Mapping Genomes

Genetic Maps

Genetic maps provide information about which chromosomes contain specific genes and precisely where the genes lie on that chromosome.

Learning Objectives

Describe the different types of genetic markers that are used in generating genetic maps of DNA

Key Takeaways

Key Points

  • Genetic mapping, often called linkage mapping, provides information about the location of a specific gene along a chromosome.
  • Gene linkage describes the phenomenon that certain genes are physically linked by being located on the same chromosome and have a tendency to be inherited together.
  • Genetic recombination involves the production of a novel set of genetic information by breaking and rejoining DNA fragments that have a great distance between them along the chromosome.
  • The construction of genetic maps is reliant on the natural process of recombination which results in the ability to identify genetic markers with variability within a population.
  • Genetic markers that can be used in generating genetic maps include restriction length polymorphisms ( RFLP ); variable number of tandem repeats (VNTRs); microsatellite polymorphisms; and single nucleotide polymorphisms ( SNPs ).

Key Terms

  • polymorphism: the regular existence of two or more different genotypes within a given species or population
  • SNP: single nucleotide polymorphism is single base pair of DNA which is polymorphic with respect to a population
  • microsatellite: any of a group of polymorphic loci in DNA that consist of repeat units of just a few base pairs
  • RFLP: restriction fragment length polymorphism is a section of DNA whose length varies among individuals and which is delimited by a base which does not occur within it

Genetic Maps

The study of genetic maps begins with linkage analysis, a procedure that analyzes the recombination frequency between genes to determine if they are linked or show independent assortment. The term linkage was used before the discovery of DNA. Early geneticists relied on the observation of phenotypic changes to understand the genotype of an organism. Shortly after Gregor Mendel (the father of modern genetics) proposed that traits were determined by what are now known as genes, other researchers observed that different traits were often inherited together and, thereby, deduced that the genes were physically linked by being located on the same chromosome. The mapping of genes relative to each other based on linkage analysis led to the development of the first genetic maps.

Observations that certain traits were always linked and certain others were not linked came from studying the offspring of crosses between parents with different traits. For example, in experiments performed on the garden pea, it was discovered that the color of the flower and shape of the plant’s pollen were linked traits; therefore, the genes encoding these traits were in close proximity on the same chromosome. The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids. Linkage analysis involves studying the recombination frequency between any two genes. The greater the distance between two genes, the higher the chance that a recombination event will occur between them, and the higher the recombination frequency between them. If the recombination frequency between two genes is less than 50 percent, they are said to be linked.

image

Crossovers and Recombination: Crossover may occur at different locations on the chromosome. Recombination between genes A and B is more frequent than recombination between genes B and C because genes A and B are farther apart; a crossover is, therefore, more likely to occur between them.

The generation of genetic maps requires markers, just as a road map requires landmarks (such as rivers and mountains). Early genetic maps were based on the use of known genes as markers. More sophisticated markers, including those based on non-coding DNA, are now used to compare the genomes of individuals in a population. Although individuals of a given species are genetically similar, they are not identical; every individual has a unique set of traits. These minor differences in the genome between individuals in a population are useful for the purposes of genetic mapping. In general, a good genetic marker is a region on the chromosome that shows variability or polymorphism (multiple forms) in the population.

Some genetic markers used in generating genetic maps are restriction fragment length polymorphisms (RFLP), variable number of tandem repeats (VNTRs), microsatellite polymorphisms, and the single nucleotide polymorphisms (SNPs). RFLPs (sometimes pronounced “rif-lips”) are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis. The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual’s DNA “fingerprint.” Certain regions of the chromosome that are subject to polymorphism will lead to the generation of the unique banding pattern. VNTRs are repeated sets of nucleotides present in the non-coding regions of DNA. Non-coding DNA has no known biological function; however, research shows that much of this DNA is actually transcribed. While its function is uncertain, it is certainly active; it may be involved in the regulation of coding genes. The number of repeats may vary in individual organisms of a population. Microsatellite polymorphisms are similar to VNTRs, but the repeat unit is very small; thus, it is often referred to as short tandem repeats(STRs). SNPs are variations in a single nucleotide.

Because genetic maps rely completely on the natural process of recombination, mapping is affected by natural increases or decreases in the level of recombination in any given area of the genome. Some parts of the genome are recombination hotspots, whereas others do not show a propensity for recombination. For this reason, it is important to look at mapping information developed by multiple methods.

Physical Maps and Integration with Genetic Maps

Physical maps display the physical distance between genes and can be constructed using cytogenetic, radiation hybrid, or sequence mapping.

Learning Objectives

Describe the methods used to physically map genes: cytogenetic mapping, radiation hybrid mapping, and sequence mapping

Key Takeaways

Key Points

  • Physical maps provide specified detail about the number of bases and physical distance that exists between genetic markers.
  • Cytogenetic mapping is a method used to construct physical maps that uses stained sections of chromosomes to approximate the distance between genetic markers.
  • Radiation hybrid mapping is a method used to construct physical maps that uses radiation or x-rays to break DNA into fragments to determine the distance between genetic markers and their order on the chromosome.
  • Sequence mapping is a method used to construct physical maps that uses already-known locations of genetic markers to determine distances in number of base pairs.

Key Terms

  • cytogenetic: of or pertaining to the origin and development of cells
  • physical map: a map showing how much DNA separates two genes and is measured in base pairs
  • expressed sequence tag: a short sub-sequence of a cDNA sequence that may be used to identify gene transcripts

Physical Maps

A physical map provides detail of the actual physical distance between genetic markers, as well as the number of nucleotides. There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping. Cytogenetic mapping uses information obtained by microscopic analysis of stained sections of the chromosome. It is possible to determine the approximate distance between genetic markers using cytogenetic mapping, but not the exact distance (number of base pairs). Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments. The amount of radiation can be adjusted to create smaller or larger fragments. This technique overcomes the limitation of genetic mapping and is not affected by increased or decreased recombination frequency. Sequence mapping resulted from DNA sequencing technology that allowed for the creation of detailed physical maps with distances measured in terms of the number of base pairs. The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome ) has sped up the process of physical mapping. A genetic site used to generate a physical map with sequencing technology (a sequence-tagged site, or STS) is a unique sequence in the genome with a known exact chromosomal location. An expressed sequence tag (EST) and a single sequence length polymorphism (SSLP) are common STSs. An EST is a short STS that is identified with cDNA libraries, while SSLPs are obtained from known genetic markers and provide a link between genetic maps and physical maps.

image

Cytogenetic Map: A cytogenetic map shows the appearance of a chromosome after it is stained and examined under a microscope.

Integration of Genetic and Physical Maps

Genetic maps provide the outline and physical maps provide the details. It is easy to understand why both types of genome mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to study the genome. Genomic mapping is being used with different model research organisms. Genome mapping is an-ongoing process; as better techniques are developed, more advances are expected. Genome mapping is similar to completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories worldwide is entered into central databases, such as GenBank at the National Center for Biotechnology Information (NCBI). Efforts are being made to make the information more easily accessible to researchers and the general public. Just as we use global positioning systems instead of paper maps to navigate through roadways, NCBI has created a genome viewer tool to simplify the data-mining process.