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Vol. 11, Issue 10, 1784-1795, October 2001
RESOURCES
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ABSTRACT |
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We present here the first fully integrated, comprehensive map of the canine genome, incorporating detailed cytogenetic, radiation hybrid (RH), and meiotic information. We have mapped a collection of 266 chromosome-specific cosmid clones, each containing a microsatellite marker, to all 38 canine autosomes by fluorescence in situ hybridization (FISH). A 1500-marker RH map, comprising 1078 microsatellites, 320 dog gene markers, and 102 chromosome-specific markers, has been constructed using the RHDF5000-2 whole-genome radiation hybrid panel. Meiotic linkage analysis was performed, with at least one microsatellite marker from each dog autosome on a panel of reference families, allowing one meiotic linkage group to be anchored to all 38 dog autosomes. We present a karyotype in which each chromosome is identified by one meiotic linkage group and one or more RH groups. This updated integrated map, containing a total of 1800 markers, covers >90% of the dog genome. Positional selection of anchor clones enabled us, for the first time, to orientate nearly all of the integrated groups on each chromosome and to evaluate the extent of individual chromosome coverage in the integrated genome map. Finally, the inclusion of 320 dog genes into this integrated map enhances existing comparative mapping data between human and dog, and the 1000 mapped microsatellite markers constitute an invaluable tool with which to perform genome scanning studies on pedigrees of interest.
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INTRODUCTION |
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The modern domestic dog features more than 300 well-defined isolated
breeding populations, most of which are readily
accessible for mapping genes involved in complex phenotypes (Ostrander
and Giniger 1997
; Galibert et al. 1998
; Ostrander et al. 2000
). Indeed, extensive canine pedigrees, coupled with an enormous diversity in
morphology and behavior, provides a valuable mechanism for understanding the genetic regulation of mammalian growth and
development. In addition, the mating of closely related individuals in
order to maximize segregation of desirable traits has led to the
propagation of autosomal recessive diseases in the modern dog, many of
which are similar or, in some cases, identical to human diseases (e.g., Dodds 1989
; Menon et al. 1992
; Sharp et al. 1992
; Stolzfus et al. 1992
;
Henthorn et al. 1994
; Zheng et al. 1994
; Acland et al. 1998
, 1999
; Lin
et al. 1999
; Veske et al. 1999
). To date, ~360 genetic diseases have
been identified in the dog, representing the largest number reported
for any nonhuman mammal (Patterson 2000
, 2001
). Genetic linkage
analysis utilizing domestic dog pedigrees, therefore, should provide a
unique and efficient mechanism for understanding the molecular and
cellular biology of human health and disease (Patterson et al. 1988
;
Ostrander et al. 2000
).
In the past three years, we and our collaborators have made major
advances in the production of a canine meiotic linkage map (Lingaas et
al. 1997
; Mellersh et al. 1997
; Neff et al. 1999
; Werner et al. 1999
)
and a radiation hybrid (RH) map (Priat et al. 1998
; Mellersh et al.
2000
). The recently published meiotic linkage map was composed of
~350 markers organized into linkage groups for 37 autosomes and the X
chromosome (Werner et al. 1999
), whereas the RH map was composed of 600 markers, including 218 genes and 382 microsatellites, organized into 77 RH groups (Priat et al. 1998
; Mellersh et al. 2000
). By taking
advantage of 216 markers mapped on both a set of three-generation
reference families (Mellersh et al. 1997
) and on a well-characterized
canine RH panel (Vignaux et al. 1999
), integration of the linkage and
RH maps has been accomplished, leading to the production of a
724-marker map (235 genes and 489 microsatellites) with a marker
spaced, on average, every 3.7 cM or 24.3 cR5000 (Mellersh et
al. 2000
). The evolutionary relationship between the canine and human
genomes is also now well established through the efforts of two
independent groups, both of whom have used bidirectional heterologous
chromosome painting to identify evolutionarily conserved regions of
human chromosomes (reciprocal Zoo-FISH; Breen et al. 1999c
; Yang et al.
