Genomics 88 (2006) 415 – 430
www.elsevier.com/locate/ygeno
A microsatellite-based genetic linkage map of the waterflea,
Daphnia pulex: On the prospect of crustacean genomics☆
Melania E.A. Cristescu a,⁎, John K. Colbourne b , Jelena Radivojac b , Michael Lynch a
a
b
Department of Biology, Indiana University at Bloomington, Bloomington, IN 47405, USA
Center of Genomics and Bioinformatics, Indiana University at Bloomington, Bloomington, IN 47405, USA
Received 8 February 2006; accepted 14 March 2006
Available online 19 April 2006
Abstract
We describe the first genetic linkage map for Daphnia pulex using 185 microsatellite markers, including 115 new markers reported in this
study. Our approach was to study the segregation of polymorphisms in 129 F2 progeny of one F1 hybrid obtained by crossing two genetically
divergent lineages of Daphnia isolated from two Oregon populations. The map spanned 1206 Kosambi cM and had an average intermarker
distance of 7 cM. Linkage groups ranged in size from 7 to 185 cM and contained 4 to 27 markers. The map revealed 12 linkage groups
corresponding to the expected number of chromosomes and covers approximately 87% of the genome. Tests for random segregation of alleles at
individual loci revealed that 21% of the markers showed significant transmission ratio distortion (primarily homozygote deficiency) likely due to
markers being linked to deleterious recessive alleles. This map will become the anchor for the physical map of the Daphnia genome and will serve
as a starting point for mapping single and quantitative trait loci affecting ecologically important phenotypes. By mapping 342 tentative
orthologous gene pairs (Daphnia/Drosophila) into the Daphnia linkage map, we facilitate future comparative projects.
© 2006 Elsevier Inc. All rights reserved.
Keywords: Crustacea; Transmission ratio distortion; Microsatellite DNA; Recombination; Genetic crosses; Comparative genomics; Daphnia; Linkage
The waterflea Daphnia pulex (Crustacea, Cladocera,
Anomopoda) is an aquatic crustacean that has been central
to ecological, toxicological, and evolutionary studies for
several decades [1]. More recently, Daphnia has been
advanced as the main nonclassical model organism for
evolutionary and ecological genomics. Its genome consists of
12 pairs of chromosomes characterized by hypercondensation
and minute size [2,3] and contains no sex chromosomes. A
previous estimate of haploid C value of 0.24 pg [4]
corroborates with subsequent genome size estimates from
the Daphnia genome sequencing project of 199 Mb, which
places the waterflea near the fruit fly (184 Mb) in terms of
genome size.
☆
Sequence data from this article have been deposited with the EMBL/
GenBank Data Libraries under Accession Nos. DQ249348–DQ249470.
⁎ Corresponding author. Fax: (812) 855 6705.
E-mail address: [email protected] (M.E.A. Cristescu).
0888-7543/$ - see front matter © 2006 Elsevier Inc. All rights reserved.
doi:10.1016/j.ygeno.2006.03.007
Genetic linkage maps have become essential tools for
many genetic and genomic studies. They are often used in
the assemblage of physical maps and in genome-wide
screenings for genetic variation. Recent progress in genetic
mapping methodologies has made it feasible to localize and
characterize single-gene traits or to dissect quantitative trait
loci (QTL). However, rapid progress is impeded by
practical difficulties associated with the lack of genetic
markers for most species or with obtaining the large size
segregating population that is required for mapping [5].
Many nonmodel organisms are very difficult to maintain
and breed in the laboratory, and the number of progeny
obtained in manipulated crosses is generally small and
inadequate for searching for association between segregating
markers and quantitative traits. Daphnia is not only well
suited to mapping studies but also has the advantage of
reproducing sexually as well as asexually. Therefore, the
recombined progeny can be maintained clonally in the lab
for a long time, which allows the mapping panel to be
shared between laboratories and used in further QTL
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M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
studies. As part of the Daphnia Genome Project, the
linkage map of D. pulex will soon become an essential tool
for large-scale studies for localizing QTL that contribute to
adaptation and speciation.
Broad-scale comparative gene mapping is an effective tool
for the study of genome evolution in phylogenetically distant
species by examining orthologous genes on interspecific
homologous chromosome segments [6,7]. Presence of
synteny could reflect the ancestral genomic organization
and could also indicate the incidence of genomic regions
resistant to linkage disruptions. Spatial comparative genomics
can also aid in transferring genetic information from
genetically well-characterized model species to less developed study organisms. However, large-scale comparative
genomic studies depend heavily on the availability of
extensive and transferable linkage maps in model as well
as nonmodel species. This approach is impeded by the lack
of a sufficiently diverse collection of genetic systems for
most taxonomic groups. For example, with the exception of
the preliminary linkage maps for the black tiger shrimp,
Penaeus monodon [8] and the white shrimp, Penaeus
vannamei [9], there are no genetic maps for crustaceans.
Moreover, most genetic linkage maps are based on dominant
markers (e.g., AFLP, RFLP, RAPD, RAPD-SSCP) that are
not easily transferable across mapping populations or species.
Microsatellites, in contrast to dominant markers, offer the
advantage of being easily transferable. In addition, microsatellites have high levels of intraspecific and intrapopulation
allele polymorphism, are ubiquitous in prokaryotes and
eukaryotes, encompass both coding and noncoding regions
of the genomes [10], and largely display a random
distribution across genomes. All of these characteristics
promote microsatellites as ideal markers.
In this paper we present the first genetic linkage map for
D. pulex based on 185 markers (most of which are
microsatellite loci) on 12 linkage groups. In addition to
discussing the recombination landscape of the Daphnia
genome we report the map location of 342 genes that show
homology to Drosophila genes. We used these coding
markers to search tentatively for conserved synteny between
the two genomes and discuss the prospect of crustacean
genomics.
Results
Linkage map
The total number of genotypes analyzed for this study was
21,546, including 185 loci and 129 individuals. The total
number of individual genotypes analyzed per locus varied
from 65 to 127, with an average of 115. A preliminary
linkage map was constructed and instances of double
crossovers were reexamined. We estimate that the data set
contains less that 1% error. Overall, 97% of the markers
tested showed detectable linkage to another marker at a lod
threshold of 4.0. The final linkage map consisted of 12
linkage groups and spanned 1206 cM with an average marker
spacing of 7 cM and with few map segments being identified
by multiple cosegregating markers. The size of the linkage
groups ranged from 6.9 to 185.3 cM (mean: 100.5 cM) and
the number of markers per linkage group varied from 4 to 27,
with an average of 15 (Fig. 1).
Genome size and coverage
We estimated a total genome length of 1367 cM using
the method of Fishman and colleagues [11], which accounts
for the terminal parts of the linkage groups by adding twice
the average spacing of markers to the lengths of each
linkage group and summing across linkage groups. Using
the method of Chakravarti and colleagues [12], in which the
length of each linkage group is expanded by (m + 1)/(m −
1), where m is the number of loci mapped, we obtained a
corrected genome length of 1398 cM. The percentage of the
genome covered by the linkage map based on these
estimations of the genome length is 87.2%. Assuming a
random distribution of markers and 12 linkage groups, we
estimate that 95% of the genome is within 3.84 cM of a
marker.
Marker distribution
Closer examination of marker distribution reveals clusters
of markers on several linkage groups (Fig. 1). The
clustered markers may not necessarily be closely spaced
physically, but may appear aggregated due to the low
recombination rate in particular regions [13,14]. Since most
linkage groups contain only one region of recombination
suppression, it is likely that these regions are associated
with centromeres. There are a few large gaps within
linkage groups (>30 cM), and it is difficult to determine at
present whether these gaps represent false linkages or
recombination hot spots. More extensive examination of
recombination suppression will require typing markers in
various crosses and the estimation of physical distance in
these regions.
Transmission ratio distortion
Using tests for random segregation of alleles at individual
loci, we determined that 21% of the 185 markers surveyed
showed significant transmission ratio distortion (TRD)
primarily due to homozygote deficiency and likely as a
result of markers being linked to deleterious recessive
alleles. Markers that showed TRD were clustered mainly in
four linkage groups (II, V, VI, and X) with linkage
group X containing almost exclusively markers that deviate
significantly from the expected Mendelian ratio.
Comparative analysis
The availability of orthologous coding markers (type 1
markers) is critical to studies of synteny and colinearity
[15]. We identified 342 putative orthologous genes between
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
417
Fig. 1. Linkage map for the crustacean D. pulex, based on genotypes for 186 microsatellite DNA markers and two protein coding loci in 129 F2 progeny. Numbers on
the left of the map framework indicate cumulative genetic distance in centimorgans (Kosambi) between markers, while codes on the right indicate marker names as
identified in Appendix A. The 12 linkage groups were arbitrarily ordered from largest to smallest and the number of loci and the corrected genetic length are indicated
above every linkage group. Markers exhibiting significant deviation from expected Mendelian segregation ratio are denoted with † and corresponding regions
exhibiting significant transmission ratio are shaded. Markers placed relative to the frame map at a log-likelihood threshold of 2.0 are denoted with ‡ and no distances
are presented, that is, their distance from other markers is arbitrary. Markers appearing on the same line are markers that cosegregate and the order of the markers on the
line is arbitrary. Horizontal interrupted lines point to specific regions of linkage groups that disassemble at a lod score greater than 6.
Daphnia and Drosophila. The majority (86.6%) of the genes
were located within 50 kb from the closest marker, with
about 5% being placed 2 kb apart from the closest marker
(Fig. 2). By examining the relative map location of
Drosophila/Daphnia pairs of genes in the two genomes
we identified a lack of synteny. The contingency table
analysis found no relationship between the linkage groups of
the two species (likelihood ratio χ2 = 25.703; df = 264;
P = 0.176). The simple cluster analysis suggests that the
null model of uniform random gene order could not be
rejected (χ2 = 8.53; df = 4; 0.1 < P < 0.05). Therefore, we
could not reject the hypothesis that the observed clusters could
have occurred by chance.
