Download The Chicken Gene Map

The Chicken Gene Map
David W. Burt and Hans H. Cheng
INTRODUCTION
Most efforts to map the genomes of birds have concentrated
almost exclusively on the domesticated chicken (Gallus
gallus) and on very few other species. Two reasons for this
bias are the importance of chicken as a major source of meat
and egg products and as a model of vertebrate development.
The first genetic linkage map of the chicken was published in
1936 by Hutt (1936) and represented the first map reported
for any domestic farm animal species. Updates of this classical map have been published periodically, with the most
recent being that of Bitgood and Somes (1993). The small
size of the chicken genome (1.2 billion base-pairs; Bloom
and others 1993) and the ability to isolate DNA from nucleated red blood cells (note: red blood cells in mammals lack
nuclei) make it well suited for gene mapping. Despite these
advantages, 6 decades of genetic linkage mapping have produced a limited map. International collaborative efforts to
produce a molecular map of the chicken genome have been
established only in the last 5 yr (Burt and others 1995,1997).
REASONS FOR MAPPING THIS SPECIES
The chicken genome is being mapped to discover genetic
markers of traits of economic value (such as meat and egg
production), to discover animal models for quantitative traits,
genetic disease, and developmental defects, and to aid studies
on the evolution of the vertebrate genome (such as chromosome evolution and speciation). Most economically important traits in poultry, such as weight, fatness, and disease resistance, are controlled by many genes located at quantitative
trait loci (QTLs1). The study of such traits requires crosses
between lines that show extreme differences in phenotypes
and large pedigrees (such as 500 or more progeny of an F 2
intercross). These types of studies are extremely difficult in
David W. Burt, Ph.D., is Principal Investigator in the Division of Molecular
Biology, Roslin Institute of Edinburgh, Midlothian, United Kingdom. Hans
H. Cheng, Ph.D., is Principal Investigator in the Avian Disease and Oncology Laboratory of the US Department of Agriculture Agricultural Research
Center, East Lansing, Michigan.
'Abbreviations used in this paper: ADW, autosomal dwarfism; BAC, bacterial artificial chromosome; FISH, fluorescence in situ hybridization; HMG1C, high mobility group protein I-C; QTL, quantitative trait locus; WL, White
Leghorn; WWW, World Wide Web; YAC, yeast artificial chromosome.
Volume 39, Numbers 2 and 3
1998
humans. However, many QTL mapping projects are under
way in poultry (Burt and others 1997), and when linkage is
established, candidate genes may be identified. Like any other
chromosomal region, QTLs and the genes encoded within
them are likely to be conserved across species. So, for example, QTLs for growth and fatness in poultry are likely to
control similar phenotypes in humans and other vertebrates.
Currently, more than 300 mutants have been described in
the chicken (Crawford 1990), and more than 80 have been
mapped. The localization and characterization of these QTLs
will increase our understanding of the basic mechanisms of
development, physiology, and oncogenesis, as well as identify new animal models of human disease.
A particular advantage of data on the chicken genome is
the evolutionary depth of comparisons between birds and
mammals, groups that diverged 350 million yr ago
(Andersson and others 1996). Sufficient data have now accumulated on the gene maps (see section below, Comparative
Gene Maps) to enable comparison of the arrangements of
genes on human and chicken genomes. In the past, one could
only speculate on map homologies based on morphological
characteristics. Information from recent maps of the chicken
genome has led to the surprising conclusion that there is
considerable similarity to the human genome (Andersson
and others 1996; Burt and others 1995, 1997).
CURRENT MAP STATUS, APPROACHES
USED TO GENERATE THE MAP, AND
ANTICIPATED FUTURE CONTRIBUTIONS
OF THE MAP
International Reference Families
International collaborations to map the chicken genome have
been based mostly on 2 reference mapping populations, 1 in
the United States (East Lansing, Michigan) and the other in
the United Kingdom (Compton). To generate the East Lansing mapping family, a single male from the inbred UCD001 Jungle Fowl line was mated to a single female from the
inbred UCD-003 White Leghorn (WL1) line to produce F,
progeny (Crittenden and others 1993). Two ¥{ males were
individually backcrossed to 10 and 8 UCD-003 WL females
to produce 208 and 192 progeny, respectively. Large quantities of blood and DNA from each animal were stored away in
aliquots. A subset of 52 progeny (1 F t male x 4 WL females)
forms the basic East Lansing mapping panel.
