Arabidopsis/Brassica napus comparative map
Parkin et al.. 1
Segmental structure of the Brassica napus genome based on comparative analysis with
Arabidopsis thaliana.
Isobel A. P. Parkin*, Sigrun M. Gulden*, Andrew G. Sharpe*, Lewis Lukens, Martin Trick§,
Thomas C. Osborn and Derek J. Lydiate*
*Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon,
SK., S7N 0X2, Canada.
University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
§John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK.
Department of Agronomy, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706,
USA.
Sequence data from this article has been deposited with the EMBL/GenBank Data Libraries
under accession nos. XXX-XXXX
Genetics: Published Articles Ahead of Print, published on July 14, 2005 as 10.1534/genetics.105.042093
Arabidopsis/Brassica napus comparative map
Parkin et al.. 2
Running Title: Arabidopsis/Brassica napus comparative map
Key Words: Brassica evolution, Arabidopsis model genome, collinearity, polyploidy
Corresponding Author:
Dr. Isobel A. P. Parkin
Saskatoon Research Centre, Agriculture and Agri-Food Canada,
107 Science Place, Saskatoon, SK., S7N 0X2, CANADA.
Tel: 1 306 956 7283
Fax: 1 306 956 7247
Email: ParkinI@agr.gc.ca
Arabidopsis/Brassica napus comparative map
Parkin et al.. 3
ABSTRACT
Over 1000 genetically linked RFLP loci in Brassica napus were mapped to homologous
positions in the Arabidopsis genome based on sequence similarity. Blocks of genetically linked
loci in B. napus frequently corresponded to physically linked markers in Arabidopsis. This
comparative analysis allowed the identification of a minimum of 21 conserved genomic units
within the Arabidopsis genome which can be duplicated and rearranged to generate the present
day B. napus genome. The conserved regions extended over lengths as great as 50 cM in the B.
napus genetic map, equivalent to approximately 9 Mb of contiguous sequence in the Arabidopsis
genome. There was also evidence for conservation of chromosome landmarks, particularly
centromeric regions, between the two species. The observed segmental structure of the
Brassica genome strongly suggests that the extant Brassica diploid species evolved from an
hexaploid ancestor. The comparative map assists in exploiting the Arabidopsis genomic
sequence for marker and candidate gene identification within the larger, intractable genomes of
the Brassica polyploids.
Arabidopsis/Brassica napus comparative map
Parkin et al.. 4
INTRODUCTION
ARABIDOPSIS thaliana (hereafter referred to as Arabidopsis) is one of almost 3500 species
which make up the monophyletic family of the Brassicaceae (PRICE et al., 1994). Arabidopsis
thus shares recent common ancestry with a large number of species of significant economic
importance, including a diverse range of vegetable and oil producing crops, the majority of
which are Brassica species. Arabidopsis is an excellent model system for the Brassicaceae, with
a small and relatively simple genome, efficient transformation system, diverse range of genetic
and genomics resources, and a completed genome sequence (ARABIDOPSIS GENOME
INITIATIVE, 2000).
Over the past ten years, plant comparative mapping has taken prominence as a powerful
tool firstly for uncovering the processes and rate of genome evolution and secondly for allowing
the transfer of genetic resources between species. Comparative mapping has been most
extensively applied to the grasses where the genetic maps of eleven species, including the model
monocot rice, have been aligned. These include 11 diverse species varying dramatically in
haploid chromosome number, genome size, and phenotype (reviewed in DEVOS and GALE,
2000). Perhaps the most striking observation from the cereal studies was the extensive genome
conservation observed between species that diverged millions of years ago. Using rice as the
basal genome, fewer than 30 conserved blocks were identified, which could be rearranged and/or
duplicated to form each of the other grass genomes. Comparative mapping studies among
members of the Brassicaceae have been more ambiguous in their conclusions, leading to on-
going discussions with regards to the level of genome duplication prevalent in modern day
Brassica cultivars and the extent of the genome rearrangements which have occurred in the
Arabidopsis/Brassica napus comparative map
Parkin et al.. 5
evolution of these cultivars from a common ancestor (LAGERCRANTZ, 1998; LAN et al.,
2000; LUKENS et al., 2003).
The present study focuses on the genome of the oilseed crop Brassica napus, which is an
amphidiploid species formed from multiple independent fusion events between ancestors of the
diploids B. rapa (A genome donor) and B. oleracea (C genome donor) (PARKIN et al., 1995;
PALMER et al., 1983; U, 1935). Polyploidy is a prevalent evolutionary mechanism within
angiosperms since it has been estimated that 30-70% of modern plant species have evolved
through a polyploid ancestor (reviewed in WENDEL, 2000). Polyploidy can occur either
through the duplication of whole chromosome complements or the fusion of related chromosome
complements, and stabilisation of the newly expanded karyotype must then take place to ensure
normal diploid inheritance. Diploidisation of the novel polyploid can occur through
chromosomal restructuring or genetic control of illegitimate recombination events or a
combination of both mechanisms. It is widely accepted that the progenitor diploid genomes of
B. napus are ancient polyploids and that large scale chromosome rearrangements have occurred
since their evolution from a lower chromosome number progenitor (SCHMIDT et al., 2001).