Discussion
This map represents the first step toward advancing
genomic studies on Daphnia, which will conclude with the
sequence of the whole genome in assembling stage at the
Joint Genome Institute.
Genetic length
The map distance spanned approximately 1206 cM and
included 185 loci and 12 linkage groups. It is therefore highly
likely that all 12 chromosomes have been marked, although
further assignment of actual chromosomes to linkage groups
will be impeded by the very difficult cytogenetics of the
Daphnia chromosomes, which are largely morphologically
indistinguishable [2,3]. Considering a genome size of
approximately 184 Mb and a genetic length of 1383 cM, it
can be inferred that 1 cM spans a physical distance of about
133 kb. The physical distance of one map unit in Daphnia is
1 order of magnitude smaller than in human or mouse [16,17]
and is more comparable with other invertebrates with small
genome size such as Bombus terrestis (∼255 kb/cM) [18] and
the honeybee Apis mellifera (∼44 kb/cM) [19]. The high
magnitude of recombination per physical distance we found
in Daphnia is consistent with the observation that the
intensity of recombination scales negatively with genome
size [20]. This is not unexpected given that chromosome
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Fig. 2. Histogram of gene distribution based on distance from the closest marker.
number is not correlated with genome size and that most
species experience one or two meiotic crossings over per
chromosome [20].
[27], which found 20–50% decrease of survivorship to
maturity or egg survivorship.
Mapping crustacean genomes
Transmission ratio distortion
The segregation of genetic traits from parents to
offspring is expected to conform to Mendel's rules.
However, deviation of transmission ratios among offspring
is often observed in interspecific crosses in animals and
plants and occasionally in intraspecific crosses [21–23]. The
mechanisms responsible for TRD are not completely
understood but may result from altered chromosome
segregation [24], differential viability of gametes, or
differential survival of different genotypes [21]. Our tests
for random segregation of alleles at individual loci revealed
that 21% of the markers showed significant homozygote
deficiency. These markers were clustered in four genomic
regions that span between 30 and 70 cM. Since our
recombinant lines experience low hatching success (∼20%),
low survivorship during first days of life (∼30%), as well
as a relatively high incidence of infertile progeny (∼10%;
excluded from the study) we suggest that the TRD was due
mainly to the high genetic load of the parental lineages,
reflected in the loss of alleles tightly linked to deleterious
recessive genes or infertility recessive genes. The magnitude
of inbreeding depression is in agreement with previous
selfing experiments in Daphnia pulicaria and Daphnia
arenata [25], Daphnia magna [26], and Daphnia obtusa
The Daphnia linkage map serves several goals. First, the
map is sufficiently dense to be used as an anchor for the
construction of the physical map of the Daphnia genome by
providing an ordered scaffold onto which “contigs” of overlapping clones can be assembled. Second, this map provides an
effective tool for genetic analysis and manipulations and could
be extended and used as an effective tool for identifying single
loci or quantitative trait loci and for underpinning the genetic
substrate of evolutionarily and ecologically significant traits
such as sex determination, response to environmental stress, and
reproductive isolation. Third, the map could be employed in
comparative linkage mapping. Of the 183 microsatellite
markers included in the map, 60 have been successfully
amplified in Daphnia species outside the D. pulex complex
(e.g., D. obtusa), and the majority of markers worked for
species within the D. pulex complex (e.g., D. pulicaria, D.
melanica). These homologous markers will make possible a
comparative synteny analysis in the genus Daphnia. Furthermore, the enrichment of the linkage map with coding markers
will enable comparative mapping with less related species for
which high-density maps are available and will instigate
comparative studies with other crustaceans for which full
genomes remain to be characterized in the near future. The
prospect of comparative genomics within Crustacea is
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
particularly appealing given that the subphylum Crustacea
includes over 50,000 described species with immense variation
in adaptations and body plans and includes many species of
high economic importance. The explosive progress in the
genomic field will likely transform small genomic projects that
involve marine crustacean species (e.g., the blue crab
Callinectes sapidus, the blue shrimp Litopenaeus stylirostris,
the white shrimp Litopenaeus vannamei, the daggerblade grass
shrimp Palaemonetes pugio [28]) into large-scale genome
sequence projects.
Search for synteny
Comparative linkage mapping has provided evidence that
genes in eukaryotic genomes are distributed nonrandomly.
For example conservation of linkage relationships was
found not only between closely related species of insects
[29], mammals, fishes, and plants but also between different
phyla. The search for residual synteny culminated with the
discovery of a few ancient syntenic gene groups spanning
vertebrates, invertebrates, and single-cell eukaryotic genomes [30]. In general, genome organization appears to be
less conserved between distantly related species (e.g.,
outside of family level). As the genomes diverge progressively, the networks of synteny are often eroded by
extensive gene duplication, gene loss, and horizontal gene
transfer [31,32]. This degeneration of homology makes
sorting between genuine remnants of ancestral gene order
and simple coincidence very difficult [33]. It does not come
as a surprise that our data suggest a lack of macrosynteny
between Daphnia and Drosophila genomes. The estimated
divergence time between Insecta and Crustacea is 666 ± 58
million years (Myr) [34], a long evolutionary history that
led to an apparent randomization of gene order. Moreover,
an extreme rate of internal chromosomal rearrangements of
0.9–1.4 chromosomal inversions fixed per million years was
found within Drosophila [31]. Based on this rate, the
authors suggest that for taxa that diverged more than 250
Myr ago information transferability will be useful only over
419
very short chromosomal distances (less than 100 kb). The
full genome sequence of Daphnia will make possible the
identification of residual synteny at a finer genomic scale.
Ecological, evolutionary, and toxicological studies on
waterfleas extend back several hundred years. The advent of
genomic advances will greatly accelerate traditional studies on
Daphnia and will open the door for new genomic approaches
and promote the establishment of emerging interdisciplinary
research areas such as ecological genomics or toxicological
genomics.
Materials and methods
Crosses
We studied the segregation of 185 polymorphic loci in 129 progeny (F2)
obtained by selfing one D. pulex (F1) interclonal hybrid (Fig. 3). To obtain
recombinants from animals that reproduce by cyclical parthenogenesis, we
first created a panel of outbred F1 isolates and selected one line that
regularly produced males and meiotic eggs under standard laboratory
conditions and whose selfed embryos required both decapsulation of
ephippia and strong stimuli to resume embryo development. The selected
F1 hybrid was clonally propagated within 10-L aquaria at 20°C under a 14 h
light:10 h dark photoperiod. These populations were maintained at densities
of approximately 1 individual per 5 ml of filtered lake water by feeding a
concentrated monoculture of green algae (Scenedesmus obliguus). Under
these conditions, Daphnia sexually produced resting eggs (ephippia), which
were collected and decapsulated. The obtained embryos were incubated for a
week in the dark at 5°C and then transferred to a 12 h light: 12 h dark
photoperiod at 15°C to stimulate the breaking of diapause. In all, 129
progeny (F2) were reared to maturity and individually cultured in 250-ml
beakers.
Genomic DNA extraction
Total genomic DNA was extracted using a CTAB extraction method [35].
Whole adult individuals were ground with a plastic pestle in a microcentrifuge
tube in CTAB DNA extraction buffer. Microcentrifuge tubes were placed in a
water bath at 65°C for 1 h. The chloroform/isoamyl alcohol (24/1) extractions
were followed by DNA precipitation, 70% ethanol washing, pellet drying, and
DNA resuspension. Samples that had a low amount of tissue were extracted with
a ProK extraction protocol [36].
Fig. 3. Crosses performed to obtain segregated progeny for map construction. To obtain a heterozygous F1 lineage, crosses were conducted with parental lineages of D.
pulex (arenata) from two Pacific coastal ponds in Oregon (LO and SL) that showed marked genetic differentiation when screened at allozyme and microsatellite loci
[50]. The recombined F2 progeny were obtained by selfing the F1 hybrid.
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Microsatellite markers and genotyping
The majority of the microsatellite markers consisted of simple or
complex di- and trinucleotide repeats. Two additional markers consisted of
protein-coding loci that show allelic length variation of more than 2 bases at
one intron region. Primers were designed either by Colbourne and colleagues
[37] or were created during this study using the programs Primer3 [38] and
MicrosatDesign [39] and trace files obtained by the Daphnia Genome
Sequencing Project (Appendix A). We employed the M13(-21) primer
genotyping protocol [40]. The forward, sequence-specific primers were 5′
extended with the M13(-21) oligonucleotide. The polymerase chain reactions
(PCR) were performed in 12-μl reactions with 10 ng of DNA template, 1×
PCR buffer with 25 nmol of Mg2+, 0.5 units of Taq polymerase, 2.5 nmol of
each dNTP, 1 pmol of the forward primer, 2 pmol of the reverse primer, and
2 pmol of the universal fluorescence-labeled M13(-21) primer. To reduce
nonspecific amplification, we used a touchdown PCR. Thermal cycle
programs included an initial denaturation step of 3 min at 95°C followed by
10 cycles of 35 s denaturation at 94°C, 35 s at final annealing
temperature + 10°C (the annealing temperature was decreased by 1°C
every cycle during each of the 9 following cycles), 45 s extension at 72°C
followed by 30 cycles of 35 s denaturation at 94°C, 35 s annealing
temperature at 48°C, and 45 s extension at 72°C, with a final extension at
72°C for 10 min. The amplified products were diluted 40- to 60-fold and
combined in groups of four to six according to their size and fluorescent
labels (NED, PET, FAM, VIC). Two microliters of the diluted PCR product
was then mixed with 8.9 μl of H2O and 0.1 μl of GeneScan–500 LIZ size
standard (Applied Biosystems, Foster City, CA, USA). Samples were
denatured for 5 min at 90°C, quickly cooled on ice, and genotyped using an
ABI 3730 and GeneMapper software v3.0 (Applied Biosystems). One allele
from each amplified locus was subsequently sequenced, to verify that the
microsatellite DNA corresponded to the expected type of repeat. Sequences
obtained in this study have been deposited with GenBank (Accession Nos.