229
To generate the Compton mapping family, a single line
151 male was mated to a single line N female to produce
progeny (Bumstead and Palyga 1992). Unlike the East Lansing mapping family, a single F, female individual was backcrossed to a line 151 male to generate the mapping family. The
consequence of using an Fj female instead of a male in the
backcross is that the Z chromosome cannot be mapped in the
Compton mapping family; however, the pseudoautosomal region of the W chromosome can be mapped. DNA from a panel
of 56 individuals forms the primary mapping panel.
Recently, a third chicken reference family was produced
in Wageningen, The Netherlands, by a collaborative effort
between Martien Groenen and Euribrid, a European poultry
breeding company. Using 2 commercial broiler lines, 10 F2
families containing a total of 456 progeny were produced
(Crooijmans and others 1996; M. A. M. Groenen, Wageningen
University, personal communication, 1998). The DNA of this
mapping family is not yet publicly available.
Genetic Markers
TABLE 1 Laboratories associated with the Chicken
Genome Project
Laboratory Director
Institution
Bernard Benkel
Centre for Food & Animal Research, Ottawa, Ontario,
Canada
INRA Centre de Recherche de
Jouy-en-Josas, France
Institute for Animal Health,
Compton, UK
University of Leicester, Leicester,
UK
Roslin Institute (Edinburgh),
Midlothian, Scotland, UK
Avian Disease & Oncology
Laboratory, East Lansing, Ml,
USA
Michigan State University, East
Lansing, Ml, USA
Michigan State University, East
Lansing, Ml, USA
Technical University of Munich,
Freising, Germany
Wageningen Agricultural University, The Netherlands
The Hebrew University of Jerusalem, Rehovot, Israel
Iowa State University, Ames, IA,
USA
University of Minnesota, St. Paul,
MN,USA
Beckman Research Institute of the
City of Hope, Duarte, CA, USA
Avian Disease & Oncology
Laboratory, East Lansing, Ml,
USA
The Hebrew University of Jerusalem, Jerusalem, Israel
National Institute of Agrobiological Resources, Ibaraki, Japan
INRA Centre de Recherche de
Toulouse, Castenet Tolosan,
France
Michele Tixier-Boicharda
Nat Bumsteada
Terry Burkea
Dave Burta
Hans Cheng
Lyman Crittenden
Jerry Dodgson
Ruedi Friesa
Genetic markers comprise the other major component required to build a genetic map. Since map development is
additive when multiple laboratories genotype markers on a
common mapping family, an early decision was made to
distribute the DNAs from the internationally recognized
mapping families (East Lansing and Compton) to interested groups. In Table 1, the major laboratories associated
with the Chicken Genome Project are listed. Each group
genotypes their markers on the reference family and sends
the data to the map curator (Hans Cheng for East Lansing
and Nat Bumstead for Compton) for marker placement.
The information is then made publicly available through
the chicken genome database, Arkdb-CHICK (D. W. Burt,
http://www.ri.bbsrc.ac.uk/).
The reference mapping populations have been typed using markers for expressed genes (that is, cloned genes and
anonymous cDNAs) and anonymous markers (random genomic clones, endogenous retroviruses, short interspersed
repeats [SINEs], or chicken repeat 1 [CR1] repeats, random
amplified polymorphic DNAs [RAPDs], minisatellites or
variable number tandem repeats [VNTRs], and microsatellites). Approximately 1200 marker genes have been mapped
on the East Lansing and Compton maps (Table 2).