What is more contentious is whether the diploids evolved through a hexaploid ancestor or
whether they were formed via segmental duplication of one or two ancestral genomes (LUKENS
et al., 2004). B. napus, a relatively young amphidiploid, is somewhat of an anomaly since it has
been established that no major chromosomal rearrangements have occurred since the fusion of
the progenitor A and C genomes, but homoeologous recombination events between these two
related genomes are common in newly resynthesised B. napus lines and have been observed at
low levels in established canola cultivars (UDALL et al, 2004; PARKIN et al., 1995; SHARPE
Arabidopsis/Brassica napus comparative map
Parkin et al.. 6
et al., 1995). It has yet to be established if B. napus has evolved or inherited a locus controlling
homologous pairing similar to the Ph1 locus in hexaploid wheat (JENCZEWSKI et al., 2003).
Comparative mapping between B. napus and Arabidopsis has thus far targeted small
regions of the Arabidopsis genome, generally identifying three collinear segments in each of the
diploid genomes for every region of Arabidopsis studied thereby promoting the idea that the
diploid Brassica species may have evolved through a hexaploid ancestor (CAVELL et al., 1998;
OSBORN et al., 1997; PARKIN et al., 2002). However, at the same time regions suggesting a
more complex relationship between the two species were also identified (OSBORN et al., 1997;
PARKIN et al., 2002). In the earliest published global comparison between one of the diploid
Brassicas, B. nigra (black mustard), and Arabidopsis, an extensive number of rearrangements
were invoked to explain how the two extant diploid genomes evolved from a common hexaploid
ancestor (LAGERCRANTZ, 1998). There have been four global comparisons of the genomes of
B. oleracea and Arabidopsis. Although all have been limited by a low density of common loci,
three identified extensive synteny between the two genomes but were inconclusive in assessing
the level of duplication of the collinear segments (LAN et al., 2000; BABULA et al., 2003;
LUKENS et al., 2003). A more recent comparison of the B. oleracea and Arabidopsis genomes
refuted the possibility of a hexaploid ancestor, citing evidence of syntenous blocks ranging in
copy number from one to seven (LI et al., 2003).
The present study describes a comprehensive comparison of a Brassica genome with that
of Arabidopsis. Sequences of 359 probes derived from Brassica and Arabidopsis that detect
1,232 genetically mapped loci in B. napus, were used to query the Arabidopsis genome,
revealing 550 homologous sequences and their inferred chromosomal positions. The data
provides strong evidence to support the hypothesis that the Brassica diploid genomes evolved
Arabidopsis/Brassica napus comparative map
Parkin et al.. 7
through a hexaploid ancestor and suggests conservation of some centromeric regions between the
two species. The postulated ancestor appears to have been formed from duplication events
which occurred subsequent to the putative global duplication events which took place between
65 and 90 million years ago during the evolution of Arabidopsis (LYNCH and CONERY, 2000;
SIMILLION et al., 2002; RAES et al., 2003). The resultant genetic and physical comparative
map can be used not only to infer genome rearrangements during the evolution of the Brassica
species but also to identify regions of the Arabidopsis genome which may harbour genes of
interest and should potentiate the exploitation of Arabidopsis genomics tools in Brassica
research.
MATERIALS AND METHODS
Genetic Linkage Analysis: Genetic linkage analysis in B. napus was carried out as described
previously except hybridisations with Arabidopsis clones were washed only at low stringency (2
X SSC, 0.1% SDS) (SHARPE et al., 1995). The B. napus population consisted of 60 doubled
haploid lines derived from crosses between a winter B. napus breeding line (CPB87/5) and a
newly resynthesised B. napus line (SYN1) as described in PARKIN et al. (1995). The genetic
map also includes loci positioned through previously described map alignments with a second
linkage map of B. napus and one of B. oleracea (PARKIN and LYDIATE, 1997; BOHUON et
al., 1996). Briefly, common parental genotypes allowed corresponding loci to be identified
between the maps through the inheritance of identical RFLP alleles. Loci mapped in only one
population which co-segregated with such common loci were positioned at that locus in the
combined map. Loci mapped in only one population positioned between common loci were
Arabidopsis/Brassica napus comparative map
Parkin et al.. 8
placed in the corresponding interval in the combined map based on their relative position in the
map of origin. The RFLP probes consisted of 213 Brassica genomic clones (pN, pO, pR, pW:
SHARPE et al., 1995), 61 Brassica cDNA clones (CA, es), 88 Arabidopsis cDNA clones (I, N,
R, Z: SILLITO et al., 2000) and six cloned Brassica or Arabidopsis genes (ACYL, CONSTANS,
FCA, HS1, oleosin: pC2, 9 desaturase: pC3). The genetic linkage map was constructed using
Mapmaker v3 with a LOD score of 4.0 (LANDER et al, 1987) and the linkage groups were
drawn using Mapchart (VOORRIPS 2002). Irregularities in meiotic pairing in the resynthesised
B. napus parental line of the doubled haploid population used for the initial and the additional
mapping, caused a non-disjunction event which prevented the accurate mapping of further loci to
linkage group N16 (PARKIN et al., 1995). A limited map of N16 derived from the alignment of
N16 from B. napus, described in SHARPE et al. (1995), and O6 from B. oleracea, described in
BOHUON et al. (1996) has been used in the present analysis. A similar alignment of N16 and
O6 was discussed in RYDER et al. (2001).
