color; many different colors are found among different individuals, with little or no differences in visual function among them.
What is the basis for the polymorphism among the varying alleles? They possess different mutations that might alter their product’s function, thus producing changes in phenotype. The population dynamics of these different alleles are partly determined by their selective effects on phenotype. If we compare the restriction maps or the DNA sequences of these alleles, they will also be polymorphic in the sense that each map or sequence will be different from the others.
Although not evident from the phenotype, the wild type might itself be polymorphic. Multiple versions of the wild-type allele can be distinguished by differences in sequence that do not affect their function and therefore do not produce phenotypic variants. A population can have extensive polymorphism at the level of the genotype. Many different sequence variants can exist at a particular locus; some of them are evident because they affect the phenotype, but others are “hidden” because they have no visible effect. These mutant alleles are usually selectively neutral, with their population dynamics mainly a result of random genetic drift.
There can be a variety of changes at a locus, including those that change the DNA sequence but do not change the sequence of the polypeptide product, those that change the polypeptide sequence without changing its function, those that result in polypeptides with different functions, and those that result in altered polypeptides that are nonfunctional.
When alleles of the same locus are compared, a difference in a single nucleotide is called a single nucleotide polymorphism (SNP). On average, one SNP occurs for approximately every 1,330 bases in the human genome. Defined by SNPs, every human being is unique. SNPs can be detected by direct comparisons of sequences from different individuals.
One aim of genetic mapping is to obtain a catalog of common variants. The observed frequency of SNPs per genome predicts that, in the human population as a whole (considering the genomes of all living human individuals), there should be more than 10 million SNPs that occur at a frequency of more than 1% (i.e., are polymorphic). (As of the end of 2015, more than 100 million human SNPs have been identified, though most of these do not fit the definition of polymorphic.)
The sequencing of complete individual genomes is now possible and allows the assessment of individual DNA-level variations, both neutral SNPs and those linked to diseases or disease susceptibilities. Although the sequencing of “celebrity” genomes (e.g., those of James Watson and Craig Venter) receive more press coverage, rapid genome sequencing  of anonymousindividuals is potentially more informative. Hundreds of individual human genomes of all major racial groups have now been sequenced, including those of Denisovans (a Paleolithic Homo species that lived more than 30,000 years ago) and Neanderthals (more than 25,000 years old). The 1,000 Genomes Project ranfrom  2008 to 2015 with the goal of identifying common human genetic variants by deep sequencing at least 1,000 human genomes; the final number was actually 2,504 anonymous huma ngenome sequences representing 26 human populations. There is now a baseline dataset that can be expanded to include individuals from populations that were not represented in the original sample.