Plant Genome Structure

Evolutionary Relatedness

Comparative Genome Mapping

Physical and Genetic Distances

Linkage Drag

Course Topics

Main Page

Physical and Genetic Distances

All distances found on a linkage maps are the product of genetic recombination and therefore are considered to be genetic distances. Two pairs of loci that are genetically the same distance apart may not be physically the same distance apart because of suppressed recombination in the region between two of the loci. Those loci where suppression of recombination does occur will physically be farther apart.

RFLP hybridizations to large fragments of DNA are necessary to accurately gauge the physical distance.These experiments are similar to other Southern hybridizations. The DNA is cut with restriction enzymes first. The choice of enzymes is important because you want to generate large fragments. For these experiments you want to cut the DNA with enzymes that recognize 8 nucleotide sequences in the target DNA. Because these sites will be rare (every 65,536 bases on average) the digestion products will range from several hundred kilobase to several megabases. Because the normal gel systems do not separate large fragments very easily, it is necessary to run pulsed-field-gel-electrophoresis. This technique was first applied to the separation of yeast chromosomes and was quickly applied to large-scale mapping experiments.

Physical and genetic distances are then resolved by hybridizing clones which define closely linked genetic markers, to DNA that has been cut with rare cutting enzymes. What you are searching for is co-hybridization of the two clones to the same restriction fragment. If two clones hybridize to the same fragment, then the maximum distance between those two clones is the size of the restriction fragment. Because you already know the genetic distance between the loci, you can correlate the genetic and physical distances in this region. The following table give the relationship between the physical and genetic distance in three species.

Species kilobases/centimorgan
Arabidopsis 139
Tomato 510
Corn 2140

But remember, these values are estimates of a single region of the genome of each species, and it is quite common to see that two regions of the same species have different amount of DNA per genetic distance.

Correlations between physical and genetic distances have also been performed using deletion stocks in wheat. A series of deletions stocks of a specific wheat chromosome were analyzed with a probes known to hybridize to that chromosome. "Each locus was assigned to the chormosome region between the breakpoint of the largest deletion where the band was present and the next larger deletion where the band was absent." (Werner et al. PNAS 89:11307-11311) The authors noted large discprencies between the physical and genetic maps of chromosomes 7B and 7D. Two loci that are located near the centromere of 7B are 7 cM apart genetically, yet the distance between the two loci spans 25% of the chromosome. Another region at the distal region of long arm of 7B which accounts for about 15 % of the chromosome is 91 cM long genetically. This points out the difference of recombination that can occur within a single chromosome.

Copyright © 1998. Phillip McClean