1999
). Specifically, Breen et al. (1999c)
and Yang et al. (1999)
propose that 68 and 73 evolutionarily conserved segments, respectively,
from the human genome can be visualized by reciprocal Zoo-FISH. Most
recently, Sargan et al. (2000)
expanded the latter of these reports and
assigned all linkage, RH, and syntenic groups from the most recently published
canine genome map (Mellersh et al. 2000
) to specific dog chromosomes.
Although the accuracy and utility of the map are evidenced by the
localization of disease loci for canine renal cancer, narcolepsy, multiple forms of retinitis pigmentosa, hematologic disorders, and
several metabolic diseases (e.g., Henthorn et al. 1994
;
Yuzbasiyan-Gurkan et al. 1997
; Acland et al. 1998
; Lingaas et al. 1998
;
Lin et al. 1999
; Jónasdóttir et al. 2000
), at this juncture those
wishing to exploit the dog system for refined mapping and cloning of
complex diseases will be met with several significant obstacles. The
placement of a marker every 3-4 cM is sufficient to ensure that genome
scans of canine families will identify linked markers, but a denser map
of more highly informative microsatellites is clearly needed for
refining regions defined by linkage, as well as to facilitate the
mapping of disease loci within highly inbred families. A more precise
understanding of the evolutionary relationship between the canine and
human genomes is needed in order that all evolutionary breakpoints may
be mapped, and data from the more comprehensively mapped human and
murine genomes used for the selection of candidate genes in the study
of diseases. The meiotic linkage and RH maps must be fully integrated
with the cytogenetic map. The latter represents a particularly
challenging task because the similarity in size and banding patterns of
many dog chromosomes renders them notoriously difficult to identify by
classical cytogenetic methods. Using conventional cytogenetics, the
International Committee for the Standardization of the Karyotype of the
Dog was able to standardize the karyotype for dog chromosomes 1-21 and
the sex chromosomes (Switonski et al. 1996
). The Committee then
assigned the chromosome-specific paint probes developed by Langford et
al. (1996)
and recommended that the chromosome numbering of Reimann et
al. (1996)
should be used for the remaining autosomes (Breen et al.
1998
, 1999a
). In this report we describe our collective effort to
produce an integrated map of the dog genome incorporating cytogenetic,
RH, and meiotic data. Building upon a newly developed set of 266 FISH-mapped chromosome-specific cosmid clones, each containing a
microsatellite marker that unambiguously identifies one of the 38 autosomes of the dog, we are able for the first time to assign all dog
chromosomes to their corresponding meiotic linkage and RH groups. The
resulting map features 1078 microsatellites, 320 gene-based markers,
and a total of 302 chromosome-specific markers, all of which are
assigned by FISH using what is now agreed upon as the standardized
chromosome nomenclature. This more than doubles the previously reported
density of markers. All known evolutionary breakpoints in the human map are assigned to the canine cytogenetic map and therefore to the RH and
linkage maps. Finally, RH mapping of proximal and/or distal markers
that were initially mapped by FISH has allowed all but four integrated
groups to be orientated. The resulting map, which features robust
anchor points on every dog chromosome and a high density of polymorphic
markers, provides an invaluable resource for the mapping and cloning of
canine genes of interest.
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RESULTS |
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In this paper we present an integrated cytogenetic/RH and meiotic map of the dog. We localized 266 microsatellite-containing cosmid clones on all dog chromosomes through FISH analysis, assigning 1500 markers by RH analysis and 354 markers by meiotic linkage analysis. Through sets of common markers, 251 RH/genetic, 102 RH/cytogenetic, and 52 linkage/cytogenetic, one or more RH groups and one genetic linkage group were assigned to each dog chromosome. This represents an integrated map with 1800 unique markers. In total, 72 RH groups are assigned to all chromosomes of the dog and 39 meiotic linkage groups are assigned to all autosomes plus the X chromosome. The resulting map (poster enclosed with this issue as Fig. 1) covers >90% of the genome.
