The remaining chapters in this book will be devoted to the process and practice of genetic mapping in the mouse. Although mapping was once viewed as a sleepy pastime performed simply for the satisfaction of knowing where a gene mapped as an end unto itself, it is now viewed as a critical tool of importance to many different areas of biological and medical research. Mapping can provide a means for moving from important diseases to clones of the causative genes which, in turn, can provide tools for diagnosis, understanding, and treatment. In the opposite direction, mapping can be used to uncover functions for newly-derived DNA clones by demonstrating correlations with previously described variant phenotypes. Mapping can also be used to dissect out the heritable and non-heritable components of complex traits and the mechanisms by which they interact. The purpose of this chapter is to provide a primer on classical genetics and to give an overview of mapping in the mouse, with further details provided in subsequent, more focused chapters.
In the prerecombinant DNA era, all genes were defined by the existence of alternative alleles that produced alternative phenotypes that segregated in genetic crosses. Today, with the use of molecular technologies, the ability to recognize genes has expanded tremendously. Monomorphic genes (those with only a single allele) can now be recognized through their transcriptional activity alone. Recognition of putative genes within larger genomic sequences can also be accomplished through the identification of open reading frames, flanking tissue-specific enhancers and other regulatory elements, internal splicing signals, and sequence conservation across evolutionary lines. Sequence-specific epigenetic phenomena such as imprinting, methylation, and DNase sensitivity can also be used to elucidate the existence of functional genomic elements.
Mouse geneticists use the term locus to describe any DNA segment that is distinguishable in some way by some form of genetic analysis. In the prerecombinant DNA era, only genes distinguished by phenotype could be recognized as loci. But today, with the use of molecular tools, it is possible to distinguish "loci" in the genome that have no discernible function at all. In fact, any change in the DNA sequence, no matter how small or large, whether in a gene or elsewhere, can be followed potentially as an alternative allele in genetic crosses. When alternative alleles exist in a genomic sequence that has no known function, the polymorphic site is called an anonymous locus. 42 With an average rate of polymorphism of one base difference in a thousand between individual chromosome homologs within a species, the pool of potential anonymous loci is enormous. Classes of anonymous loci and the methods by which they are detected and used as genetic markers will be the subject of Chapter 8.
A genetic map is simply a representation of the distribution of a set of loci within the genome. The loci included by an investigator in any one mapping project may bear no relation to each other at all, or they may be related according to any of a number of parameters including functional or structural homologies or a pre-determined chromosomal assignment. Mapping of these loci can be accomplished at many different levels of resolution. At the lowest level, a locus is simply assigned to a particular chromosome without any further localization. At a step above, an assignment may be made to a particular subchromosomal region. At a still higher level of resolution, the relative order and approximate distances that separate individual loci within a linked set can be determined. With ever-increasing levels of resolution, the order and interlocus distances can be determined with greater and greater precision. Finally, the ultimate resolution is attained when loci are mapped onto the DNA sequence itself.
The simplest genetic maps can contain information on as few as two linked loci. At the opposite extreme will be complete physical maps that depict the precise physical location of all of the thousands of genes that exist along an entire chromosome. The first step toward the generation of these complete physical maps has recently been achieved with the establishment of single contigs of overlapping clones across the length of two complete human chromosome arms (Chumakov et al., 1992; Foote et al., 1992). By the time this book is actually read, it is likely that complete contigs across other human — as well as mouse — chromosomes will also be attained. However, it is still a long journey from simply having a set of clones to deciphering the genetic information within them.
There is actually not one, but three distinct types of genetic maps that can be derived for each chromosome in the genome (other than the Y). The three types of maps — linkage, chromosomal, and physical — are illustrated in Figure 7.1 and are distinguished both by the methods used for their derivation and the metric used for measuring distances within them.
The linkage map, also referred to as a recombination map, was the first to be developed soon after the re-discovery of Mendel's work at the beginning of the 20th century. Linkage maps can only be constructed for loci that occur in two or more heritable forms, or alleles. Thus, monomorphic loci — those with only a single allele — cannot be mapped in this fashion. Linkage maps are generated by counting the number of offspring that receive either parental or recombinant allele combinations from a parent that carries two different alleles at two or more loci. Analyses of this type of data allow one to determine whether loci are "linked" to each other and, if they are, their relative order and the relative distances that separate them (see Section 7.2).
