540
Chicken Genome
as introns and may not have any effect on
gene function. For example, a frequent
genetic
marker
is
based
on
variation
in so-called
microsatellite sequences
.These
are common and are based on simple
sequence repeats (e.g. ACACACA
...
)that
vary in length from individual to individual
and may or may not be associated with a
gene; they are therefore called
anonymous
genetic markers
.
The ±rst genetic linkage map for chick-
ens based on DNA markers was published
by Bumstead and Palyga in 1992 and was
based on a cross between two partially
inbred White Leghorn lines. Progress in
creating a chicken genetic map (a con-
sensus genetic map) accelerated when
laboratories decided to pool efforts and
concentrate on a few pedigrees (refer-
ence mapping families). The most fruitful
pedigrees were the East Lansing and Wa-
geningen populations. The East Lansing
population consisted of only 52 back-
cross animals derived from a partially
inbred jungle fowl and a highly inbred
White Leghorn line. The resolution of
this cross was low, between 5 and 7 cM.
The Wageningen population consisted of
456 F
2
intercross animals derived from
a cross between two broiler dam lines
with origins from the White Plymouth
Rockbreed
.W
i
thmoreprogeny
,theres
-
o
lu
t
i
ono
fth
i
sc
r
o
s
sw
a
sh
i
gh
e
r
,ab
ou
t
1 cM. This is equivalent to about 300 kb
or 5 to 10 genes. As an example, Fig. 2
shows the genetic map of chromosome
5 derived from the East Lansing and
Wageningen reference mapping popula-
tions.
Early maps were based on various ge-
netic markers (RFLP (restriction fragment
length polymorphism), RAPD (randomly
ampli±ed polymorphic DNA), CR1-repeats
and classical markers). Since then, most
markers have been based on microsatellite
sequences and AFLPs (ampli±ed length
fragment polymorphisms). Recently, more
markers based on SNPs (single-nucleotide
polymorphisms) have been used. Since
many markers were in common between
these various maps, it was possible to
calculate a consensus map comprising
2012 loci and spanning 4000 cM. The con-
sensus map still consists of 51 linkage
groups, many probably representing the
same microchromosome. So far, 32 of
the linkage groups have been assigned
to a speci±c chromosome by Grif±n and
all chromosomes now have a landmark
probe.
5
Physical Maps
The resolution of physical mapping varies
widely depending on the technique used,
from 10 Mb in FISH mapping, 0.1 to
1 Mb in RH mapping, 0.1 to 1 Mb for
BAC (bacterial arti±cial chromosome) and
YAC (yeast arti±cial chromosome) physical
maps, and to individual nucleotides in
genome sequencing.
5.1
Cytogenetic Maps
Themostreliab
letechniquefor
in situ
hy-
bridization to reveal physical location on
a chromosome has been FISH, where the
DNA probe (e.g. a BAC clone) is labeled
with a fluorescent dye. The location of
the labeled probe is detected under the
microscope after it has hybridized to its
complementary DNA strand on a speci±c
chromosome. Earlier experiments using
radioactive
in situ
hybridization tended to
be incorrect due to the technical challenges
of the method. When combined with the
availability of large genomic clones, FISH
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