Sequence Analysis: Brassica genomic or cDNA clones were sequenced from each end using the
BigDyeTM
v2 Terminator cycle sequencing kit according to the instructions of the manufacturer
and subsequently the reactions were run out on an automated ABI377 DNA Sequencer (Applied
Biosystems, Foster City, CA, USA). The Brassica sequences were analysed using Sequencher
(Gene Codes Corp, Ann Arbor, MI, USA) to trim vector sequence, identify overlaps and
generate contigs. Brassica and Arabidopsis sequences were analysed for homology to the TIGR
Arabidopsis pseudo chromosome genomic sequence version 5.0
(ftp://ftp.tigr.org/pub/data/a_thaliana/) using the BLAST programs of the National Center for
Biotechnology Information (http://www.ncbi.nlm.nih.gov/) housed on a Linux server. Low
complexity sequences were filtered in the BLAST analysis, and default values for cost
Arabidopsis/Brassica napus comparative map
Parkin et al.. 9
(mismatch cost = -3.0), reward (match reward= 1.0), and wordsize (11 bp) were selected. The
default gap opening penalty (5.0), and the gap extension penalty (2.0) were also selected. Perl
script was used to extract the base pair position in the Arabidopsis genomic sequence of each
HSP (high scoring segment pairs), identified with BLASTN, for each clone where the primary
HSP had an E value of less than or equal to 1E-07 (Table I, supplemental data).
RESULTS
Comparative map of Brassica napus and Arabidopsis: Genetic linkage mapping of restriction
fragment length polymorphisms (RFLPs) identified with 183 Brassica and Arabidopsis cDNA
clones added a further 646 loci to the published aligned map of B. napus (BOHUON et al., 1996;
PARKIN and LYDIATE, 1997). The complete B. napus linkage map is presented in Figure 1
and consists of 1317 genetic loci distributed over nineteen linkage groups with a combined map
length of 1,968 cM.
The genetic linkage map was generated from segregating loci detected by 368 DNA
clones, 274 of which were derived from anonymous Brassica genomic or complementary DNA,
five were Brassica homologues of known genes and the remaining 89 clones were derived from
Arabidopsis cDNA. Sequence data was obtained for 267 of the anonymous Brassica clones and
BLASTN analysis was used to identify homologous loci within the Arabidopsis genome for each
clone. A fairly low expect (E) value was used as the exclusion cut off (1E-07) (supplemental
data, Table I). The low E value was adopted to maximise the number of number of markers
positioned, since the majority of the probes were derived from genomic, potentially inter-genic,
DNA. Two hundred and fifty-eight of the Brassica clones displayed homology to 404 regions
Arabidopsis/Brassica napus comparative map
Parkin et al.. 10
within the Arabidopsis genome, with an average sequence identity of 86% over all aligned
highest scoring pairs (HSPs). The majority of these hits were to genic regions and the most
similar Arabidopsis gene was identified for each clone (supplemental data, Table I). A less
stringent E value can lead to the identification of a large number of small non-specific regions of
homology (LUKENS et al., 2003). Fifty-eight of the 258 clones identified regions of similarity
with bit scores lower than 82, a value suggested as a cut-off for identifying orthologous
sequences within the Arabidopsis genome for Brassica markers (LUKENS et al., 2003). For 11
clones these lower scoring hits represented their only or primary region of homology within the
Arabidopsis genome, the data for these clones was included in the comparative analysis
described below. The remainder of the low scoring hits represented secondary or tertiary regions
of homology which generally fell within predefined duplicated regions within the Arabidopsis
genome (ARABIDOPSIS GENOME INITIATIVE, 2000), and these data did not impact on the
comparative analysis. Ten of the Brassica genomic clones showed no significant homology to
the Arabidopsis genomic sequence at an E value of 1E-07, one clone, pR113, mapped to the
Arabidopsis genome over multiple adjacent HSPs, but with an E value of 1E-06. Subsequent
BLASTX analysis of the remaining nine clones identified related sequence for two clones, pR30
and pN87, which showed significant (1E-44 and 1E-94 respectively) homology to an annotated
retroelement pol polyprotein sequence (At3g29156). Perhaps not surprisingly neither of these
clones mapped to syntenous regions between the two genomes (see below).