Genetic Linkage Maps
The status of each genetic map is continually changing, but
at the time of this writing (October 1998), the status is as
follows (Table 3). On the East Lansing map, 98% of loci are
linked to at least 1 other locus containing 830 loci in 39
linkage groups, for a total length of 4061 cM with an average
marker spacing of 5 cM. On the Compton map, 96% of loci
are linked to at least 1 other locus containing 420 loci in 36
linkage groups, and the total length is 4262 cM with an aver230
Martien Groenena
Jossi Hillel
Susan Lamont
Abel Ponce de Leon
Marcia Miller
Eugene Smith
Morris Soller
Hideaki Takahashi
Alain Vignala
'Members of the European CHICKMAP group.
age marker spacing of 10 cM. On the Wageningen map, 98%
loci are linked to at least 1 other locus containing 471 microsatellite loci in 28 linkage groups, and the total length is 3682
cM with an average marker spacing of 8 cM. The total genetic length of each map was estimated (D. W. Burt unpublished) from a summation of the genetic distance between
loci (recombination fractions were converted to genetic distance using the method of Kosambi 1944) and using an end
correction to adjust for failure to sample telomeric regions
(Morton 1991). Cytological data suggest that the total genetic length of the chicken genome is 2800 to 3300 cM
(Bitgood and Shoffner 1990; Rodionov and others 1992).
ILAR Journal
TABLE 2 Genetic markers on the chicken mapa
Marker type
Total
SINES'3 or CR1fa repeats
Endogenous retroviruses
VNTRsb or minisatellites
Random genomic clones
RAPDsb
Classical genes
cDNAs of unknown function
cDNAs of known function
Microsatellites associated with genes
Total number of genes
Anonymous microsatellites
Total number of microsatellites
Total number of markers
45
37
52
109
68
10
37
92
43
182
634
677
1127
netic maps of the 2 sexes can be compared in the Wageningen
map; and as in other species, the genetic map of the heterogametic sex (female in birds) is shorter than the genetic map of
the homogametic sex (male in birds), but only by 1% (M. A.
M. Groenen, Wageningen University, personal communication, 1998).
A second major goal is to isolate and map sufficient
microsatellite markers to cover the entire genome for whole
genome mapping studies. So far, 677 microsatellites have
been mapped, at an average spacing of 9 cM and with a range
of 6 to 20 cM (Cheng and Crittenden 1994; Cheng and others
1995; Crooijmans and others 1996, 1997; Gibbs and others
1997).
Physical Maps and Resources
a
Data from Arkdb-CHICK, October 1998.
b
CR1, chicken repeat 1; RAPD, random amplified polymorphic DNA;
SINES, short interspersed elements; VNTR, variable number of
tandem repeats.
Thus, the current genetic maps are almost complete, although
there is still some uncertainty due to problems associated
with microchromosomes.
One goal is to assign sufficient common markers to enable cross-comparison between maps. Significant progress
has already been made with 28 consensus linkage groups
defined from an expected total of 39, with 46 linkage groups
in total (Table 4). However, many small linkage groups remain to be associated—7 on the Compton map and 12 on the
East Lansing map. The order of markers on all maps is in
general agreement, although the Compton map is larger than
either the East Lansing map or the Wageningen map. Ge-
Physical maps show the location of markers on individual
chromosomes and provide landmarks for the assignment and
orientation of linkage groups to specific chromosomes. Integration of the physical and genetic maps helps to support
marker order, resolve discrepancies, and determine the coverage of maps. Chicken chromosomes are very numerous
(2n=78) and are classified into macrochromosomes or microchromosomes based on their size. The larger macrochromosomes are easy to differentiate based on their morphology; however, the microchromosomes are too small to be
recognized individually using current banding techniques.