A chromosomal assignment is accomplished whenever a new locus is found to be in linkage with a previously assigned locus. Distances are measured in centimorgans, with one centimorgan equivalent to a crossover rate of 1%. The linkage map is the only type based on classical breeding analysis. The term "genetic map" is sometimes used as a false synonym for "linkage map"; a genetic map is actually more broadly defined to include both chromosomal and physical maps as well.
The chromosome map (or cytogenetic map) is based on the karyotype of the mouse genome. All mouse chromosomes are defined at the cytogenetic level according to their size and banding pattern (see Figure 5.1), and ultimately, all chromosomal assignments are made by direct cytogenetic analysis or by linkage to a locus that has previously been mapped in this way. Chromosomal map positions are indicated with the use of band names (Figures 5.2 and 7.1). Inherent in this naming scheme is a means for ordering loci along the chromosome (see Section 5.2).
Today, several different approaches, with different levels of resolution, can be used to generate chromosome maps. First, in some cases, indirect mapping can be accomplished with the use of one or more somatic cell hybrid lines that contain only portions of the mouse karyotype within the milieu of another species' genome. By correlating the presence or expression of a particular mouse gene with the presence of a mouse chromosome or subchromosomal region in these cells, one can obtain a chromosomal, or subchromosomal, assignment (see Section 10.2.3).
The second approach can be used in those special cases where karyotypic abnormalities appear in conjunction with particular mutant phenotypes. When the chromosomal lesion and the phenotype assort together, from one generation to the next, it is likely that the former causes the latter. When the lesion is a deletion, translocation, inversion, or duplication, one can assign the mutant locus to the chromosomal band that has been disrupted.
Finally, with the availability of a locus-specific DNA probe, it becomes possible to use the method of in situ hybridization to directly visualize the location of the corresponding sequence within a particular chromosomal band. This approach is not dependent on correlations or assumptions of any kind and, as such, it is the most direct mapping approach that exists. However, it is technically demanding and its resolution is not nearly as high as that obtained with linkage or physical approaches (see Section 10.2.2).
The third type of map is a physical map. All physical maps are based on the direct analysis of DNA. Physical distances between and within loci are measured in basepairs (bp), kilobasepairs (kb) or megabasepairs (mb). Physical maps are arbitrarily divided into short range and long range. Short range mapping is commonly pursued over distances ranging up to 30 kb. In very approximate terms, this is the average size of a gene and it is also the average size of cloned inserts obtained from cosmid-based genomic libraries. Cloned regions of this size can be easily mapped to high resolution with restriction enzymes and, with advances in sequencing technology, it is becoming more common to sequence interesting regions of this length in their entirety.
Direct long-range physical mapping can be accomplished over megabase-sized regions with the use of rare-cutting restriction enzymes together with various methods of gel electrophoresis referred to generically as pulsed field gel electrophoresis or PFGE, which allow the separation and sizing of DNA fragments of 6 mb or more in length (Schwartz and Cantor, 1984; den Dunnen and van Ommen, 1991). PFGE mapping studies can be performed directly on genomic DNA followed by Southern blot analysis with probes for particular loci (see Section 10.3.2). It becomes possible to demonstrate physical linkage whenever probes for two loci detect the same set of large restriction fragments upon sequential hybridizations to the same blot.
Long-range mapping can also be performed with clones obtained from large insert genomic libraries such as those based on the yeast artificial chromosome (YAC) cloning vectors, since regions within these clones can be readily isolated for further analysis (see Section 10.3.3). In the future, long-range physical maps consisting of overlapping clones will cover each chromosome in the mouse genome. Short-range restriction maps of high resolution will be merged together along each chromosomal length, and ultimately, perhaps, the highest level of mapping resolution will be achieved with whole chromosome DNA sequences.
In theory, linkage, chromosomal, and physical maps should all provide the same information on chromosomal assignment and the order of loci. However, the relative distances that are measured within each map can be quite different. Only the physical map can provide an accurate description of the actual length of DNA that separates loci from each other. This is not to say that the other two types of maps are inaccurate. Rather, each represents a version of the physical map that has been modulated according to a different parameter. Cytogenetic distances are modulated by the relative packing of the DNA molecule into different chromosomal regions. Linkage distances are modulated by the variable propensity of different DNA regions to take part in recombination events (see Section 7.2.3).
In practice, genetic maps of the mouse are often an amalgamation of chromosomal, linkage, and physical maps, but at the time of this writing, it is still the case that classical recombination studies provide the great bulk of data incorporated into such integrated maps. Thus, the primary metric used to chart interlocus distances has been the centimorgan. However, it seems reasonable to predict that, within the next five years, the megabase will overtake the centimorgan as the unit for measurement along the chromosome.