To position the Arabidopsis clones accurately relative to the Brassica sequences all the
clones were compared to the Arabidopsis pseudo-chromosome sequence using BLASTN
analysis. In total, 550 loci were physically positioned within the Arabidopsis genome based on
sequence identity (an average of one comparative marker every 214 Kb). These same clones
Arabidopsis/Brassica napus comparative map
Parkin et al.. 11
identified 1,232 RFLP loci on the genetic linkage map of B. napus (an average of one
comparative marker every 1.6 cM). In Figure 1 each of the B. napus genetic loci has been colour
coded according to the most significant BLASTN hit for the probe which detected that locus.
Forty-two percent of the RFLP clones probes showed sequence similarity to more than one
region of the Arabidopsis genome. Some of the mapped homologous loci in B. napus may
represent orthologues of these secondary hits within the model genome. Brassica loci whose
position within a conserved block in Arabidopsis was dependant upon such secondary hits are
colour coded according to the appropriate duplicate hit and are identified in italics in Figure 1.
All of the B. napus linkage groups were composed of loci identified by probes related to
sequence from each of the five Arabidopsis chromosomes (Table 1 and Figure 1). If the
Brassica genomes evolved through simple polyploidy from a lower chromosome ancestor
similar to Arabidopsis, it might be expected that the comparative loci mapped within the B.
napus genome would be equally represented across the Arabidopsis genome. However, the
number of loci originating from each Arabidopsis chromosome was not evenly distributed with
significantly fewer loci than expected detected by probes showing homology to Arabidopsis
chromosomes 2 and 3 and significantly more loci than expected detected by probes with
homology to Arabidopsis chromosome 5 (p<0.001 for a goodness-of-fit test) (Table 1). This
non-random distribution could be a function of a reduction in chromosome number in the
Arabidopsis lineage and/or a function of gene loss occurring after genome duplication events
within Arabidopsis.
Identification of conserved blocks between Arabidopsis and B. napus: For each B. napus
linkage group it was possible to identify blocks of conserved synteny between B. napus and
Arabidopsis/Brassica napus comparative map
Parkin et al.. 12
Arabidopsis which represent chromosomal segments that have been maintained since the
divergence of Arabidopsis and Brassica from a common ancestor (Figures 1 and 2).
A conserved block is defined as a region that contains several closely linked homologous
loci in both the Arabidopsis and Brassica genomes. Each block has a minimum of four mapped
loci with at least one shared locus every 5 cM in B. napus and at least one shared locus every 1
Mb in Arabidopsis. Using these criteria, each conserved block contained on average 7.8 shared
loci and had an average length of 14.8 cM in B. napus and 4.8 Mb in Arabidopsis. Together the
blocks covered almost 90% of the mapped length of the B. napus genome. The average physical
distance covered in the Arabidopsis genome per 1 cM of genetic distance in the B. napus genome
was calculated for every pair of comparative markers identified within the conserved blocks
(Figure 3). The distribution was skewed with 35% of the intervals tested giving a ratio of 1 cM
of the B. napus genetic map to 100,000 bp or less of Arabidopsis sequence, with a median ratio
of 1 cM to 160,767 bp.
Based on the conserved blocks, 21 segments were identified within the Arabidopsis
genome which could be duplicated and rearranged to form the skeleton of the B. napus genome
(Figure 1, Figure 2). Although coverage of the two genomes is extensive there are areas where
marker density is limited, specifically the regions spanning the Arabidopsis centromeres (Figure
2). The low copy number sequences utilised in the Brassica mapping would be expected to have
lower levels of similarity to centromeres, since they tend to be located within gene poor
transposable element rich regions (ARABIDOPSIS GENOME INITIATIVE, 2000).
Comparative genome organisation: The organisation of the B. napus genome in comparison to
the Arabidopsis genome as depicted in Figures 1 and 2 has been summarised for each of the
linkage groups. Due to the close homology between the A (N1-N10) and C (N11-N19) genomes
Arabidopsis/Brassica napus comparative map
Parkin et al.. 13
of B. napus, the primary homoeologues in B. napus (described in PARKIN et al., 2003) are
indicated in the comparison.
N1/N11: These two B. napus linkage groups are homologous along their entire length. The top
half of each linkage group shows significant homology to the long arm of Arabidopsis
chromosome 4 (block C4B) with one inversion, previously noted in CAVELL et al. (1998),
disrupting the collinearity between the two genomes. The inversion appears to be specific to
N1/N11, and is not present in the homologous regions of linkage groups N3/N17 and N8/N18
where copies of block C4B were found. The lower half of N1/N11 is homologous to the top arm
of Arabidopsis chromosome 3 (block C3A). This block is also strongly conserved on N5/N15
and N3/N13. In each case the distal end of the Arabidopsis chromosome corresponds with the
terminal end of the linkage groups. At the breakpoint between the two large stretches of
collinearity there are three markers that span the centromere on Arabidopsis C3 and additional
markers that do not identify a conserved region. One gross chromosomal rearrangement would
be sufficient to generate N1/N11 from the blocks defined in Figure 2.