The Z and W chromosomes are the sex chromosomes. A
standard G-banded karyotype was developed by a committee
consisting of J. Bitgood (United States), K. Ladjadi (France),
F. A. Ponce de Leon (United States), and M. Tixier-Boichard
(France) as an aid for comparing physical maps of the macrochromosomes (Ponce de Leon and others 1993). Some linkage groups have been assigned to specific chromosomes by
TABLE 3 Size of genetic linkage groups on the international reference maps
East Lansing,
M l , size
(cM)
Linkage
group
No. of
markers
1
2
3
4
5
6
7
8
Z
155
103
76
57
47
31
26
26
57
522
497
338
218
211
122
146
103
222
12.9
12.2
8.3
5.4
5.2
3.0
3.6
2.5
5.5
252
830
1682
4061
41.4
100.0
(%a)
w
MIC C
Total
Exp %
male
genome b
20.5
14.7
11.2
8.8
5.2
3.4
3.3
2.4
8.2
0.0
22.3
100.0
No. of
markers
Compton,
UK, size
(cM)
(%a)
69
58
51
38
26
9
20
5
738
462
331
433
171
120
149
162
17.3
10.8
7.8
10.2
4.0
2.8
3.5
3.8
12
132
420
95
1601
4262
2.2
37.6
100.0
Exp %
female
genomefa
20.8
15.1
11.5
9.1
5.3
3.5
3.4
2.5
4.2
1.4
23.2
100.0
••Percentage of the total genome.
b
Expected percentage of DNA content based on direct measures of fluorescence (Smith and Burt 1998) (data from Arkdb-CHICK, October 1998).
C
MIC, microchromosomes.
Volume 39, Numbers 2 and 3
1998
231
TABLE 4 Comparison of East Lansing, Ml, and Compton, UK, genetic linkage groups
Linkage
group
East Lansing
size (cM)
Z
222
w
1
2
3
4
5
6
7
8
16
C21
C22
C24
C26
C30
C32
C34
E04
El 7
E24
E32
E38
E41
a
522
497
338
218
211
122
146
103
48
21
8
0
4
35
74
Compton
size (cM)
95
738
462
331
433
171
120
149
162
80
31
0
0
4
84
11
11
0
Chr.
type
Linkage
group
East Lansing
size (cM)
MAC a
MIC
MAC
MAC
MAC
MAC
MAC
MAC
MAC
MAC
MIC
MIC?
MIC?
MIC?
MIC?
MIC?
MIC?
MIC?
MIC?
MIC?
MIC?
MIC
MICa?
MIC
E47
E52
E54
E56
E57
E58
E16C17
E18C15
E22C19
E25C31
E26C13
E27C36
E29C09
E30C14
E31C25
E35C18
E36C06
E40C29
E46C08
E48C28
E49C20
E50C23
E53C34
E59C35
14
54
107
8
14
24
52
38
88
45
62
50
85
63
117
39
117
35
83
90
90
39
105
47
Compton
size (cM)
68
50
81
42
0
40
65
5
92
171
22
142
186
16
58
66
48
33
124
73
Chr.
type
MIC?
MIC
MIC?
MIC?
MIC?
MIC?
MIC?
MIC
MIC?
MIC?
MIC?
MIC?
MIC
MIC
MIC
MIC
MIC
MIC?
MIC
MIC
MIC
MIC?
MIC
MIC
MAC, macrochromosomes; MIC, microchromosomes.
in situ hybridization. In particular, linkage groups have now
been assigned to macrochromosomes 1 through 8, Z, and W.
Specific physical clones (that is, cosmid, PI bacteriophage
artificial chromosome, and bacterial artificial chromosome
[BAC1] clones) are being used to integrate the genetic and
physical maps of microchromosomes. Using 2-color fluorescent in situ hybridization (FISH1), it has been possible to
differentiate 16 of the 30 microchromosomes (Fillon and
others 1996a,b). It should be possible to define all
microchromosomes using a set of reference probes within
the next 3 yr. A World Wide Web (WWW1) page is maintained at the Roslin Institute (Edinburgh, United Kingdom)
as part of the European CHICKMAP project to share information and probes for physical mapping (Jacqueline Smith,
http://www.ri.bbsrc.ac.uk/). This site currently contains information on more than 214 physically mapped clones. It is
our aim to assign and orient all genetic linkage groups to
specific macro- or microchromosomes. An example is the
integration of the genetic and physical maps of chromosome
5 shown in Figure 1.
Numerous laboratories around the world have or are in
the process of developing physical resources for physical
map building and gene isolation as shown in Table 5. The
yeast artificial chromosome (YAC1) and cosmid clones are
232
available on gridded nylon filters from the Berlin Genome
Centre (http://www.rpd.de/).