Cytogenetic Map
Chromosome-Specific FISH Probe Selection
The cytogenetic localization of 266 microsatellite-containing cosmid clones (designated AHT-Kxxx, AHT-Hxxx, or LEI-xxx) was determined by analysis of FISH data. Chromosome assignments were made according to the nomenclature of the International Committee for the Standardization of the Dog Karyotype (Switonski et al. 1996RH Map: Marker Characteristics
Microsatellite Markers
A total of 1078 anonymous markers are now positioned on the canine RH map, of which 786, 20, and 272 are based upon di-, tri- and tetranucleotide repeats, respectively (Table 1). Polymorphism for each marker was evaluated either by heterozygosity (Het) or PIC values; 50% had Het or PIC values >0.5 (indicated by a triple star in Fig. 1) and 20% (mainly the tetranucleotide repeats) had Het or PIC values >0.75. The markers are randomly distributed throughout the autosomes and also the X chromosome. The 561 most polymorphic markers have an average distribution of 1 per 42 cR5000 (4.2 Mb), so indicating that, on average, any point on the map is now within 10 cM of a highly polymorphic marker.
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Gene-Based Markers
The 320 gene-based markers were composed of 252 dog gene markers (Priat et al. 1999Chromosome-Specific Markers
End sequencing of FISH-mapped chromosome-specific cosmid clones was used to derive 68 novel chromosome-specific markers. These markers were added to 35 previously identified FISH mapped markers, 12 of which (connected by green lines in Fig. 1) were reported by Werner et al. (1999)
on CFA 4, DLAA9 on CFA 12, ROM1 on CFA 18, RHO on CFA 20, RB1 on CFA
22, and RTB on CFA 27). Data from all 103 chromosome-specific
markers were typed in duplicate.
Radiation Hybrid Mapping
The 900 new markers added here, as compared with the map reported by
Mellersh et al. (2000)
, were typed on the 118-cell-line RHDF5000-2
panel (Vignaux et al. 1999
). Data from these markers were added to the
previous 600-marker RH map (Mellersh et al. 2000
) and computed using
the MultiMap software. Pairwise linkage analysis at
LOD > 8.0 resulted in 89 RH groups. A total of 1413 out of 1500 markers were incorporated into these RH groups, with the remaining 87 markers remaining unlinked. The presence among RH markers of 102 chromosome-specific markers allowed 72 of the RH groups to be linked to
one another resulting in 40 larger groups, each of which was assigned
to a specific dog chromosome (Fig. 1). The 17 remaining orphan RH
groups, which include 2-12 markers, have a cumulated size of 586 cR5000, representing only 2.5% of the map (data not shown).
The marker order for each RH group was obtained using Multipoint
analysis. The order was initially determined using an LOD score
of >3.0 (likelihood odds = 1000/1), resulting in a framework map
consisting of 579 markers (45%). These markers are underlined in
Figure 1. All remaining markers were then integrated relative to the
framework markers to give the comprehensive map presented here. For RH
groups presenting inconsistent ordering data, the initial pairwise
analysis was repeated using a higher LOD score value (LOD > 9) that
resulted in the formation of more RH groups. Ordering could then be
carried out by multipoint analysis. The number of RH markers assigned
to each autosome ranged from 67 markers (CFA 1) to a minimum of 8 (CFA
38), with the smallest dog chromosome, Y, having only 4 markers. The
size of RH groups assigned to each chromosome ranged from 1272 cR5000 (CFA 1) to 112 cR5000 (CFA 38), with 17 cR5000 for the Y chromosome. The total size of the RH map is
23,428 cR5000 with 1413 markers mapped to 1354 unique
positions. Thus, the average intermarker distance is 17 cR5000. Compared with the previously reported RH map
(Mellersh et al. 2000
), the present map represents a 2.5-fold increase
in marker density, and decreases the average intermarker distance 1.5-fold.
Using maximum likelihood predictions, the canine genome has been
estimated to be 26.5 M (Neff et al. 1999
). The total length of the RH
map presented here is 23,428 cR5000. Taking into account the
cR/kb correspondence (see below) and the correspondence of 1 Mb/1 cM,
the total size of the RH map thus amounts to 23.5 M. This map,
therefore, is estimated to cover 88% of the canine genome. In
agreement with this coverage estimate, only 7% of the markers remain
unlinked at this point of the RH-map construction.
Meiotic Map: Marker Characteristics
Chromosome-Specific Microsatellite Markers
We selected 38 chromosome-specific cosmid clones (one per autosome) for the isolation of microsatellites. DNA prepared from these clones was shotgun-cloned into M13, and (CA)n-positive subclones were sequenced to identify a microsatellite repeat sequence. In Table 2 we present the primer sequences and optimized PCR conditions for all selected chromosome-specific microsatellite loci.