DQ249348–DQ249470).
Linkage analysis
To assemble linkage groups by maximum-likelihood we used MapMaker/
Exp v3.00 [41]. Genotype data were entered in both phases to satisfy the
requirements of the software (the absence of phase information does not
impact the results of the software). All markers were tested for significant
deviation from Mendelian segregation using a χ2 test (α = 0.01). Markers
that showed significant TRD were double checked for genotyping errors and
reliability. Marker clusters were initially identified using a LOD of 4 and after
excluding TRD markers. To minimize the number of false linkage groups, the
stability of each linkage group was further tested by gradually increasing the
lod score to 8. For example, two large groups supported by LOD 4 were
subsequently broken up by increasing the minimum LOD to 5 and 6,
respectively. The most likely order of markers in each linkage group with
nine or fewer markers was determined by calculating the maximum-likelihood
map, and the corresponding map's likelihood for each possible order of
markers using the “compare” command. For all other linkage groups with
more than nine markers, the “order” command was used to obtain the
sequence of markers with unique placement with the criteria for finding
highly informative markers set to 4 maximum distance, 100 minimum
individuals. The “try” command was used to determine the most likely
placement of the orphaned markers, and subsequent orders were tested using
the “ripple” command with “error detection” and “use three point” options
enabled. The distances between neighboring markers were calculated using
the multipoint analysis implemented in the “map” command. The Kosambi
mapping function that incorporates the possibility of crossover interference
was used to convert recombination frequencies into map distances [42]. The
linkage map was drawn using MapChart software [43].
Dealing with genotyping errors
Since even small fractions of genotyping errors can artificially increase
the total length and influence the marker order of the map, we employed
several different approaches to estimate and minimize genotyping errors.
For example, 15 randomly chosen markers and six F2 progeny were
sequenced and genotyped twice. Based on the duplicated data, we
estimated an average genotyping error to be less than 1%. The genotyping
data were scored independently by two persons, and differences were
compared and resolved. In general, discrepant data points were left as
unscored. Moreover, the data were analyzed with the “error detection”
algorithm enabled, and genotypes with LOD-error values of about 1.0 or
greater were considered candidate mistyping errors [44] and were double
checked.
Genome size and coverage
To calculate an estimate of the total map length (Gl) for the genome, we
used the methods of Fishman and colleagues [11] and Chakravarti and
colleagues [12]. These estimates were subsequently averaged and used to
estimate the expected distance of a gene from the closest of n random
markers, E(m) [45,46].
Sequence comparisons between Daphnia and Drosophila
As a first attempt to identify conserved chromosomal regions between
crustacean and insect genomes, we mapped the locations of putative
Drosophila orthologous genes onto the Daphnia genetic map by first
annotating the available genome sequence assembly provided by H.
Shapiro and the Joint Genome Institute. This preliminary assembly—at the
halfway point of the Daphnia Genome Sequencing Project—consisted of
3804 scaffolds (23,428 contigs) with a total length of 184 Mb. The length
weighted average of the scaffold sizes (N50) was 776.2 kb. Putative
Daphnia genes were identified by aligning the Drosophila proteome to the
scaffolds using the tBLASTn program [47], with a grid-aware version of
the NCBI software developed by P. Wang at Indiana University,
implemented on the TeraGrid (http://www.teragrid.org/). This analysis was
performed and archived by Don Gilbert at wFleaBase [48]. We required
that a protein show a significant similarity (cutoff of E was 10−10) to be
considered an ortholog. We next positioned the microsatellite markers
relative to the annotated genes using the BLASTn program on a local
computer. For each of the markers mapped onto scaffolds, we then
extracted the gene identities for the two best, nonoverlapping, matches to
fly proteins flanking the microsatellite, for a maximum of four positioned
genes. The relative placements of these genes on the Daphnia linkage
groups and Drosophila chromosomes were compared to identify broad-scale
syntenic relationship between the two genomes. First, we used a
contingency table analysis to test for associations at the linkage group
level between the two genomes. Test of significance were performed by a
likelihood ratio χ2 test in JMP IN 5.1 [49]. Second, we conducted simple
cluster probabilities. We calculated the probability of finding a cluster
association between genes linked to a particular marker in the focal species
(Daphnia) and their orthologs in the reference genome (Drosophila) under
the model of random gene order.
Acknowledgments
We thank members of the Lynch and Rieseberg labs for
engaging discussions. We are grateful to C. Scotti Saitagne
and T. Crease for helpful comments and suggestions on
the manuscript and to X. Hong and D. Gilbert for data
mining support. E. Williams, A. Seyfert, A. Wolf, V.
Cloud, and B. Molter helped with Daphnia maintenance.
This project was financed by grants to M.L. from the
National Science Foundation (DEB-0196450 and EF0328516) and by a postdoctoral fellowship to M.E.A.C.
from the Natural Sciences and Engineering Research
Council of Canada.
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
421
Appendix A. List of primers used in the study