Comparative Gene Map
The ultimate map is the DNA sequence itself. In the Human
Genome Project, the entire DNA sequence of the human
genome is expected to be complete by 2003. Sequencing the
entire genome is not a priority in poultry and other livestock
species; however, comparisons between human and poultry
maps will provide links to the human DNA sequence. With
many genes now mapped in the chicken, it is possible to
make comparisons between the maps of chickens and mammals (Andersson and others 1996; Burt and others 1995,
1997; Girard-Santosuosso and others 1997; Jones and others
1997; Smith and others 1996, 1997). An example is a comparison of chicken chromosome 3 and its human and mouse
homologous chromosomes (Table 6). Such comparisons will
make it possible both to deduce the evolution of the vertebrate genome and to infer gene assignments to specific chromosomes. At the time of this writing, 220 conserved genes
have been mapped in the chicken, and the following comparative data have been recorded (D. W. Burt, Roslin InstiILAR Journal
1.1
COM0016
COM0015
LEI0082-RDL0247
RDL0253
RDI_0008- f 1 S U 0 0 0 1
COM0013-LE10077^riCU0038
COM0012-.COri0156
HUJ0007
RYR3-LEI0109=fiDL0312COM0089E
COri0070
MCU0029
COM0089E
RDL0233-DNCL«
MCW0081-DNCL-RDL0233
MCU0026
RDL0166
-COri0125E
FIGURE 1 Integration of genetic and physical maps of chromosome 5 (Arkdb-CHICK, October 1998).
tute, 1998, unpublished): 69 human-chicken and 92 mousechicken chromosome homologies (1 or more loci); 44 human-chicken and 46 mouse-chicken conserved syntenies (2
or more loci); 44 human-chicken and 22 mouse-chicken conserved segments (2 or more uninterrupted loci). Using this
sample of conserved linkage data, we have estimated the
expected number of conserved segments to be 79 to 116
human-chicken, 120 to 204 mouse-chicken, and 176 mousehuman (D. W. B., Roslin Institute, 1998, unpublished data;
DeBry and Seldin 1996). Given that 20 to 24 chromosome
pairs are so frequently found in fish and mammals (Morizot
1994), we assume that the ancestral vertebrate genome probably had a karyotype consisting of approximately 24 chromosome pairs. If true, then we can estimate the number of
chromosome rearrangements since a common ancestor to be
71 human-chicken, 131 mouse-chicken, and 152 mousehuman. These results suggest that there have been extensive
rearrangements during the evolution of rodent genomes at a
rate far greater than that found in birds or other mammals
(Andersson and others 1996; D. W. Burt, Roslin Institute,
1998, unpublished). This apparent stability of the avian genome is supported by early work on the conservation of the
TABLE 5 Physical mapping resources
Laboratory
Country
Type of library
Reference
Nat Bumstead
Rima Zoorob
CHICKMAPb
UK
France
European Union
YACa
BACa, PACa
BAC, cosmid
Ann Gibbins
Canada
BAC
Toye and others 1997
Zoorob and others 1996
R. Fries and M. A. M. Groenen, personal
communication, 1997, 1998
Zimmer and Gibbins 1997
a
BAC, bacterial artificial chromosome; PAC, P1 bacteriophage artificial chromosome; YAC, yeast artificial chromosome.
As part of the European CHICKMAP project.
b
Volume 39, Numbers 2 and 3
1998
233
Genetic Markers
TABLE 6 Conservation of synteny, segments, and
gene order
MYCN
ODC1
GSTA2
BMP5
EEF1A
FYN
PLN
ESR
TCP!
T
Chicken
Human
Mouse
3
3
3
3
3
3
3
3
3
3
2
2
6
6
6
6
6
6
6
6
12
12
9
9
4
10
10
10
17
17
46
55
76
86
95
117
125
157
158
161
p24.3
p25
pi 2
q12-q13
q14
q21
q22.1
q25.1
q25-q27
q27
4
6
43
42
Sa
23
S
10
8
4
S, mapped using synteny data.
avian karyotype (Tegelstrom and others 1983). The high degree of conservation found between the gene maps of the
human and the chicken has great practical and evolutionary
significance for the chicken and other vertebrate genomes.