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Meiotic Linkage Mapping
Microsatellites from each of the 38 dog autosomes were genotyped on
dog reference families that have been described previously (Mellersh et
al. 1997
), and the data were merged with those from the previous
meiotic linkage map described by Werner et al. (1999)
. We identified 39 linkage groups, containing a total of 350 markers. Of these 38 groups
could be assigned to a chromosome via a chromosome-specific microsatellite marker. An additional linkage group did not contain a
chromosome-specific microsatellite and could not, therefore, be
conclusively assigned to a chromosome (data not shown).
The chromosome-specific microsatellites could be assigned to their respective linkage groups with varying levels of significance. For 32 autosomes, CFA 1-12, 14-27, 29, 31, 33, 35-37, the chromosome-specific microsatellites were linked to other microsatellites in the corresponding group with LOD scores >5.0, indicating significant evidence of linkage. Meiotic linkage data for the six remaining chromosomes were as follows: the chromosome-specific microsatellite for CFA 13 (AHTH310) was linked to one other marker (FH2394) in the group with a LOD score >4.0, and to multiple other markers in the same group with LOD scores >3.0. The markers representing CFA 28 (AHTK135), CFA 32 (AHTH327), and CFA 34 (AHTH163) were each linked to a single marker (LEI006, CPH2, and FH2377, respectively) in their corresponding groups with a LOD score >3.0. For CFA 30 (LEI-1F11) and CFA 38 (AHTH91), the best two-point LOD scores were 2.709 (to PEZ7) and 2.912 (to FH2244), respectively. However, RH data for these two markers did enable them to be assigned to their respective groups with significant LOD scores (>8.0), thus validating the assignment of the whole group.
The Integrated Map: Integration of the Three Maps
The use of FISH analysis to integrate the RH and meiotic maps with the cytogenetic map is illustrated in Figure 2. A comparison of the RH, meiotic, and cytogenetic maps shows that they are highly concordant. The only observed discrepancies in the colinearity between the maps is the inversion of a segment containing four markers on CFA 4, and 20 inverted pairs of markers distributed on other autosomes. Chromosome-specific FISH-mapped markers were RH-mapped on all chromosomes as follows: 8 dog chromosomes harbor 3-6 probes, 20 have 2 probes, and 12 chromosomes have 1 probe. RH/meiotic groups could be readily orientated on 33 chromosomes owing to the localization of at least one FISH probe at one end of the chromosome. Another chromosome, CFA 19, could be oriented because of syntenic conservation between human and dog chromosomes. The maps for the remaining four autosomes (i.e., CFA 21, CFA 32, CFA 35, and CFA 36), each harboring one midchromosome probe, and for the two sex chromosomes cannot as yet be orientated (Fig. 1).
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By comparing the size in megabases of a chromosome (deduced by the
bivariate flow-sorting measurements of Langford et al. 1996
) to the
size of the RH group harboring FISH markers located at the two ends of
the chromosome (this was possible for CFA 1, CFA 10, CFA 12, CFA 14, and CFA 20), a correspondence of 1 cR5000 for 100 kb was
calculated. This result compares well with those reported for human and
murine genomes at comparable radiation doses (McCarthy et al. 1997
;
Stewart et al. 1997
).
Coverage of the Integrated Map
Our data indicate that RH groups span the length of all but three autosomes, CFA 32, CFA 36, and CFA 38, for which we observed a clear difference between the size of the chromosome and that of the corresponding RH group. Specifically, CFA 32 and CFA 36 are each composed of one RH group, covering approximately half of the chromosome, whereas CFA 38 is covered by one RH group representing approximately one-third of the chromosome. The X chromosome is more poorly covered by two RH groups and four single markers. Regions not covered by the RH map can be estimated to 200 Mb, or ~8% of the total genome size. However, unlinked markers and orphan RH groups are likely to fill the gaps.