Accession Nos. AYxxxxxx correspond to primers developed by Colbourne and colleagues [37], while Accession Nos. DQxxxxxx
correspond to primers developed during this study.
Pr. code
Primer name
LG
Accession no.
Allele size
Left primer
Right primer
d001
d002
d003
d004
d005
d006
d007
d008
d009
d010
d011
d012
d013
d014
d015
d016
d017
d018
d019
d020
d021
d023
d024
d025
d026
d027
d028
d029
d030
d031
d033
d034
d035
d039
d040
d041
d042
d043
d044
d045
d047
d048
d049
d050
d051
d053
d054
d055
d057
d058
d059
d061
d062
d063
d064
d065
d066
d067
d068
Dp149
Dp321
Dp24
Dp28
Dp463
Dp70
Dp74
Dp1498
Dp48
Dp71
Dp123
Dp146
Dp91
Dp126
Dp147
Dp339
Dp62
Dp143
Dp337
Dp170
Dp295
Dp460
Dp231
Dp298
Dp1486
Dp156
Dp385
Dp430
Dp319
Dp240
Dp421
Dp304
Dp475
Dp40
Dp1489
Dp137
Dp208
Dp330
Dp1494
Dp1493
Dp395
Dp199
Dp144
Dp1491
Dp193
Dp300
Dp115
Dp21
Dp78
Dp112
Dp196
Dp1487
Dp111
Dp1495
Dp1490
Dp142
Dp1492
Dp308
Dp53
I
II
III
II
X
XI
I
III
I
III
IX
VI
V
VI
II
II
II
IV
III
VI
IV
X
V
VI
Unlk
VII
VI
IV
V
V
Unlk
X
VI
I
VII
III
V
IX
II
VIII
II
I
III
II
Unlk
I
III
V
IV
VII
III
VI*
III
I
III
VIII
III
III
VIII
AY619162
AY619341
AY619034
AY619038
AY619486
AY619081
AY619085
DQ249470
AY619059
AY619082
AY619135
AY619159
AY619102
AY619138
AY619160
AY619359
457/462
253/263
209/213
379/387
302/307
272/278
358/362
215/241
361/364
155/164
257/271
388/393
316/319
173/178
429/433
174/178
503/538
376/388
156/158
273/285
212/216
296/300
232/235
347/352
270/292
153/156
318/320
198/203
191/196
266/268
288/291
379/384
262/265
404/409
169/174
232/234
341/358
152/156
343/346
312/314
224/225
316/320
235/239
184/187
183/188
324/326
281/284
238/242
463/466
356/359
268/275
359/379
443/457
420/426
176/182
357/362
336/343
231/237
352/356
ACACAGACCCGCCATCCATT
ACTCCAGATCGAGGTGTTGG
TGGCGGGCGGAATAGTTTG
GAAGGCGAAACATAAATAAAACAC
TCGCCGATGAAAATACTCC
ATGGGGCGGAATCAATCAC
TGCGCCGCGATGTTTTCC
CACGATACGGCGGATTTTGT
TCAATCCCATCATCCCATC
CGCGCAACTCTTTCTATTATAC
GGCATCCTCCCAGTAATTGA
GCATTGCAGGTGGCATTTTC
CGTACCGCAAGAGGATAGGA
TGCGTGAATCCGTGATATTTGA
AGAGGGAGACCCGCTTCGTT
CGCCTCCCTCCGTCTATTCT
AGCAAATGGGGTGACTCG
CTCAGCAACCAGGACCGTTG
GGTCACCTCCTCTTCGCTCTCCTC
TTGTTGTCGGAACGATGACG
CCGCGCTCTAACCGCTAAAT
GCCAAAAGCCCAAGGTAAGG
CCCAAACGATTGTAAAAATAAAAAGA
TGCTGCTTCTTTTTGGGCAT
GTCAACGATCGAATCGGACT
TATTGCCGGGTCGTCAGTCT
CCTGTTTCACCTAGCCCACG
AGAGTGGGCGAACGAACAAA
GGCCCCAGCAGTTCCTTATT
CGCGAATACCCCTCTTTGTG
GCTCGACACACCGGTTAAGG
CGGCGTGCCAGGAGATCTAT
CGTAAATAAACCGAGGCGCA
CTATACAGCGGCTTCGGCAC
TCAACACAACGGATTTGGAA
AGCAAACGACGCACGAAAAT
GGGACCGGACATGTGTTGTT
GGGTTTTGGAGGCGAACTCT
CCACTCTGCGGGAAATGAAC
ACACAACCATCCGGCATCTT
GGAGACCAAACCATTGCCTG
ATTTCCCTGGGACGCTTGTT
ATTGTTGTTTGCGTCCGAGG
GTAACGTGCGTGCATGTGTG
ACTCGACGGGAGCAGAATGA
GTTGGCGACTCTCTCGCATT
CGGACGTGTCAATGAACGAA
GACGGAATTCAATAGAGAGAAAAATG
GCTGCAAAGCGGAAAAATTG
TTTGCCCATTTTAGCGGTTG
CCAGCAGACGAGCCAAATTC
CCTCTTTGGCTCTGATTTCG
TCTATTGAACGACCGAGACG
GAAACTGGCTTGCAGCTGAT
CAGCTGGTCCCCAAACCATA
GCGACTTGACCCAACCAGAA
TGATGCGGGTCTCGAGTTTT
GTGACGATGTCCGCACCTTT
CGGTAGACGGCCAACAAGTC
ACATGTGCCGGACTCGTGAT
TAGCGAGAGGCGAAGAAGAG
ACTTTCCGACCGGTTTCTTCTTG
AACCCCGGCGTGAATCC
CAGCAAATAAGCCCGTGTG
GAGGCGCATCGGCTAAAAAG
TGCGACCGACTTATGAACCAACTG
TCAAAACGGCAACATGGAGA
CCGCATCAATTATCTTTTTCTG
AACGACCAGGCGCTCTAC
TTAGCCAGCCCTCAGAAAAA
ATGCCAAGTCTTCCCCTCCA
ATCTCTCCCCGAAAGGAAGA
TCGATTGGGATCCAGCCAGT
ACAGCTCCGCCAAACAAACA
CCCAGCGTGTGACATCTCAAT
ATGGCGTGGAATAAAGAATGTT
ACCTGGAACCTGCAATGACG
ACAAGTCGTGCGCAGTTTCCAATC
ACCACAGCGGGACAAGAGAA
GAGAAATCCTCCCGTTTGGG
GAGCGATGTACACGCACGAG
GACACGGCCGAGATGAAATC
GGCCGACAGCCCTTATATCC
TGACCGCCAGGAAATAAATC
GATGCGCCAACAGCATATCA
CTTTTGCTTATGCCCTCCCC
CGGAGAAAAACACGGACGAAG
CATCATGGCATCAGCCAAAA
GTGCATTCCCCTTTGGATGA
ACCCCAAAAATATGCTGCCA
CCCAAACGCGATTATGCAAT
GCTCAAATGGAGAAATGGCG
TGGCTGCTGCGATATCAAAA
ATTGTGCTGGGAGCTAGGTT
TGCAAGGTATTCAGCGACGA
ACCCCTCACGACCCTTCTGT
AGTGTTGTCCAGCCGCAACT
TCACAGTTGTGATGGACGGC
CGAGCGAATTAAGCGGTCTG
TCAATGCGAAATTCGAGACG
TCGATTGGCTTTGATCGCTT
AAAAGGGCGGAGTGTGTTGA
CGAAAAATACCGCAACGCTC
AACCACAGCCGCTCAACTTC
CACCCAGACTCTCGTTCGCT
CGGTCGTAAATCAACTCCGC
GACACGGGAAGCGTTTGAAG
ACCGGTCTGGGTCAAACCTT
CCTGCGAGGGTCAATATCCA
CGGAAGCTTGGGATTCCTTT
GGCGACGTGTTGAGTTTCTT
CGTGAGGTCGAAACCAAAAT
ATTCCCATGGGTGGCCTAAA
ACACCGGGGGAGATTACACC
GGGAGATCGTGAGCGAACCT
CCAGCAGACGAGCCAAATTC
TCCGTCTTCTCCTCACGACG
GCTAAATTTCTCCCGCTGGC
AY619156
AY619357
AY619183
AY619313
AY619483
AY619247
AY619316
DQ249461
AY619169
AY619408
AY619453
AY619339
AY619257
AY619444
AY619322
AY619498
AY619051
DQ249462
AY619149
AY619223
AY619350
DQ249466
DQ249465
AY619418
AY619214
AY619157
DQ249464
AY619207
AY619318
AY619127
AY619031
AY619089
AY619124
AY619210
AY619123
DQ249467
DQ249463
AY619155
AY619327
AY619064
(continued on next page)
422
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
Appendix A (continued )
Pr. code
Primer name
LG
Accession no.
Allele size
Left primer
Right primer
d069
d070
d071
d072
d073
d074
d075
d076
d077
d078
d079
d081
d082
d083
d084
d085
d086
d087
d088
d089
d090
d091
d092
d093
d094
d095
d096
d097
d098
d099
d100
d101
d102
d103
d104
d105
d106
d107
d108
d109
d111
d112
d113
d114
d115
d116
d117
d118
d119
d120
d121
d122
d123
d124
d125
d126
d127
d128
d129
d130
d131
d132
d133
d134
d135
Dp224
Dp325
Dp311
Dp1496
Dp361
Dp389
Dp530
Dp564
Dp559
Dp616
Dp557
Dp605
Dp581
Dp641
Dp687
Dp642
Dp693
Dp648
Dp660
Dp675
Dpl1/87
Dp655
Dp808
Dp721
Dp770
Dp785
Dp571
Dp572
Dp589
Dp609
Dp775
Dp802
Dp725
Dp729
Dp742
Dp779
Dp830
Dp867
Dp813
Dp821
Dp907
Dp848
Dp883
Dp884
Dp840
Dp878
Dp887
Dp621
Dp632
Dp637
Dp1485
Dp50
Dp1497
Dp117
Dp815
Dp838
Dp696
Dp726
Dp746
Dp754
Dp612
Dp895
Dp786
Dp553
Dp985
II
II
IV
X
VI
II
III
I
VIII
III
II
IV
III
X
IV
VI
XI
V
IX
IV
V
I
XI
V
III
II
I
III
I
IX
V
I
II
I
II
IV
IV
VII
III
II
VI
II
VIII
I
I
IV
VIII
IX
V
II
VIII
III
II
II
VI
V
X
XII
II*
I
VI
III
VII
I
VI
AY619240
AY619345
AY619331
DQ249468
AY619383
AY619412
DQ249359
DQ249441
DQ249443
DQ249382
DQ249361
DQ249406
DQ249391
DQ249429
DQ249455
DQ249364
