"Frontmatter". In: Plant Genomics and Proteomics

P
HYSICAL AND
G
ENETIC
M
APS
The genetic map is an ordering of the regions of the genome according 
to the rates of recombination that occur along each of the chromosomes, 
the genetic distance being the frequency with which recombination occurs
between two points on the chromosome. There is not a specific relationship
between the genetic distance and the physical distance between the same
5 0
3. S
E Q U E N C I N G
S
T R AT E G I E S
Isolate High molecular weight DNA
Isolate DNA
Partial digest with restriction
enzymes or shearing
Make large insert BAC libraries
Fragmentation, fractionation
Rack libraries for automation
Clone fragments
Isolate BAC DNA
Sequence fragments
BAC fingerprinting
Build contigs
Contig building
Link to some type of scaffold
(EST links, BAC end sequences,
physical map)
BAC library filter hybridizations (optional)
With EST, oligo overgos etc 
Use of synteny to order regions
MTP development
Shotgun sequencing of BACs
Assembly of sequence reads
Build of contig sequences
Crossing gaps — PCR, linking libraries
Finished sequence
Annotation
FIGURE 3.1.
Flowcharts for various sequencing approaches.

---

two points because the recombination rate is not constant over the length 
of the chromosomes. A more extreme example of a lack of correspondence
between genetic and physical distance is found in humans, where the genetic
maps for males and females have the same linear order but do not have the
same values for the distances between equivalent points because there is a
difference in recombination rate in the two sexes, the rate being higher in
females than in males. The density of markers on the genetic map for most
organisms has increased rapidly with the use of DNA-based polymor-
phisms. The genetic map is generated by the scoring of numerous poly-
morphisms in populations segregating for those markers. The larger the
number of individuals scored in the population, the more precise the loca-
tion of any particular marker becomes and the greater confidence can be
placed on the specific order of a series of closely linked markers. 
The physical map, on the other hand, is the linear order of the sequences
linking the ends of each chromosome with overlapping regions of DNA. This
is done by fragmenting the whole genome into pieces and then trying to
reassemble the pieces into a single continuous molecule for each chromo-
some. When complete, each chromosome would consist of a single compos-
ite strand made up from a large number of smaller, overlapping fragments.
In generation of the physical map, some of the regions will provide special
problems. For example, regions that contain long sequences of tandem
repeats, such as the genes for the large ribosomal RNAs, cannot be linked in
a linear order, because the array is longer than any single subfragment and
each repeat is essentially identical. However, a knowledge of the number of
repeats and the number of chromosomal sites over which these repeats are
spread can facilitate an estimation of the length of the region containing the
repeats.