The size of meiotic linkage groups in Figure 1 approximates to their
chromosome length for all but eight autosomes: CFA 6, CFA 17, CFA 19, CFA 21, CFA 24, CFA 32, CFA 34, and CFA 36. Coverage of chromosomes by
their corresponding meiotic linkage group is 60% for CFA 19 and CFA
21, 50% for CFA 6 and CFA 24, 30% for CFA 17 and CFA 32, 20% for CFA
36, and 10% for CFA 34. The X chromosome is covered at 50%. However,
by combining data from the RH and meiotic linkage maps, only half of
both CFA 32 and CFA X and two-thirds of CFA 36 are not represented in
the integrated map. A summary of the relevant statistics of the
integrated map is shown in Table 3.
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Comparative Mapping
For each dog chromosome presented in Figure 1, we have illustrated
the regions of evolutionarily conserved chromosome segments that were
observed in the Zoo-FISH studies of Breen et al. (1999c)
. Although Yang
et al. (1999)
used a different chromosome nomenclature from that
recently endorsed (International Society for Animal Genetics 2000, G. Dolf, DogMap Chairman, pers. comm.) and in use here, correspondence
between the two chromosome numbering systems was tentatively identified
by Sargan et al. (2000)
. Our localization of 320 gene markers on the RH
map has now verified this correspondence. This has allowed us to
confirm that these two studies were grossly comparable in their
assessment of the distribution of human conserved chromosome segments
throughout the dog karyotype. We observed differences in five cases.
Four differences were at the proximal end of CFA 4, CFA 18, and CFA 31 and the telomeric end of CFA 25. This was because of the lack of
visible signal at the centromeric and telomeric ends of the dog
chromosomes reported by Breen et al. (1999c)
, a phenomenon that has
also been reported for other species (Jauch et al. 1992
; Wienberg et
al. 1992
; Nash et al. 1998
). However, hybridization signals were
observed in these regions by Yang et al. (1999)
, and we have now
confirmed the presence of these regions by identification of
corresponding type I markers in the RH map. The additional information
for these four regions provided by Yang et al. (1999)
is therefore
included in Figure 1, highlighted with (Y) beside the data. A fifth
difference was observed toward the distal end of CFA 10, where Yang et
al. (1999)
reported a small block of HSA 12 between blocks of HSA 22 and HSA 2 reported by Breen et al. (1999c)
. This finding has not yet been confirmed by RH mapping. Zoo-FISH data between dog and human identified no fewer than 67 (Breen et al. 1999c
) or 75 conserved chromosome segments (Yang et al. 1999
). RH mapping of dog genes whose
human locations are known has thus far allowed the detection of 65 conserved segments.
For 229 RH-mapped dog genes, the human localization of the putative
ortholog was known. All but two dog chromosomes (CFA 32 and CFA 36)
harbor at least one (and up to 22) gene marker for which a physically
mapped human ortholog is known. The absence of any mapped gene on CFA
32 and CFA 36 precluded the use of the RH data for comparative
assessment of these two autosomes. Conserved syntenic fragments between
dog and human are indicated in Figure 1, with colored boxes to the
immediate left of the RH markers. Apparently 18 dog chromosomes
correspond to only one human fragment each, that is, CFA 8/HSA 14q, CFA
12/HSA 6pq, CFA 14/HSA 7pq, CFA 21/HSA 11pq, CFA 22/HSA 13q, CFA 23/HSA
3pq, CFA 24/HSA 20pq, CFA 27/HSA 12pq, CFA 28/HSA 10q, CFA 29/HSA 8q,
CFA 30/HSA 15q, CFA 33/HSA 3q, CFA 34/HSA 3q, CFA 35/HSA 6p, CFA 37/HSA
2q, CFA 38/HSA 1q, X/X, and Y/Y. Another 13 dog chromosomes (CFA 7, CFA 9, CFA 10, CFA 11, CFA 13, CFA 15, CFA 16, CFA 17, CFA 18, CFA 19, CFA
20, CFA 26, and CFA 31) correspond to two human fragments each, and the
remaining 9 dog chromosomes correspond to three or four different human
chromosomal fragments each. In contrast, only four human chromosomes
share exclusive conserved synteny with a dog chromosome (HSA 14/CFA 8, HSA 20/CFA 24, HSA 21/CFA 31, and chromosome X). The remainder are
split into two to eight chromosomal segments (e.g., HSA 1 is split into
eight fragments in the dog, corresponding to regions of CFA 2, CFA 4, CFA 5, CFA 6, CFA 7, CFA 15, CFA 17, and CFA 38; Breen et al. 1999c
;
Yang et al. 1999
).