N2/N12: These two linkage groups are homologous along their mapped length. PARKIN et al.
(2002) previously described the relationship between N2/N12 and Arabidopsis C5, where the
upper region of N2/N12 is homologous to the top 8 Mb of Arabidopsis C5 (block C5A) and an
inversion on Arabidopsis C5 has moved block C5E to lie adjacent to block C5A. This pattern of
C5A-C5E is conserved on linkage groups N3/N13 and N10/N19. The same inversion moved
blocks C5B and C5D to the bottom of N2/N12. N2/N12 share a region of homology with
Arabidopsis C1, block C1E, adjacent to which are five markers that flank the centromere on
Arabidopsis C4. Two further small conserved regions were identified on N2/N12, C3B and C5F.
Arabidopsis/Brassica napus comparative map
Parkin et al.. 14
One inversion on Arabidopsis C5 and three insertion/deletion/translocation events represent the
least number of rearrangements, which could generate the present organisation of N2/N12.
N3(N17)/N13: The homology of N3/N13 to C5 is described above, below which N3/N13 share
homology with Arabidopsis C2 (block C2BC). Block C2BC on N3/N13 was defined by a lower
density of comparative markers, which were further rearranged by an inversion, compared to the
duplicated copies of C2BC found on N4/N14 and N5. The lower end of C2BC on N3/N13,
which borders the centromere on C2, lies adjacent to a conserved block originating from the
centromeric region of Arabidopsis C4 (block C4A). Below C4A, N3/N13 share homology with
block C3A as described above. At the junction of C3A, which lies proximal to the centromere on
C3, N3 is no longer homologous to N13 but instead shares homology with linkage group N17
and Arabidopsis C4 as described above. The remainder of linkage group N13 has no clear
region of homoeology in the B. napus A genome. However, in relation to Arabidopsis this region
of N13 shares homology with the blocks flanking the centromere of C3 (C3B-C3C), block C1B
and block C4B. In the area which would be homologous to the centromeric region of C3 there
are eight markers with homology to different Arabidopsis chromosomes, three of which flank the
centromere on C2. At least three gross chromosomal rearrangements and two inversions are
necessary to generate N3 from the identified conserved blocks, assuming C3ABC has been
essentially conserved one additional translocation/insertion would be necessary to generate N13.
N4/N14/N5: The majority of N4 and N14 (65% and 75% of the mapped length, respectively)
and the upper half of N5 share homology with Arabidopsis C2. The organization of N14
suggests that of an isocentric chromosome with the upper and lower arms sharing numerous
common markers mapped in inverse orientation with respect to each other. The top of N4 and
the homoeologous central section of N14 show small blocks of collinearity with Arabidopsis C3,
Arabidopsis/Brassica napus comparative map
Parkin et al.. 15
C4 and C5; N14 has one additional block from C1. Three gross chromosomal rearrangements
are sufficient to describe the organisation of N4 and one additional inversion and two
translocation/insertions would describe N14.
N5/N15/N6: The lower half of N5 and N15 as described above (for N1/N11) are collinear with
the long arm of Arabidopsis C3. At the centre of N5/N15, the markers originate from
Arabidopsis C1, with comparative markers flanking the centromere on C1. This central region
on N15 is part of a larger block which is collinear with the upper arm of Arabidopsis C1 and the
homoeologous region of B. napus N6. One and two large chromosomal rearrangements would
generate the present organisation of N15 and N5 respectively.
N6/N17: The lower half of N6 shows homology to sections of Arabidopsis C5 and C3. The
region from block C5B to the bottom of N6 is homoeologous but inverted with respect to N17.
There are two markers on N6/N17 (CA129 and es1732) that identify sequences on the short arm
of Arabidopsis C2; there was insufficient marker data from this region to identify a conserved
block, however fine mapping of a dwarf gene in B. rapa has subsequently aligned this region of
N6 with the short arm of Arabidopsis C2 (MUANGPROM and OSBORN, 2004). It is to be
expected that for regions such as these, flanking the Arabidopsis centromeres where there is a
dearth of comparative markers, further conserved blocks will be identified. The comparison of
N6/N17 to Arabidopsis is complex relative to other B. napus linkage groups and at least five and
six chromosomal rearrangements need to be invoked to generate N6 and N17, respectively.
N7(N16)/N17: The top of N7/N17 are homologous to the short arm of Arabidopsis C2 including
comparative markers which flank the centromere on C2. Homoeology between N7/N17 breaks
down after block C1B, where the lower half of N7 is homologous with N16 and Arabidopsis C1.
Due to the constraints of the mapping population (refer to Materials and Methods) there are
Arabidopsis/Brassica napus comparative map
Parkin et al.. 16
limited markers mapped to N16, making the number of rearrangements difficult to interpret. The
data suggests that at least three translocations/deletions/insertions of conserved blocks have
taken place to give N7 and at least one chromosomal rearrangement gave rise to N16.
