Chicken Genome
543
genome. Such clones are difFcult to main-
tain and analyze, so most contig-building
projects nowadays use the simpler and
more stable BAC system. In preparation
for sequencing the chicken genome, many
laboratories have constructed a number
of BAC libraries with various enzyme
combinations. The library by Crooijmans
et al. was constructed with the restric-
tion enzyme
Hind
III and contains 50 000
clones or Fvefold coverage of the genome.
Recently, three BAC libraries were con-
structed (
Hind
III,
Eco
RI, and
Bam
HI),
each consisting of about 40 000 clones.
Methods used to create contigs vary
and depend on using a simple and rapid
method to identify a shared characteristic,
such as the presence of a PCR product
(STS or sequence tagged site), or more
simply, an overlapping DNA Fngerprint.
These Fngerprints can be generated in
sophisticated ways (e.g. using A±LPs) or
more simply, by restriction digests of
the BAC clones (
Hind
III,
Bam
HI,
Eco
RI,
etc.). Because the genomic inserts in these
clones are large, many DNA fragments are
observed for each clone after restriction
digestion. The images are usually captured
using imaging software and the results
analyzed semiautomatically.
Currently,
partial
BAC
contigs
have
been built for chicken chromosomes 10,
13, and 24, and when integrated with
other data (sequence sampling data, ge-
netic maps, RH maps, etc.), reveal gene
maps of high resolution. Zhang et al.
Fig. 4
Example of BAC contigs (ctg87, 1829 kb)
for the chicken physical map. Example of chicken
BAC contig anchored to the chromosome 1
genetic map of the chicken genome. This contig
consists of 142 clones from three source BAC
libraries, contains 903 unique Fngerprint bands,
and is estimated to span 4.01 Mb. The clones
preFxed with h were from the HindIII BAC
library, with b from the BamHI BAC library and
with r from the EcoRI BAC library. The contig was
anchored to the region around 361 cM of the
chromosome 1 genetic map using Fve DNA
markers – MSU0301, ADL0037, GCT0013,
GCT0033, and ROS0081. The highlighted clones
indicate the positive clones identiFed by DNA
marker hybridization. (Reproduced by kind
permission of Chengwei Ren, Mi-Kyung Lee, Bo
Yan, Jerry B. Dodgon, and Hong-Bin Zhang).
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