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DISCUSSION |
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Great strides have been made over the past few years toward the
development of a canine genome map. Prior to this study, however, there
were a number of limitations associated with the canine map.
Chromosomal assignment of meiotic linkage groups had been made for only
19 of the 38 dog autosomes (Mellersh et al. 2000
), with the remainder
being referred to as anonymous linkage groups. In addition, the
chromosomal orientation of the meiotic linkage and RH groups was
largely unknown. Furthermore, estimates of genome coverage had been
entirely theoretical, and little was known about the extent to which
the RH and meiotic linkage maps extended along the length of their
respective chromosomes. In this study we have addressed these issues.
We have conclusively assigned 266 cosmid clones to their specific dog
chromosomes, by FISH, using the chromosome numbering system endorsed by
the ISAG 2000 DogMap workshop (G. Dolf, DogMap Chairman, pers. comm.).
Because all the cosmid clones had been prescreened to contain a
microsatellite repeat, they represent not only additional
chromosome-specific genetic markers but also the key resource that
enabled us, for the first time, to integrate the canine meiotic linkage
and RH maps with the cytogenetic map.
Meiotic linkage data from 38 chromosome-specific microsatellite
markers, derived from these clones, were used to anchor meiotic linkage
groups to each of the 38 autosomes. RH mapping of 102 chromosome-specific markers similarly allowed us to assign 72 RH groups
to all chromosomes comprising the dog karyotype, and provide an
integrated cytogenetic, meiotic linkage, and RH map of the dog.
Moreover, FISH mapping of other previously RH-mapped markers strengthen
the chromosomal assignments made in this study, for example,
GALK1, RARA, THRA1, NF1, and
KRT17 on CFA 9 (Werner et al. 1997
; Miller et al. 1999
),
C04107 on CFA10 (Van der Sluis et al. 1999
), PROP1 on
CFA11 (Lantinga-van Leuween et al. 2000a
), and PIT1 on CFA31
(Lantinga-van Leuween et al. 2000b
). Sixteen of the 19 integrated
assignments reported by Werner et al. (1999)
and Mellersh et al. (2000)
are in agreement with the nomenclature used in this study. However,
there are three discrepancies in chromosome nomenclature. In this
report the chromosomes we refer to as CFA 17, CFA 23, and CFA 27 were
described by Werner et al. (1999)
and Mellersh et al. (2000)
as CFA 15, CFA 22, and CFA 16, respectively. Reciprocal exchange of probes from
both laboratories now confirms that the nomenclature used here is
correct (P. Werner and M. Breen, data not shown). Also in this study,
when possible, we used RH and meiotic linkage mapping to position
chromosome-specific markers that had been FISH-mapped to both the
proximal and distal ends of each chromosome. This approach allowed us
to orientate all but four of the integrated RH and meiotic groups on
the chromosomes to which they have been assigned. The exceptions are
those groups assigned to CFA 21, CFA 32, CFA 35, and CFA 36, which will
require additional markers to reveal their true orientations. In the
previous meiotic (Werner et al. 1999
) and RH (Mellersh et al. 2000
)
maps, calculation of the coverage was based on theoretical
considerations. Integration of the RH, meiotic, and cytogenetic maps
allowed a more accurate assessment of chromosome coverage, as is
demonstrated clearly in Figure 1. Good coverage is evident for all
autosomes, with the exception of half of CFA 32 and X as well as
two-thirds of CFA 36. The integrated RH/cytogenetic map would,
therefore, confirm genome coverage >90%. Chromosomes for which the
map coverage is less than complete can now be targeted by specific
efforts to provide full coverage. For instance, the meiotic linkage
maps for three chromosomes in particular, CFA 6, CFA 19, and CFA 24, appear to be short (to varying extents) at the proximal and/or distal
ends, and the map for CFA 17 appears not to represent the distal half
of the chromosome. In all these cases we will aim to select the markers
at the ends of both the RH and meiotic maps, in order to isolate BAC
clones that may then be FISH-mapped to determine the true extent of the
chromosome coverage of the existing maps.