DQ249353
DQ249387
DQ249372
DQ249413
268/272
184/192
134/136
156/159
313/323
129/133
155/161
256/265
231/241
189/199
156/163
288/295
323/327
290/294
208/211
318/320
164/176
328/337
124/129
279/287
233/236
262/271
216/223
236/244
272/283
189/195
166/168
126/130
236/241
250/285
141/148
124/129
261/264
134/138
236/242
145/149
300/308
218/224
240/252
304/307
268/288
175/181
251/255
219/223
272/278
317/323
220/227
119/124
287/289
234/238
397/416
204/211
306/312
236/240
291/295
256/259
306/327
229/233
165/172
279/299
240/254
258/263
140/144
197/202
251/254
TCTCTGCCACCCCAACAAAT
GCACCGAAAACCCAATCAAA
TCCACCTCCTTCCTCACCAA
CCCATCTCACACCAGCAACA
GGCGGCAACATCCAAAGTAA
GCGAAGAAAAGCTGGTGGTG
TCCTGTCAATTTCCCCAGAG
TGGGAGGATCGATAAAAACG
TGTGGAACAGATGGCGACTA
CGGAAACTTGTGAGTGGGTT
GCTCTGTTCTCTGGGCAAAC
AGTCCGGAATTGACACCATC
AACTCAATTCGGAATCACGG
TTTTTCTCCGTGTCTTTGGG
AAAAACGGCCAAGAAAAAGG
CCGGGATATGAATGTTTCTCA
AACAGATTTGTTTGCAGGGG
GGAAATGAAAAATGGGACGA
TTTCACAACTGCTTTGGCTG
CGCGACATGACTCAAAACAC
GAGGGATTTGTGTAGGTGC
CGTACTAGGCCACTTTCGCT
TGTTGTTGCATGACGAATCC
TGAAATGATGATGTCGTCGC
TTTGCCGAGTACCAGTAGGG
CAGAATCCTTTGCTTTTCGC
CTGGAGAGCGTCCTGCTACT
CGCTTGGAAGAAAAGAAACG
AAAAGGCCCAGTCGAAATCT
CCCATCGGTTGTGTAGGTTT
GTAGCGTTGGTTGCTCATCA
AGTGATGGGCTCCTTTGATG
ATCAGCATTCACGACACAGC
GGCCAATAACAGCCGAAATA
TGTATATCGCCGTGTGATGG
TTTACCGTTAGCTTGACCGC
TGCTAATCATGTGGGCGATA
TCGTGAGTGAGGTAAGTGCG
GGGGTCCTTCGGTCATTATT
GCACACAACCAACCACAAAA
GCGACACAGCGAAGGTAAAT
TTTATCGCATTTTATGGGGC
CCCCTTTTGCTTTTGTGTGT
TCTGTGGAAAACTCTCGGCT
CATGCCGGTAAACGTCTCTT
ACGGAAAACAAGCCATTCTG
TCATAGTCACAACGGCCTCA
ACTCGACACAAGCGGAAAGT
ATGTCAGCCGAAAAAGGCTA
CAAAGATCCGCAAAAGAACC
TAGTTGTTGGCTTGCGATG
CGGTCAACAGCGATAAATG
TCTCTTTTCCGTGTTTCCCG
CGAAAGAAGAAACGGCAGTC
TCGCGTTTCACAATCTCTTG
TTGGCTCCTTCACAATTTCC
CGTGGCATTCTGCTGAACTA
GAAAACGCTGCCAGAGAGAT
CCCATCATCTGTCCGTTTTT
CTCAGGAGCTGGTGGCTAAC
TATCGCATTATCCATTCGCA
ATTTTGTTTCGTGGGGTCTG
CCTATTTGCATCGTCGGTTT
ATTGGTGGAATGAGTCGAGC
GCACTGCTCCTCTCCTCCTA
TCATCACCGGTACATCGCAG
TTTGTCCGCACCCATATTCC
GCGCGGCAGTGAAATAAATC
AAAAGGCTGGTCCCGATTGT
CCTGCTTCCAGTCCAAAACG
TCCATGGGAAAATCACTGCC
GCTGGAGATGGGTGATTCAT
AACCGATCACGTAAGTTGGC
CACTCTCAACGATCCAAGCA
GACGGTTCCATTTGCTGATT
TCAAAACCAGCAACAGCAAG
CGAAAATTCTTCCCTCCTCC
CCCACCGATTTTGATGTTTC
AGCTCATTTTGATGGATGCC
CACTCCACGGGAGAAGGATA
GACGACTGCGTGATACAGGA
AGGAAAACTAATCGCCGGAT
GATCCCTTTAAGGACACGCA
TGCTGCGTGTGTTTATGTGA
TATAGTGCGACTTTGTGCCG
ATGAGCCAAAAGAGCTGC
ATTTTCCCGAATCCTATCCG
ACTGAGAGCAATGCCGAATC
CGAGCAGCAATGAGATGTGT
TGCAGCATATCCATCTCAGC
GCCACCCTTTTAATAAGCCG
CAAAACCTCCCCTCAAGTCA
AGTCCGGAGAAAGGATGGAT
ACTCCCTCGACTTCTGACCA
CTTGTGGTCCTTGTTCGGTT
ACCTGCAAAAGACCCACATC
CTCTTCCCTCGATCAGTTGC
CTTTTCACGAAATGCGACAA
AGTGAAGAAGACGACGCCAG
ATGTGTCTGTGCGTGCGTAT
TGCGTGTTTTGGGTGTTCTA
ATCAGCATTCAGTCGTGCTG
CCCGTCATCAAAAGGAGAAA
GGGTAATTACGACCCGTGTG
GACCTCAGCAATATAGCCCG
GTCATCGTTGTCGTGTGGAC
ACAAGTTTCACAAGGCCCAG
CCTCCTGGTCGGATTACAGA
CACCTACCGGCTGAAATTGT
GATTGCGAGTAGTTGCCCAT
ACGGACACAATGGGTCTAGC
CACGTCTTCATTTCCAGGCT
AAAGGGAGGAGCTGAAATCC
GTCAAAGGGAAGATGACCGA
AGCAAGCCCCCTCTCTACTC
CTTTATTAACCAGGGTAGTATGC
AGTCCGATGATGCCACTG
CCTGCGAAATAGCAACCCTG
AGGTCCTTCGTGACTCGTCT
CAGGACCATAAAGTCCCGAA
ACACCGTGACCTTTTCGTTT
CGTGAAGCAACAGAGGGAAT
GAGGAGGAAACGGGAGAAAC
CTTGTGATGCATGCGCTAGT
AGCACAAATATCTGACCCCG
ATAAGACCGTGACGATTCCG
GCAAAGGCGAGAAAGAGAGA
GGCTTGGATGAACGTCAAAT
GGCATGCCGTTACAAATTCT
CGGGCGACAAACGATATAAT
DQ249403
DQ249447
DQ249408
DQ249438
DQ249374
DQ249456
DQ249369
DQ249385
DQ249442
DQ249394
DQ249363
DQ249418
DQ249439
DQ249421
DQ249405
DQ249414
DQ249426
DQ249404
DQ249440
DQ249409
DQ249400
DQ249366
DQ249351
DQ249401
DQ249355
DQ249362
DQ249444
DQ249420
DQ249457
DQ249460
AY619061
DQ249469
AY619129
DQ249384
DQ249396
DQ249448
DQ249424
DQ249436
DQ249452
DQ249459
DQ249454
DQ249431
DQ249383
DQ249349
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
423
Appendix A (continued )
Pr. code
Primer name
LG
Accession no.
Allele size
Left primer
Right primer
d136
d137
d138
d139
d140
d142
d143
d144
d145
d146
d147
d148
d149
d150
d151
d152
d153
d154
d155
d156
d157
d158
d159
d160
d161
d162
d163
d164
d165
d166
d167
d168
d169
d170
d171
d172
d173
d174
d175
d177
d178
d179
d180
d181
d182
d183
d184
d186
d187
d188
d189
d190
d191
d192
d193
d195
d196
d197
d198
d199
d200
Dp998
Dp936
Dp957
Dp924
Dp967
Dp1040
Dp1148
Dp1232
Dp1325
Dp1397
Dp1041
Dp1155
Dp1236
Dp1160
Dp1238
Dp1327
Dp1350
Dp1059
Dp1185
Dp1311
Dp1328
Dp1338
Dp1050
Dp1123
Dp1302
Dp1346
Dp1368
Dp1262
Dp1404
Dp1300
Dp1354
Dp1372
Dp1058
Dp1290
Dp1309
Dp1396
Dp1112
Dp1266
Dp1363
Dp1276
Dp1278
Dp1376
Dp1409
Dp1073
Dp1144
Dp1056
Dp1079
Dp1057
Dp1080
Dp1195
Dp1347
Dp1399
Dp1391
Dp1351
Dp1189
Dp969
Dp1005
Dp1048
AO5
AO92
P1N22
III
XII
I
IV
II
VI
IV
VI
IX
Unlk
III
I
IX
VIII
VI
VI
VI
VI*
IV
IV
VII
II*
Unlk
V
X
II
I
V
VIII
VII
I
IV
III
I
IX
IV
XI
I
II
III
IX
IV
IV
I
XII
II
XII
X
XII
I
VII
VI
VII
VIII
I
II
II
II
VI
X
III
DQ249350
DQ249392
DQ249399
DQ249419
DQ249377
DQ249370
DQ249453
DQ249380
DQ249437
DQ249433
DQ249371
DQ249427
DQ249375
DQ249395
DQ249348
DQ249445
DQ249389
DQ249402
DQ249354
DQ249390
DQ249446
DQ249415
DQ249434
DQ249410
DQ249358
DQ249381
DQ249356
DQ249451
DQ249450
DQ249352
DQ249398
DQ249368
DQ249393
DQ249432
DQ249360
DQ249430
DQ249388
DQ249386
DQ249407
DQ249357
DQ249376
DQ249378
DQ249435
DQ249367
DQ249423
DQ249412
DQ249422
DQ249416
DQ249425
DQ249379
DQ249417
DQ249449
DQ249428
DQ249397
DQ249365
DQ249373
DQ249458
DQ249411
251/260
183/190
310/313
133/140
269/272
176/180
325/333
296/304
272/277
196/113
286/292
221/229
195/197
193/195
266/269
299/301
239/247
251/257
199/201
217/223
243/251
299/302
215/217
156/158
210/214
260/268
199/201
211/220
190/202
259/273
232/251
292/296
194/198
275/278
213/219
307/313
259/282
137/140
259/261
289/294
255/259
307/309
199/206
209/214
304/316
302/304
212/215
313/316
208/212
151/162
343/347
272/277
306/319
226/244
278/289
308/312
272/282
192/194
624/633
524/528
173/178
AGGTGCAATTACCGATCCAG
GCCAGGTCAGAAAATTGGAA