Recently, Groenen and coworkers (Ruyter-Spira and others forthcoming) have taken advantage of the comparative
map to identify a candidate gene for a single gene mutation,
autosomal dwarfism (ADW1), a recessive mutation that results in reduced adult body weight. Using bulked segregant
analysis with microsatellite markers, the ADW locus was
localized to chromosome 1. This particular region shares a
conserved segment with mouse chromosome 10, which is
significant because in mouse, a mutant phenotype, pygmy, is
similar and maps to this region. Since the pygmy phenotype
is the result of a mutation in the high mobility group protein
I-C (HMGI-C1), it is a very good candidate gene for the ADW
chicken mutant. This hypothesis is supported by physical
mapping of the chicken HMGI-C gene to the same location
as the microsatellite that is linked to ADW.
Another example of using comparative QTL mapping is
the recent, published study on Salmonella resistance in species as distantly related as mouse and chicken (Hu and others
1997). This study identified the genes NRAMP1 and TNC as
genes that could account for one third of the early differential
resistance to infection with Salmonella in the chicken.
A realistic goal for the next 5 yr is to achieve an average
marker density of 1 to 2 cM. The accomplishment of this
goal will require 3000 or more markers to be placed on a
framework map. With more than 1500 unique markers already scored on 1 or more of the chicken genetic maps, we
are already halfway toward this goal. In addition to increasing the number of markers, the selected markers should have
a high level of utility (greater than 70% heterozygosity).
One common problem of all the maps is that of marker
order. To resolve this dilemma, markers must be pooled into
"bins." The order of the bins can be determined, and hopefully, increases in the number of meiotic breakpoints (for
genetic linkage mapping) or radiation-induced breakpoints
(for radiation hybrids) will minimize the size of these bins
for greater accuracy. The large resource populations currently being used for QTL mapping with 500 to 2000 progeny will also help to resolve these closely linked markers.
Microsatellite markers are ideal for whole genome scans;
however, their numbers are limited in birds and are often 10fold less abundant than in humans (Primmer and others
1997). For high-resolution mapping, it will be necessary to
use other marker types, such as amplified fragment length
polymorphisms (Vos and others 1995) and single nucleotide
polymorphisms (Kruglyak 1997).
Comparative Map
A natural outcome of mapping more type I markers onto the
genetic map will be a higher resolution comparative map. A
realistic goal in the next 5 yr is to map at least 2000 markers
of genes with human homologues. Faster ways of mapping
genes are needed and might result, for example, in increased
use of FISH and radiation hybrids. In addition, the use of
fiber-FISH may help to resolve gene order on the microchromosomes, often difficult by genetic linkage because of
the large number of progeny needed to detect the rare recombinants on these small chromosomes. Comparative maps
between different avian species should be possible by ZOOFISH, using sorted or microdissected chromosomes. It may
even be possible to compare chicken and human chromosomes by ZOO-FISH.
ANTICIPATED FUTURE CONTRIBUTIONS
OF THE MAP
Integration of Genetic and Physical Maps
The chicken is an ideal livestock species for QTL studies
since the relatively short generation time, the ability to produce large families, and the relatively low rearing costs are
all very favorable characteristics. With the development of
the first generation molecular maps, large-insert libraries,
and databases, the chicken genome project has made significant progress in spite of the limited number of investigators
and limited monetary resources. However, despite initial successes, much remains to be accomplished.
Efforts will continue to integrate the East Lansing, Compton,
and Wageningen genetic maps. All the data are or will be
available on Arkdb-CHICK (http://www.ri.bbsrc.ac.uk/).
Determination of genetic map completeness and identification of the microchromosome-associated linkage groups must
come from the integration of the physical and genetic maps.
Extended physical contig maps may be achievable for some
portions of the map given the expected 3000 or more markers on the genetic map. If we assume that each cM is -400 kb
234
ILAR Journal
or 1 YAC in length, then many regions may have marker
densities of 1 cM or less that are amenable to contig building.