The meiotic linkage groups assigned to seven chromosomes (CFA 21, CFA
32, CFA 33, CFA 34, CFA 35, CFA 36, and CFA 38) do not yet contain a
sufficient number of appropriately placed markers to accurately
determine the extent of chromosome coverage. We are therefore pursuing
these chromosomes from a comparative angle by targeting type I markers
that have been mapped in the corresponding evolutionarily conserved
chromosome segments as identified by Breen et al. (1999c)
and Yang et
al. (1999)
.
The present study provides a significant advance in the development of
an effective genome map of the dog. The genome-wide integration of the
meiotic and RH maps with the cytogenetic map, together with the
increase in the number and density of RH-mapped markers, will improve
our ability to use the canine genome to identify important genes in
major ways. It will now be possible to assign accurately markers linked
to canine disease genes to their corresponding position in the human
genome, using the set of conserved genes presented in this study in
combination with previously established gross levels of conserved
synteny, reported by Breen et al. (1999c)
and Yang et al. (1999)
. This,
in turn, will provide a mechanism for identifying appropriate
positional candidate genes whose disease-causing roles can subsequently
be investigated. In addition, the significant increase in the number of
informative microsatellites on the RH map will facilitate the direct
identification of a disease-associated gene from that of a linked
marker. The 561 polymorphic di- and tetranucleotide microsatellites in
the integrated map will provide complete coverage of the dog genome
because any position in the genome is within an average of 10 cM of at
least one of these microsatellites. Finally, this integrated map will
facilitate the cloning of desired genes, because it allows us to
exploit the dog as a powerful new genetic system for mapping complex
traits that have been difficult to identify through corresponding
studies of human families.
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METHODS |
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Generation of Chromosome-Specific Data
A dog cosmid genomic library in pWE15 (Stratagene) was gridded
manually and screened for the presence of CA/GT repeats, using high
stringency, as described previously (Holmes et al. 1993
). A total of
2304 cosmids were screened, and 328 (26%) were found to be positive.
DNA from all positive clones was prepared using either a QIAprep
(QIAGEN) or Wizard Plus SV (Promega).
Fluorescence in Situ Hybridization (FISH)
Metaphase chromosomes of the dog and all probes were prepared for FISH as described by Breen et al. (1999b)Image Acquisition and Chromosome Assignment
Images were acquired and processed using a FISH workstation comprising a fluorescence microscope (Axiophot, Zeiss) equipped with an FITC/Texas Red/DAPI excitation filter set and a cooled CCD camera (KAF 1400, Photometrics), both driven by dedicated software (SmartCapture, Vysis Inc.). The digital image of each DAPI-stained metaphase spread was processed using a high-pass spatial filter to reveal enhanced DAPI bands. Each clone was assigned to a chromosome band according to the DAPI-banded nomenclature of Breen et al. (1999a)RH Map Data
Generation of RH Markers
Accession numbers and marker characteristics appear at http://www-recomgen.univ-rennes1.fr/doggy.html. Microsatellite markers with the motif (CA)n were isolated from a small-insert dog genomic library (Jouquand et al. 2000b
(Pi)2, with
Pi corresponding to allele frequencies. Dog gene
markers and dog ESTs from a retinal cDNA library were retrieved from
public databases. Primers were designed utilizing the
Primer3 program.
Chromosome-Specific Markers
Sequence information was obtained from at least one chromosome-specific cosmid clone per chromosome and, where possible, from at least two clones that had been FISH-mapped to proximal and distal ends of the corresponding chromosome. For each chromosome-specific marker, sequence data were generated from the corresponding cosmid clone, in the flanking regions of each microsatellite locus. For all these markers, primers were designed to amplify fragments of 200-500 bp under unique PCR conditions, as described previously (Priat et al. 1999RH Typing and RH Map Construction
Markers were typed on the RHDF5000-2 dog/hamster radiation hybrid panel. This panel, consisting of 118 hybrids, was selected from the original RHDF5000 panel (Vignaux et al. 1999
ln(1
), where
is the breakage frequency. Distances are referred to as centirays (cR5000), in reference to the 5000-rad value used to construct the panel.
Meiotic Linkage Data
A subset of 38 chromosome-specific cosmid clones was processed to characterize their respective microsatellite markers.