N8/N18/N9: The whole of N8 appears to be homoeologous with N18, and is syntenous with
Arabidopsis C1C, C4B and C1AB; however block C1AB is inverted on N18 with respect to N8.
The remainder of N18 is homoeologous to the lower portion of N9 and is syntenous with
Arabidopsis C3D, C2B, a fraction of C1B and C1A. The latter block forms part of an internal
duplication on N18. One insertion of block C4B into the centromeric region lying between
C1AB and C1C and two inversions (in C4B) could describe N8. The same insertion of C4B
found on N8, duplication of C1A and translocation/insertion of C3D would generate N18.
N9/N19/N10: N10 and N19 share a region which is syntenous with Arabidopsis C5 as described
above (for N2/N12). The end of C5E, which coincides with the break in homology between
N10/N19, separates a region of apparent conservation between the two species from one which is
fragmented. The tops of N9 and N19 share loci from comparative markers which are assigned to
a number of blocks, running from the top of N9/N19 in the order C4A-C5B-C5F-C1D-C5D-
C4A. There is no clear region of homology in the B. napus C genome for the top of N10, which
is syntenous with Arabidopsis C1. N9 has the most complex segmental pattern of all the linkage
groups necessitating at least nine chromosomal rearrangements to generate the mapped group.
One inversion on C5 (as described for N2/N12) and one translocation would explain N10, one
inversion and six further rearrangements would explain N19.
At least seventy-four translocations, fusions, deletions or inversions of the 21 conserved
segments found within the Arabidopsis genome are necessary to generate the present day B.
napus genome. However, 28 of these rearrangements are common to both the A and C genomes
Arabidopsis/Brassica napus comparative map
Parkin et al.. 17
of B. napus, suggesting they occurred prior to their divergence from a common ancestor. As
described above, a number of the breakpoints between conserved segments correspond to
previously defined translocation end points which separate the A and C genomes of B. napus
(PARKIN et al., 2003). In a number of instances the junctions of conserved blocks coincide
with telomeric or centromeric regions of Arabidopsis suggesting centric fission and fusion have
played a role in the chromosomal restructuring.
Duplication within the Brassica Genome: Counting the number of times a single Arabidopsis
region is found within the B. napus genome provides an estimate of the level of genome
duplication within Brassica compared to the model genome. Each conserved chromosomal
segment was represented between four and seven times within the B. napus genome (Table 2).
However, the organisation of the different duplicated copies of each block varied with respect to
each other, either by the presence of additional rearrangements (see description for N1/N11
above) or by the number of comparative markers (see description for N3(N17)/N13 above). In
Arabidopsis, 81% of the comparative loci positioned on the genome mapped to conserved
regions present in at least six copies within the B. napus genome (Table 2). Eighty-six percent of
the mapped length of the B. napus genome, which was arranged in conserved blocks, was found
in at least six copies (Table 2). These results corroborate previous suggestions based on more
limited data that the Brassica diploid genomes have evolved through a hexaploid ancestor.
However, the presence of seven copies of some Arabidopsis regions within the B. napus genome
suggests that further segmental duplication events may have occurred subsequent to any
polyploidy event(s).
Consequences of duplication within the Arabidopsis genome: The majority of the conserved
Arabidopsis blocks, including those known to be part of duplicated regions within Arabidopsis,
Arabidopsis/Brassica napus comparative map
Parkin et al.. 18
are each found between five and seven times within the B. napus genome. Effectively this means
that the duplicated regions of the Arabidopsis genome are found between ten and fourteen times
within the B. napus genome, similarly recent physical mapping carried out in B. napus identified
twelve regions within the B. napus genome homologous to a small duplicated region of the
Arabidopsis genome (RANA et al., 2004). These data suggest the large segmental genomic
duplications found within Arabidopsis occurred in the common ancestor of the two lineages prior
to the formation of a Brassica hexaploid ancestor. These data are also consistent with the fact
that the last round of genome duplication is believed to have occurred in Arabidopsis between 65
and 90 million years ago (LYNCH and CONERY, 2000; SIMILLION et al., 2002; RAES et al.,
2003) whereas the separation of the Arabidopsis and Brassica lineages is dated somewhere
between 12 and 24 million years ago (KOCH et al, 2000).
Since the divergence of these two species one would expect the independent loss of
redundant duplicate genes from both species. Several such losses were observed from the
Arabidopsis genome. For example on N1 and N11, the upper parts of the linkage groups are
collinear with the long arm of Arabidopsis chromosome 4 (Figure 1). Nonetheless, a number of
Brassica loci were identified by probes (IC06, CA87, pN52, pN67) originating from Arabidopsis
chromosome 2. Although these probes were found in regions identified as being duplicated
between chromosomes 2 and 4 of Arabidopsis (http://www.tigr.org/tdb/e2k1/ath1/
Arabidopsis_genome_duplication.shtml) they showed no homology to Arabidopsis chromosome
4 sequence. Thus, Brassica has maintained duplicate copies of these sequences within the
region equivalent to chromosome 4, whereas Arabidopsis has lost them.