ATTCTTTTGCCCCCTTTGAC
GCAACCAGAAAGGGAGAGTG
CTCGTCCAGCTCTCTGCTCT
CTGGCTCATCCACTCACTCA
AAAAGGGAAACGTTCGAGGT
TATGCACGCGTATCCTTGAA
CCTGTAGGGAAAACACCCAA
TCGACAACTACAACAACGCC
GCACAGTCAGGAATGGGATT
CGAGCACACGTTCTTTCTCA
TATCGATCCCACTTTACGGC
CGCTCTGCTTAATACGGTCC
TTCATAGGGGGTGAGACTGC
TTGACCTCTCATCCCCACTC
CGAAGCGGTGGAGAAAAATA
TGTGTCTGGGCTACCAACTG
TAATAATGGACCCATCGGGA
ATCCCGTTTTGCTTCTCTCA
ATTTTCGATGGTGAAGACGG
TCTCTGCGGATGACACACTC
GACCCTGGCTGTGCTGTAAT
GACGCGGTCAACCTGTTC
TTTGTATCCTCGGCGTAAGG
GCTTCGGTACACGACCAAAT
ACACGTTCCGCGAATCTAAC
TCTCGACGAGGTGTTGACAG
GCCAGTAATTGAGCCTCCAG
GGCGTTTGAATTAACCGAGA
AGCTTCACCAAGGCAAAGAA
GCCTTTGAGAGAAGATCGGA
AATTCAATGAAATCCACGCC
ACATTCGGAGGGTCATGAAG
AAGGACGACATCTGGCAATC
GTTCTGCTGACCCAATTGCT
CCACCAACCGACGCTATAAT
CTCAAGGCTCACCAGAGGAC
CAATATTCGTCTTCCTCCGC
TCACGCCCACAAGATGTAAA
CACGTGACCGTTGTTTTGAC
CCCCTACACCACTCATGTCC
ACGAGCTGCAGGTCAGAGAT
CGGGCCAATACTTATGTCGT
GACTTGAACGAGTCTTGCCC
ACGTCCAGTTTGCCTCAATC
TTCTAGCTAACCGCCAGGTG
GCAAAACCCCCTACAAAACA
GTCGACGAGATGGGAATGTT
GTGAACCCAACCGAGACAGT
CCAACAGTGGAAAAGCCATT
TGCCATATATGTTGCTTGCG
ATAGCCACCGGTGTAGATGG
CAGCAGCCATTTAGGAGGAG
AATTTCGCATATGCTTTGGC
TATCACGGACATCGTGTGGT
GGATTTCCCCCTTACCAAAA
TCACCGGCTTCTTTCTTTTC
ATTGCTCTGGCCGTTACAAG
TCAAGTACAAAACCTCCTTTCAA
TCGTTATGGCAACAGTCGAG
CAGCAGAAGGTGGAATGACA
AGAGACGCCAAAGTGAAGGA
TGCTACCCGGGTTAAGAAGA
TCCAAATCTCCACCAACAGA
CCTACGATAACAGGCCGAAA
TCCTCTATGCACACTGGTGG
GGACGTTTCGCAGAAAAGAG
GCGTTCTTCTTCCGCTTATG
ACAGCAGAGCACAGCACATC
ATTTGAATTTTGCTGCCGAC
TGATTCCACAAAGCCAACAA
CGCACGTTAATCACCGAATA
CTGGCCACCATCAGACTTTT
AATGTCCCCCATGCATTAAA
GGGTGACGCAAAAGAAAGAG
AGTCCCAGCCACACAGGTAG
ACCAGTCCGAGATTTATGCG
TGAAGAAAACCGGAGACGAC
GGAAATTGTCCGTCCTTTCA
TATCTTCATCCATCCTCCGC
CAGTGTTCCACAAGTGTCCG
CGATGAATTGACGACGTGAC
CGCATGCAGTAATGGAGCTA
CTCATCCGCTGTCTCATTCA
TTCCTATTCCAAATGGTCGC
ACTGTTCGGTTGCTTCGAGT
GATGTGATGACCAACAACGG
TGGCGCAGTAGAAAATGTTG
CCGTTTCTGTCCAAAAGGAA
CAAAGTGCGCTGTTCCACTA
GCTTGCTGGTTGCTGTTGTA
CCTTGGAGGCAAATGAAAA
CCATGACCATAAGTGGGTCC
GGAGCCAGTTGAGAGCAAAG
AATCGATCAGAACCGACACC
GCCGTAAGGTTATTACGCGA
CGAACGACAAGCGAGTGATA
GGTCTCTCAAGTCGACCAGC
AATGTGTCAATGCGCAACAT
TCCTTCTGCTGTCCGCTATT
GTCTACATACAAGGGGCGGA
TAAGTTATCCGGTCCGATGC
GCGTGTGTGTACCGGTGTAG
GATGTGCCATCAGTTGAACG
ACCTACGCCTGGTCATCAAC
GGATGACTAAATCCGCTCCA
TGCGAGAGAGAAAACACACG
TACCCCCACCAAGAGATTCA
CGAAAATCCCAGGAAATCAA
CCGGGGAATCAATGTTACAC
CACGCAGAAAGAGCATTCAA
AGGAAAGAGACAGACTGGCG
ACGTAAAAAGGGGATACGCA
GGCCGAGTTGTCTTGTGTTT
TTCACGTTGTGTCCCTTTGA
ATGGTTTCCCCTTTTGCTCT
GATTCAGCGGGAAAAATTCA
CTGGACCATCATGGGTTTTC
AACGGTCTCGGATTTCTCCT
CCACAATAGGTGTATTCTTGGAAC
AACTTTCCGACCGGTTTCTT
424
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
Appendix B. List of putative homologs
Daphnia
E value
Marker
Gene ID
Lk
Distance from closest marker
d076
Dp564a
Dp564b
Dp564c
Dp589a
Dp589b
Dp1290a
Dp1290b
Dp199a
Dp199b
Dp199c
Dp199d
Dp571a
Dp571b
Dp884a
Dp884b
Dp884c
Dp884d
Dp1073a
Dp1073b
Dp553a
Dp553b
Dp553c
Dp553d
Dp802a
Dp802b
Dp802c
Dp1495a
Dp1495b
Dp1495c
Dp1495d
Dp1189a
Dp1189b
Dp300a
Dp300b
Dp300c
Dp1368a
Dp1368b
Dp1368c
Dp149a
Dp149b
Dp149c
Dp149d
Dp754a
Dp754b
Dp754c
Dp754d
Dp655a
Dp655b
Dp655c
Dp74a
Dp74b
Dp74c
Dp74d
Dp1155a
Dp1155b
Dp1195a
Dp1195b
Dp1195c
Dp957a
Dp957b
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
190.5
202.5
–17,065
9324.5
9311
–8936.5
–9023.5
27,065
25,031.5
–17,445.5
–23,100
25,700.5
–13,319
4669
4706.5
–5988.5
–8336
–26,589
–59,034.5
32,439
–2393
–32,572.5
–83,360
15,728
–9214
–16,655.5
2553
207
–2733.5
–8001
–7020.5
–16,057
22,026
–53,458
–107,243
18,981
15,315.5
–14,648.5
3492.5
8360
–82,749
–89,930.5
25,450
20,070
–18,863
–61,827
15,999
15,897
–5332
64,023.5
45,856.5
–3672
–3651
135,223.5
133,927
6819
–11,925
31,409.5
19,149.5
10,729
d098
d170
d048
d096
d114
d181
d134
d101
d063
d193
d053
d163
d001
d130
d091
d007
d148
d188
d138
8E–14
1E–12
7E–17
1E–31
1E–26
4E–13
9E–17
1E–13
3E–11
9E–20
1E–38
4E–61
7E–24
3E–37
8E–30
2E–53
2E–53
7E–44
4E–80
9E–15
9E–30
3E–18
7E–30
0
2E–11
7E–27
3E–65
5E–40
6E–17
0
8E–19
5E–18
2E–44
2E–36
2E–105
2E–30
2E–47
2E–53
2E–25
3E–11
7E–50
3E–37
9E–43
3E–45
2E–141
4E–19
5E–72
1E–35
1E–18
2E–11
5E–17
3E–34
2E–52
1E–36
2E–61
1E–18
3E–86
2E–82
2E–18
1E–14
Bit score
78
74
64
137
121
75
87
77
70
99
84
237
100
157
132
185
122
127
300
80
131
93
132
461
70
106
231
144
87
752
95
92
110
152
136
106
127
211
90
66
156
154
72
185
197
95
234
104
91
70
90
146
206
152
236
93
171
257
72
65
Drosophila
Gene ID
Cytology
CG32770-PA
CG3367-PA
CG11212-PA
CG4427-PA
CG3065-PA
CG17198-PA
CG17197-PA
CG14780-PA
CG31873-PA
CG5411-PA
CG18104-PA
CG10952-PA
CG32532-PA
CG11202-PA
CG6604-PA
CG8003-PA
CG9633-PA
CG3045-PA
CG3896-PA
CG17029-PA
CG4637-PA
CG32593-PA
CG8376-PA
CG31671-PA
CG1756-PA
CG6391-PA
CG11949-PA
CG1228-PD
CG8441-PA
CG3725-PB
CG5590-PA
CG7887-PA
CG13348-PA
CG17187-PA
CG6137-PA
CG7831-PA
CG4212-PB
CG12758-PA
CG33041-PA
CG14698-PA
CG32654-PC
CG7359-PA
CG31860-PA
CG8787-PA
CG5594-PD
CG7452-PA
CG11870-PA
CG6114-PA
CG8627-PA
CG7420-PA
CG5155-PA
CG5069-PA
CG3668-PA
CG32072-PA
CG33110-PA
CG2108-PA
CG9318-PA
CG32592-PA
CG10237-PB
CG7231-PB
X
X
2R
2L
2R
3R
3R
X
2L
2R
X
X
X
X
2L
3L
3R
2R
2R
3L
3R
X
2R
2L
X
3L
2R
3L
2R
2R
3R
3R
2R
3R
2L
3R
2L
2R
2R
3R
X
X
2L
2R
2R
3L
3R
3L
3L
2L
2L
3L
2R
3L
3R
3R
2L
X
2L
2L
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
425
Appendix B (continued )
Daphnia
Marker
Gene ID
Lk
Distance from closest marker
d197
Dp1048a
Dp1048b
Dp1048c
Dp1048d
Dp725a
Dp725b
Dp848a
Dp848b
Dp848c
Dp967a
Dp967b
Dp967c
Dp785a
Dp785b
Dp785c
Dp742a
Dp742b
Dp1497a
Dp1497b
Dp1494a
Dp1494b
Dp821a
Dp821b
Dp325a
Dp325b
Dp325c
Dp321a
Dp321b
Dp321c
Dp395a
Dp395b
Dp147a
Dp147b
Dp1056a
Dp1056b
Dp1056c
Dp1056d
Dp224a
Dp224b
Dp224c
Dp557a
Dp557b
Dp557c
Dp557d
Dp117a
Dp117b
Dp117c
Dp117d
Dp1346a
Dp1346b
Dp1346c
Dp1346d
Dp308a
Dp308b
Dp71a
Dp71b
Dp71c
Dp71d
Dp572a
Dp572b
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
II
III
III
III
III
III
III
III
III