Subcloning and Identification of Microsatellite Markers
DNA from at least one clone per chromosome was subjected to restriction digestion with Sau3A1, HaeIII, or Alu1, and the resulting fragments were subcloned into either the BamH1 site of M13mp18 or the HincII site of M13mp19 (Oncor Appligene). Single-strand preparations or PCR products were sequenced from either end of the insert, with M13 primers using an ABI-377 sequencer (PE Biosystems). For clones in which the CA/GT repeat lay outside the region of readable sequence, a set of six primers [(GT)10N, where N = A, C, or T; (TG)10N, where N = A, G, or C] was used to sequence outward from the repeat to identify flanking sequences suitable for the design of primers to amplify the microsatellite. Microsatellites characterized at the Animal Health Trust are denoted by the prefix AHT, and those characterized at the University of Leicester are denoted by the prefix LEI.Design of Suitable Locus-Specific PCR Primers
PCR primers were designed either manually or with the aid of the program PRIMER v3. All primers were synthesized commercially (Genset; Amersham Pharmacia Biotech). PCR reactions were carried out on an MJ-Tetrad thermal cycler. Microsatellites were typed either by incorporation of fluorescently labeled dUTP during the PCR and analyzed on an ABI-377 sequencer with GENESCAN and GENOTYPER software (PE Biosystems) or by end-labeling of one primer with [
33P]dATP using T4 polynucleotide kinase.
Genotyping of Chromosome-Specific Microsatellites
Microsatellites were genotyped on a panel of canine reference pedigrees described previously (Mellersh et al. 1997Meiotic Linkage Map Construction
Genotyping data from our panel of chromosome-specific microsatellites were merged with data from previous studies (Werner et al. 1999Human/Dog Comparative Mapping
Orthologous human genes have been defined by BLAST
searches (Altschul et al. 1990
) against public databases (GenBank "nr" and "HTGS") in February 2001; default BLAST
criteria were used. Chromosomal locations have been found in GeneAtlas (http://www.citi2.fr/GENATLAS) and LocusLink
(http://www.ncbi.nlm.nih.gov/LocusLink).
Web Sites
Comprehensive data of the integrated map (tables and figures) and the characteristics of all markers will appear on the following linked Web sites: http://www-recomgen.univ-rennes1.fr/doggy.html, http://www.aht.org.uk/cytogenetic-map/dog.html, and http://www.fhcrc.org/science/dog_genome/dog.html.
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ACKNOWLEDGMENTS |
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We thank Sally Debenham and Philip Ricketts (Animal Health Trust) for technical help. Canine genome analysis at the Animal Health Trust and the University of Leicester is generously supported by the Guide Dogs for the Blind Association. F.G. is supported by funds from CNRS, Conseil Regional de Bretagne, and the American Kennel Club/Canine Health Foundation. We thank Thierry Giffon and Edouard Cadieu for their help in RH mapping as well as Stephane Dréano for sequencing and Bruno Coutard, Valérie Lelaure, and Hervé Cartron for their help in microsatellite isolation, and Tara Matise for her help in the use of the MultiMap package. E.A.O. is supported by grants from the American Kennel Club/Canine Health Foundation, the American Cancer Society, and a Burroughs Wellcome Fund Award for Excellence in Innovative Genomics. C.S.M. is generously supported by a fellowship from Ralston Purina. We are grateful to the American Kennel Club Canine Health Foundation and Ralston Purina for sponsoring the production of the integrated map as a poster. We also thank the Geraldine Rockefeller Dodge Foundation.
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FOOTNOTES |
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5 These authors contributed equally to this work.
6 Corresponding authors.
E-MAIL mtbreen{at}hgmp.mrc.ac.uk; FAX 44-1638-750794
E-MAIL Francis.Galibert{at}univ-rennes1.fr; FAX 33-2993-36200.
Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.189401.
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REFERENCES |
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|
|
|---|
gene microdeletion demonstrates that canine X-linked severe combined immunodeficiency is a homologue of the human disease.
Genomics
23:
69-74[CrossRef][Medline].
-L-iduronidase.
J. Biol. Chem.
267:
6570-6575
5 chain of collagen type IV.
Proc. Natl. Acad. Sci.
91:
3989-3993Received March 21, 2001; accepted in revised form July 25, 2001.