In some instances the duplications evident within the Arabidopsis genome have made it
difficult to identify the most similar region shared between the two species. For example, loci on
Arabidopsis/Brassica napus comparative map
Parkin et al.. 19
B. napus linkage group N19, show strong homology to both chromosome 5 block C and to the
duplicated region on Arabidopsis chromosome 1 block D (Figure 4).
Conservation of chromosome landmarks between the two species: The position of each
Brassica centromere has yet to be accurately determined relative to the genetic linkage maps.
However, RFLP mapping of artefactual telocentric chromosomes in Brassica aneuploids placed
the centromere of linkage group N12 between markers pW177E3 and pO5b, the centromere of
group N13 between pW181a and pN96b and the centromere of group N14 between markers
pN151b and pW130a (KELLY, 1996). Additionally, integration of the cytogenetic and genetic
linkage maps of B. oleracea positioned the centromere of linkage group O1 (equivalent to N11)
between markers pN152E1 and pO168E1 (HOWELL et al., 2002).
In the proposed centromeric region of N12 four coincident markers were mapped with
homology to Arabidopsis sequences that span the centromere on chromosome 4, suggesting
conservation of chromosome position between the species. It is possible that with sufficient
marker data the Arabidopsis centromeric positions could be used to predict functional and
ancestral centromeric regions in Brassica chromosomes. The latter would arise, since a
hexaploid derived from a lower chromosome progenitor, which likely had between 5 and 8
chromosomes, would have originally had between 15 and 24 functional centromeres, which were
then reduced to 10 and 9 in the Brassica A and C genomes respectively. As in the case of N12,
there were a number of instances where the density of markers across the Arabidopsis
centromere was insufficient to identify a conserved block in B. napus. However, the loci
identified by these same markers were tightly linked in B. napus and in the case of N11, N12 and
N13 there was further cytological evidence suggesting the centromere location. These putative
centromeric regions have each been indicated in Figure 1. As evidenced by numerous small
Arabidopsis/Brassica napus comparative map
Parkin et al.. 20
segments of collinearity flanking these provisional centromeric regions on N11, N12 and N14, it
appears the neighbouring regions are prone to rearrangements and evolve rapidly compared to
more distal regions.
The karyotype of B. oleracea indicates that linkage group O7 (equivalent to N17) is an
acrocentric chromosome and has a strongly hybridising 45S locus at the terminus of the short
arm (HOWELL et al., 2002). This region of N17 shows homology to the short arm of
Arabidopsis chromosome 2 and coincidently one of the two NOR regions of Arabidopsis also
maps to the terminus of the short arm of chromosome 2 (FRANZ et al., 1998).
DISCUSSION
In the present study, by allowing minor disruptions in conserved regions it was possible
to identify 21 conserved blocks within Arabidopsis which could be replicated and rearranged to
cover almost 90% of the mapped length of B. napus. A minimum number of 74 gross
rearrangements, with 38 in the A genome and 36 in the C genome, can be estimated to have
separated the two lineages since their divergence 14-24 million years ago (mya) (KOCH et al,
2000). This lies between two previously published figures derived from Brassica Arabidopsis
comparative mapping, which were 19 chromosomal rearrangements separating B. oleracea from
Arabidopsis (LAN et al., 2000) and 90 separating B. nigra from Arabidopsis (LAGERCRANTZ,
1998). Detecting rearrangements is influenced by a number of variables including the number
and type of available comparative markers, the level of polymorphism within a mapping
population and the method of determining synteny between species. For LAN et al. (2000) the
lower figure was probably due to a low density of comparative markers and for
LAGERCRANTZ et al. (1998) the much higher figure was due in part to the approach used to
Arabidopsis/Brassica napus comparative map
Parkin et al.. 21
identify syntenous regions, with no allowance made for minor disruptions of collinearity, and
was exacerbated by the inclusion of markers thought to be single copy in Arabidopsis but now
known to be multi-copy. Comparing estimates of the level of rearrangements in lineages is
problematic because of the inherent difficulties in comparing between data sets and due to
variation in the estimated divergence times. With that proviso, considering the data presented
here, the level of rearrangement observed in the Brassiceae tribe, as represented by the A and C
genomes of B. napus, is relatively high when compared with related species from the
Brassicaceae family. Recently the genetic maps of Capsella rubella (Lepideae tribe) and
Arabidopsis lyrata (Sisymbrieae tribe) have been compared to the sequence map of A. thaliana
(BOIVIN et al., 2004; KUITTINEN et al., 2004). Based on the comparison to the A. thaliana
genome, analysis of the two maps indicates equivalent linkage group organisation, with the eight
chromosomes of C. rubella, A-H, aligning with the A. lyrata chromosomes, AL1-AL8,
respectively. This demonstrates that both species evolved from a common ancestor. A. lyrata
and C. rubella are estimated to have diverged from Arabidopsis 5 mya and 10 mya, respectively
(BOIVIN et al., 2004; KUITTINEN et al., 2004). A limited number of major chromosomal
rearrangements, approximately 6-13, separate these two species from A. thaliana. In addition, no
major rearrangements have separated A. lyrata from C. rubella. Although it is not possible to
align all the conserved blocks identified in this study with the C. rubella and A. lyrata genomes,
the junctions of a number of the rearrangements identified between these two species and A.
thaliana correspond to the ends of conserved blocks identified in this study. However, none of
the chromosomal rearrangements which separate A. lyrata and C. rubella from A. thaliana
appear to be common to the Brassiceae lineage.