56,229.5
48948
–80630
–87140.5
52270
42399.5
71981
–8424
–8578.5
5339
–2648
–11117.5
26949
11729.5
–39510.5
–152051
–167340
21739.5
108988.5
1273.5
–157339
21056
17434.5
16654
4725.5
–12084
–4395
–12581.5
–36222.5
219974.5
217175
–147333
–147333
15914
8665
–10642.5
–17949
762.5
–23129.5
–23321.5
9498
5901.5
–3713.5
–21283.5
17754
10235.5
–94337.5
–96940
23530.5
381
–8928.5
–12343.5
–11527.5
–68392
14823.5
11127.5
–20793.5
–21960.5
–11633.5
–11639.5
d102
d112
d140
d095
d104
d123
d044
d109
d070
d002
d047
d015
d183
d069
d079
d124
d162
d067
d010
d097
E value
Bit score
3E–66
0
8E–31
7E–24
1E–25
5E–27
9E–11
1E–85
3E–50
4E–133
7E–88
3E–32
2E–36
6E–145
7E–57
5E–33
2E–68
9E–21
2E–22
6E–47
6E–17
6E–21
5E–26
2E–11
3E–53
8E–17
8E–108
2E–38
5E–39
9E–28
5E–32
2E–33
3E–22
9E–77
4E–30
2E–11
2E–23
2E–48
4E–54
6E–19
7E–39
4E–39
3E–22
4E–13
9E–53
4E–86
3E–49
2E–58
4E–25
1E–53
4E–73
2E–15
5E–20
5E–41
1E–22
4E–28
5E–15
8E–26
7E–38
3E–26
172
763
135
95
97
111
69
317
201
200
327
85
152
309
187
134
70
62
89
186
60
50
119
72
160
88
394
163
164
82
88
143
107
114
115
70
70
195
213
95
83
162
106
77
172
318
168
113
71
144
276
62
101
142
107
125
79
87
159
119
Drosophila
Gene ID
Cytology
CG3335-PA
CG32659-PA
CG4482-PA
CG30077-PA
CG2968-PA
CG5586-PB
CG13338-PA
CG10037-PA
CG12287-PB
CG7729-PA
CG9932-PA
CG18735-PA
CG15455-PA
CG1973-PA
CG12287-PB
CG4896-PC
CG3057-PA
CG16988-PA
CG5708-PA
CG13880-PA
CG7861-PA
CG3388-PA
CG8246-PA
CG31868-PA
CG11396-PA
CG32843-PA
CG11895-PA
CG17941-PA
CG6977-PA
CG7484-PB
CG32486-PD
CG5893-PA
CG18024-PA
CG2248-PA
CG32296-PA
CG6398-PA
CG7058-PA
CG7245-PA
CG13758-PA
CG12370-PA
CG4980-PA
CG5502-PA
CG11324-PB
CG4096-PA
CG6661-PA
CG3576-PA
CG1316-PA
CG4802-PA
CG14435-PA
CG8127-PB
CG6502-PA
CG4293-PA
CG31772-PA
CG1147-PA
CG8882-PA
CG12524-PA
CG32854-PA
CG10447-PA
CG33473-PB
CG4427-PA
3L
X
2L
2R
X
3R
2R
3L
2L
3L
2L
2R
X
3R
2L
2L
2L
3L
2L
3L
2R
2R
2R
2L
3L
2R
2R
2L
3R
3L
3L
3L
2L
3L
3L
X
X
2L
X
2R
3R
3R
2L
X
3L
X
3L
2R
X
3L
3L
X
2L
3R
2L
3L
3R
2L
2R
2L
(continued on next page)
426
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
Appendix B (continued )
Daphnia
Marker
Gene ID
Lk
Distance from closest marker
d169
Dp1058a
Dp1058b
Dp1058c
Dp1058d
Dp581a
Dp581b
Dp1276a
Dp1276b
Dp1276c
Dp1276d
Dp24a
Dp24b
Dp24c
Dp50a
Dp50b
Dp50c
Dp616a
Dp616b
Dp616c
Dp337a
Dp337b
Dp137a
Dp137b
Dp770a
Dp770b
Dp770c
Dp144a
Dp144b
Dp144c
Dp813a
Dp813b
Dp530a
Dp530b
Dp530c
Dp530d
Dp1041a
Dp1041b
Dp1041c
Dp675a
Dp675b
Dp311a
Dp311b
Dp311c
Dp1311a
Dp1311b
Dp1311c
Dp1372a
Dp1372b
Dp1372c
Dp605a
Dp605b
Dp605c
Dp687a
Dp687b
Dp687c
Dp878a
Dp878b
Dp878c
Dp878d
Dp924a
Dp924b
Dp924c
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
III
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
52101
9846
–5671
–27067.5
28718
–7459
12613
2226
–8114.5
–18421
3262
3166
–68468
39212.5
4067.5
–30719
38810
41379
–38333
8886
–11791
34639
–6913
6447
–17856
–13992
28708.5
25622.5
24421
110323
9902
13177
7064
–75127.5
–78117.5
3800
1565
–4048
–72164.5
–133679
38474.5
3023
–8461
26980
18589
–46309.5
24744.5
–3219.5
–26742.5
17114.5
–92654
–92628.5
13888.5
10037.5
–33502.5
79044
28568.5
–24207.5
–32396.5
13882
8373
–16436
d082
d177
d003
d122
d078
d019
d041
d094
d049
d108
d075
d147
d089
d071
d156
d168
d081
d084
d116
d139
E value
Bit score
6E–19
2E–30
3E–27
4E–80
8E–18
1E–38
5E–19
2E–144
2E–26
2E–76
2E–51
3E–54
1E–58
8E–44
0
6E–139
1E–26
1E–17
2E–18
6E–70
4E–143
9E–24
2E–99
2E–34
8E–47
6E–22
3E–13
6E–75
1E–19
3E–107
5E–92
6E–14
8E–31
4E–44
4E–20
3E–11
6E–65
4E–11
2E–58
8E–21
5E–32
2E–38
6E–29
3E–13
8E–58
3E–102
5E–43
3E–32
4E–27
7E–54
7E–15
6E–40
2E–12
0
7E–30
5E–53
1E–94
5E–51
0
2E–24
6E–25
1E–47
95
103
124
205
82
164
98
515
72
138
156
162
192
151
275
136
121
91
95
264
308
112
367
148
190
107
52
201
99
390
341
64
136
132
63
62
249
70
206
72
125
108
125
49
156
276
171
140
123
211
82
165
50
474
132
124
348
203
424
115
115
98
Drosophila
Gene ID
Cytology
CG12096-PA
CG8913-PA
CG8967-PA
CG8274-PA
CG3738-PA
CG9907-PA
CG9071-PB
CG9907-PA
CG6632-PA
CG11093-PA
CG7293-PA
CG10642-PA
CG13567-PA
CG1099-PA
CG32096-PB
CG32823-PB
CG14575-PA
CG9918-PC
CG31643-PA
CG10160-PA
CG8983-PA
CG10421-PA
CG7749-PA
CG31690-PA
CG6445-PA
CG4509-PB
CG5454-PA
CG30421-PA
CG5798-PA
CG13900-PA
CG1449-PA
CG12943-PA
CG32180-PB
CG8070-PA
CG13533-PA
CG3251-PA
CG1951-PA
CG5053-PA
CG1810-PA
CG3026-PA
CG14885-PA
CG33135-PA
CG7301-PA
CG11077-PA
CG13188-PA
CG3011-PA
CG5177-PA
CG3048-PA
CG31794-PA
CG1434-PA
CG31392-PA
CG3956-PA
CG31251-PA
CG7908-PA
CG33227-PB
CG9601-PA
CG12630-PA
CG31612-PA
CG11579-PA
CG3291-PA
CG7404-PB
CG12908-PB
X
3R
2R
2R
2L
X
2R
X
X
4
3L
3L
2R
2L
3L
X
3L
3R
2L
3L
2R
3R
3L
2L
3L
3R
3R
2R
3R
3L
4
2R
3L
2R
2R
2L
3R
3R
X
X
3R
2R
3R
4
2R
X
2L
2L
2L
X
3R
2L
3R
3R
2R
3R
2L
2L
X
X
3L
2R
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
427
Appendix B (continued )
Daphnia
Marker
Gene ID
Lk
Distance from closest marker
d179
Dp1376a
Dp1376b
Dp78a
Dp78b
Dp78c
Dp1185a
Dp1185b
Dp1185c
Dp779a
Dp779b
Dp779c
Dp779d
Dp830a
Dp830b
Dp830c
Dp830d
Dp143a
Dp143b
Dp1409a
Dp1409b
Dp1409c
Dp1396a
Dp1396b
Dp1396c
Dp838a
Dp838b
Dp91a
Dp91b
Dp91c
Dp91d
Dp240a
Dp240b
Dp240c
Dp231a
Dp231b
Dp231c
Dp231d
Dp231e
Dp231f
Dp319a
Dp319b
Dp721a
Dp721b
Dp721c
Dp648a
Dp648b
Dp648c
Dp632a
Dp632b
Dp632c
Dp632d
Dp170a
Dp170b
Dp642a
Dp642b
Dp298a
Dp298b
Dp1040a
Dp1040b
Dp985a
Dp985b
Dp985c
Dp985d
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
IV
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
V
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
–3973
–28672
38541
33408.5
–8539.5
40877
–12647.5
–11501
13615
9052.5
–22483.5
–30722
8076
–7733.5
–34552.5
–36094
37275.5
–126653
18790
–3003.5
–42284.5
16648
13223.5
–29271.5
52613.5
17672.5
55597
3088.5
–5328.5
–11690
2597.5
–9348
–13927.5
35164
–62561.5
–137939
25412
3396.5
–7972
–63727
–109689
10441
7425.5
–33049
34072.5
–9844
–28493
85367.5
35435