Physical Resources
Gridded bacterial artificial chromosome (BAC1) libraries
have been produced and are now available (contact:
Martien [email protected] or http://www.zod.wau.nl/
vf/chickensite/chicken.html). Chromosome-specific libraries
produced by chromosome sorting or microdissection will be
available for marker isolation and ZOO-FISH studies. Efforts are under way to create radiation hybrid panels for high
throughput gene mapping.
Bioinformatics
Access to marker and map information will continue to be
provided by the ARKdb-CHICK genome database. This site
is under continuous development and will provide access to
other marker and map types, such as radiation hybrid maps
and physical contigs based on YAC and BAC clones. Links
to sequence databases will be improved to provide database
searches for gene homologies.
Genetic Maps of Other Avian Species
A project to produce a microsatellite map of the turkey genome began in April 1997 as a collaboration between the
Roslin Institute and British United Turkeys. This map will be
made available to interested groups in the same way as has
been done with the chicken reference families (DNA, databases, and so forth). We hope that maps on other species
(such as quail and ducks) will also be started for developing
comparative maps among avian species.
USES OF THE MAP AND ACCESSIBILITY
Genome projects are inherently more efficient when they are
the result of group effort, coordinated primarily through formal projects, shared resources and information, and joint
meetings. In Europe, the Economic Community has funded a
CHICKMAP project, started in early 1996 under the coordination of Dave Burt (Roslin Institute). This group aims to
develop tools and resources for QTL mapping in poultry
(genetic markers and maps, physical maps and resources,
comparative maps, and genome databases), as well as to integrate the strengths of many laboratories involved in chicken
genomics. Information on genetic markers, genetic maps,
physical maps, and so forth are provided free from the
CHICKMAP WWW pages (http://www.ri.bbsrc.ac.uk).
Physical resources such as filters of gridded cosmid and YAC
clones are being distributed by the Berlin Genome Centre
Volume 39, Numbers 2 and 3
1998
(http://www.rzpd.de/). A gridded BAC library is also available (address provided in Physical Resources). In the United
States, East Lansing serves as the Poultry Coordination Center of the National Animal Genome Research Program. Besides distributing the East Lansing reference family, microsatellite primer kits are also distributed. Currently, there is a
"Population Tester Kit" containing fluorescently labeled
primers to amplify 9 highly polymorphic microsatellites and
intended for use in other avian species or first-time users of
microsatellite markers. The ability to obtain informative
markers in other avian species has been variable and is probably
dependent on the genetic distance from chicken. Additionally, 3 "Comprehensive Mapping Kits" contain fluorescently
labeled primers for more than 500 microsatellite markers
roughly spaced over the entire chicken genome.
Databases are the main vehicles for sharing scientific
information. The bioinformatics group at the Roslin Institute has developed a generic livestock genome database,
ARKdb (Archibald and others 1996), with the chicken as
one of the represented species. Using the Internet, researchers can access information on maps, markers, sequences,
references, and so forth through a graphic interface (http://
www.ri.bbsrc.ac.uk/). The Roslin site is linked to the East
Lansing site, which also maintains a WWW site (http://
poultry.mph.msu.edu) that contains the latest East Lansing
map and other marker information. These 2 sites, as well as
many others, are linked and are readily accessed on the
WWW.
Regular meetings (such as the 1998 Plant and Animal
Genome meeting in San Diego, California, and the 1998
International Society of Animal Genetics meeting in New
Zealand), newsletters (such as Poultry Genome Newsletter),
and electronic bulletin boards (such as ANGENMAP) also
provide effective sources of information.
CONCLUSION
The chicken genome project has achieved its initial goals,
and it appears that the momentum will continue in the foreseeable future.
ACKNOWLEDGMENTS
We thank the many colleagues and sponsors engaged in the
various multinational collaborations to map the genomes of
poultry. Genome research at the Roslin Institute is supported
by funds from the Ministry of Agriculture, Fisheries and
Food, the Biotechnology Sciences Research Council, and the
Commission of the European Communities. H. H. C. is supported by the US Department of Agriculture (USDA) Agricultural Research Service and grants from the USDA, the
US-Israel Binational Research and Development Fund, and
the US-Israel Binational Science Foundation. The USDA
also provides financial support for public resources.
235
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