–3190
–18027
47966
4888.5
8130
–1233.5
23948
19955.5
–2428.5
–11258
39883.5
29575
–6196.5
–7143
d057
d155
d105
d106
d018
d180
d172
d126
d013
d031
d024
d030
d093
d087
d119
d020
d085
d025
d142
d135
E value
Bit score
4E–58
1E–122
9E–30
9E–41
2E–14
1E–38
9E–98
2E–25
2E–42
3E–126
1E–18
1E–18
6E–44
1E–29
2E–12
6E–21
0
2E–45
4E–31
9E–29
6E–31
3E–92
1E–139
3E–32
5E–16
0
4E–43
4E–28
0
1E–27
1E–18
6E–84
2E–65
5E–98
6E–21
3E–30
4E–14
6E–40
2E–104
3E–17
1E–96
1E–17
1E–63
7E–17
4E–18
3E–16
3E–69
3E–61
2E–13
2E–72
1E–119
3E–139
5E–84
1E–38
1E–138
2E–69
1E–24
7E–61
4E–28
9E–136
5E–19
2E–14
0
147
316
89
101
82
162
182
94
124
452
85
94
138
131
56
71
233
71
135
128
93
196
218
116
87
195
143
126
550
125
95
108
123
205
104
100
79
166
304
55
152
67
246
89
89
87
198
176
75
181
163
310
129
119
306
154
102
110
125
301
96
80
716
Drosophila
Gene ID
Cytology
CG7323-PA
CG31729-PB
CG8201-PA
CG11376-PA
CG8949-PA
CG31304-PA
CG7913-PB
CG32568-PA
CG7619-PA
CG2017-PA
CG31842-PA
CG6530-PA
CG10733-PA
CG6187-PA
CG8407-PA
CG9705-PA
CG2637-PA
CG11236-PA
CG7383-PA
CG4717-PA
CG5352-PA
CG6388-PA
CG7415-PC
CG3756-PA
CG16932-PA
CG2999-PB
CG15218-PA
CG13287-PA
CG5033-PA
CG11798-PA
CG32137-PB
CG6969-PA
CG5585-PA
CG9191-PA
CG16779-PA
CG9717-PA
CG15553-PA
CG31721-PA
CG10639-PA
CG8383-PA
CG1598-PA
CG10198-PA
CG10198-PA
CG31646-PA
CG31779-PA
CG4853-PA
CG7369-PA
CG2864-PA
CG14469-PA
CG2316-PA
CG2845-PA
CG10080-PA
CG10754-PA
CG2061-PA
CG6335-PB
CG2827-PA
CG8965-PA
CG9379-PA
CG10075-PA
CG8344-PA
CG6476-PA
CG5810-PA
CG8896-PA
3L
2L
2R
2L
X
3R
3R
X
3L
3R
2L
2R
3L
2L
2R
3L
2L
2L
3L
3L
2L
2L
3R
2L
2R
4
2L
3L
2R
2R
3L
3R
3L
3L
3R
3R
3R
2L
2L
3R
2R
3R
3R
2L
2L
2R
3L
X
2R
4
X
2R
3L
X
X
2R
2L
3R
3L
2R
3R
3R
2R
(continued on next page)
428
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
Appendix B (continued )
Daphnia
Marker
Gene ID
Lk
Distance from closest marker
d190
Dp1399a
Dp1399b
Dp361a
Dp361b
Dp385a
Dp385b
Dp385c
Dp385e
Dp1327a
Dp1327b
Dp1327c
Dp1350a
Dp1350b
Dp1328a
Dp1328b
Dp1328c
Dp112a
Dp112b
Dp867a
Dp867b
Dp1300a
Dp1300b
Dp1347a
Dp1347b
Dp156a
Dp156b
Dp156c
Dp53a
Dp53b
Dp142a
Dp142b
Dp559a
Dp559b
Dp559c
Dp559d
Dp887a
Dp887b
Dp887c
Dp1493a
Dp1493b
Dp1351a
Dp1351b
Dp1351c
Dp1278a
Dp1278b
Dp1278c
Dp1278d
Dp1309a
Dp1309b
Dp1309c
Dp1325a
Dp1325b
Dp1325c
Dp1325d
Dp330a
Dp330b
Dp330c
Dp330d
Dp660a
Dp660b
Dp660c
Dp696a
Dp696b
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VI
VII
VII
VII
VII
VII
VII
VII
VII
VII
VII
VII
VII
VII
VII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
VIII
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
IX
X
X
–1017.5
–1271
5524.5
5499
21330
21321
–26501.5
–27266.5
36898
–50400.5
–100573
37195.5
29528
17411.5
–719.5
–23947.5
5916.5
–3182.5
1371.5
–4314.5
–4460.5
–6004.5
–3925
–55154.5
27339.5
25583.5
–52957.5
–1204
–50894
88658
40984
53796.5
53780
–2070.5
–2067.5
92744.5
15464
–24426
7055.5
6111.5
72150
–6458
–6479
2824.5
2818.5
–19811
–24238.5
35445
–16322.5
–25927.5
6561.5
3599
–2632.5
–9520
34298.5
3722
–14486
–31731.5
32427
19668
–16563.5
–1916.5
–15365
d073
d028
d152
d153
d157
d058
d107
d166
d189
d027
d068
d065
d077
d117
d045
d192
d178
d171
d145
d043
d088
d127
E value
Bit score
1E–20
6E–26
8E–62
5E–68
9E–19
9E–31
3E–14
1E–10
7E–49
5E–19
3E–44
5E–32
1E–78
4E–38
7E–13
0
2E–63
1E–61
4E–81
5E–61
1E–62
1E–14
1E–43
6E–21
3E–20
2E–12
1E–20
6E–22
5E–81
8E–34
1E–39
7E–26
3E–26
2E–32
6E–16
2E–48
2E–50
2E–84
2E–27
2E–25
2E–21
5E–40
2E–89
2E–23
2E–13
1E–46
1E–45
5E–11
1E–125
2E–54
2E–42
9E–47
1E–17
5E–75
2E–26
1E–56
7E–28
2E–32
6E–16
3E–14
9E–54
1E–75
2E–20
101
118
239
259
94
136
81
68
196
67
101
139
138
144
75
355
157
207
171
119
102
80
179
73
100
73
102
77
132
145
104
118
120
140
83
151
201
313
120
57
104
167
282
107
73
187
134
68
453
164
175
189
90
199
84
199
127
140
62
81
138
142
101
Drosophila
Gene ID
Cytology
CG31543-PC
CG30036-PA
CG4125-PA
CG3653-PA
CG14305-PA
CG3105-PA
CG6324-PA
CG8994-PA
CG9650-PB
CG3817-PA
CG3633-PA
CG2977-PA
CG7035-PA
CG32920-PB
CG2851-PA
CG2747-PA
CG8282-PA
CG17923-PA
CG9738-PA
CG33304-PA
CG1100-PA
CG32147-PA
CG32577-PA
CG32578-PA
CG5488-PA
CG6545-PA
CG5488-PA
CG7902-PA
CG10220-PA
CG6488-PA
CG3373-PA
CG9428-PA
CG6898-PA
CG7535-PA
CG6112-PA
CG5970-PA
CG2102-PA
CG3157-PA
CG9344-PA
CG5846-PA
CG7121-PA
CG3228-PA
CG3225-PA
CG6870-PA
CG3566-PB
CG9175-PA
CG8400-PA
CG3672-PA
CG15288-PB
CG7269-PA
CG14120-PA
CG11887-PA
CG15604-PA
CG9163-PA
CG4787-PA
CG10693-PB
CG10693-PB
CG32423-PB
CG9109-PA
CG12290-PA
CG6551-PA
CG8205-PD
CG4713-PA
3R
2R
X
X
3R
2R
X
2R
X
3R
2R
X
X
3R
2L
3R
2L
4
3R
2L
3R
3L
X
X
X
3R
X
3R
2R
2L
3R
2R
3R
3R
3L
2R
3R
2L
2R
2L
2L
X
2L
2L
X
2L
2R
3L
2L
2L
3L
2R
X
X
3R
3R
3R
3L
2L
3R
X
2R
2L
M.E.A. Cristescu et al. / Genomics 88 (2006) 415–430
429
Appendix B (continued )
Daphnia
Marker
Gene ID
Lk
d023
Dp460a
Dp460b
Dp460c
Dp304a
Dp304b
Dp1496a
Dp1496b
Dp1302a
Dp1302b
Dp1057a
Dp1057b
Dp1057c
Dp1057d
Dp641a
Dp641b
Dp641c
Dp641d
Dp808a
Dp808b
Dp808c
Dp808d
Dp70a
Dp70b
Dp70c
Dp70d
Dp1112a
Dp1112b
Dp1112c
Dp936a
Dp936b
Dp1144a
Dp1079b
Dp1079c
Dp1079d
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
X
XI
XI
XI
XI
XI
XI
XI
XI
XI
XI
XI
XII
XII
XII
XII
XII
XII
d034
d072
d161
d186
d083
d092
d006
d173
d137
d182
E value
Bit score
2E–19
4E–21
3E–14
7E–19
9E–12
9E–76
1E–12
7E–18
1E–73
7E–66
6E–97
7E–32
8E–28
2E–38
4E–25
5E–25
1E–60
1E–84
5E–71
7E–31
2E–155
0
8E–133
3E–81
5E–138
9E–59
7E–86
2E–21
5E–103
4E–71
4E–15
2E–22
6E–91
1E–112
58
103
79
48
70
285
77
94
200
253
357
138
73
124
115
113
212
315
269
136
168
222
475
303
233
230
178
102
375
182
84
104
338
410
Distance from closest marker
51284.5
7620.5
–86107.5
13685
12564.5
38824.5
20675
–7307
–34144
49005
48972
–5131
–10203.5
39475.5
5580
–15435.5
–20074
40318
40274.5
–11911.5
–14853.5
82401
46862.5
–33190
–46643.5
24553.5
9834
–16578
–52736
–54685
5402.5
22188
10770.5
–4970
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