Arabidopsis/Brassica napus comparative map
Parkin et al.. 22
The fact that the majority of the identified conserved segments are found in at least six
copies in B. napus, and 81% of the comparative loci, which define the conserved blocks in
Arabidopsis, are mapped to these triplicated regions, is consistent with a proposed hexaploid
ancestor for the diploid Brassica progenitor. However, it could still be argued that the observed
pattern of duplicated segments is the result of several smaller independent segmental
duplications following a single whole genome duplication event, a mode of evolution which
would require a significant number of independent duplication events. Polyploidy has been a
prevalent mechanism of evolution within the angiosperms and it has been estimated that 30-70%
of species having undergone at least one round of chromosome doubling during their
evolutionary development (reviewed in WENDEL, 2000). There is also well documented
evidence for extensive chromosomal rearrangements in newly resynthesised Brassica polyploids
(SONG et al, 1995; PARKIN et al, 1995). Thus genome triplication followed by a small number
of insertions/deletions/translocations would provide the simplest explanation for the present
structure of the Brassica diploid genome.
In this study, the overall picture is one of conservation of gene content and gene order
between the genomes of Arabidopsis and B. napus. The average length of the conserved blocks
identified between the two species was 14.8 cM in B. napus and 4.8 Mb in Arabidopsis.
However, for at least seven B. napus linkage groups half their mapped length was equivalent to
one conserved region of the Arabidopsis genome. Undoubtedly the Brassica genomes have
undergone restructuring during their evolution from a common ancestor of Arabidopsis, but this
has not prevented the maintenance of large stretches of similarity, in some cases equivalent to 9
Mb of contiguous Arabidopsis genomic sequence. In a number of instances the comparative
mapping provisionally suggests correspondence of centromere positions between the two
Arabidopsis/Brassica napus comparative map
Parkin et al.. 23
species. The large conserved regions found across the different genomes, punctuated by
numerous smaller blocks of similarity suggest there are preferential regions for chromosome
breakage and subsequent rearrangements.
The publication of the genome sequence of Arabidopsis has opened up many avenues of
research with the expectation that these endeavours would have applications in the study of the
more complex genomes of crop plants (ARABIDOPSIS GENOME INITIATIVE, 2000). The
complete sequence allowed the resolution of the exact physical positions for some 30,000 genes,
50% of which have no known function, and any of which could hold the key to understanding a
number of important agronomic traits. The comparative map suggests that the model genome of
Arabidopsis can be widely exploited to infer the genetic basis of traits in its economically
valuable Brassica crop relatives. In the identified conserved regions, the Arabidopsis genomic
sequence should be an excellent resource for identifying useful markers, targeting the genic
regions, since they show on average 86% sequence identity. Accurately mapping the genes
controlling target phenotypes in large segregating Brassica populations should allow candidate
genes to be inferred from the Arabidopsis sequence. However, due to the duplicated nature of
the Brassica genomes it will be difficult to predict whether any particular Arabidopsis gene will
have been maintained in all the duplicate copies. Comparative genomic sequencing in other plant
species suggest that there will have almost certainly been numerous rearrangements at the level
of microsynteny (BENNETZEN and RAMAKRISHNA, 2002). Limited physical mapping in B.
oleracea only identified one potential inversion and one gene in a non-syntenic position;
however, there was obvious interspersed gene loss from the different triplicated regions
(O'NEILL and BANCROFT, 2000). In addition, recent physical mapping in the B. napus
genome uncovered a similarly small number of disruptions in the microsynteny but evidence of
Arabidopsis/Brassica napus comparative map
Parkin et al.. 24
changes in gene content between the homologous Brassica segments compared to the
homologous Arabidopsis regions (RANA et al., 2004). Genomic sequence data of such regions
from Brassica species will allow the extent to which the duplicate copies have been conserved to
be determined, provide insights into the mechanism underlying the rearrangements
differentiating the different copies and allow an estimate of the relative age of the different
duplication events.
This research was funded by the Saskatchewan Agri-Food Innovation Fund. We would like to thank Cambridge
Plant Breeders, Twyfords and Advanta who supported the development of the Brassica RFLP probes (pN, pO, pR)
and the construction of the genetic linkage maps of B. napus described in Parkin et al. (1995) and Sharpe et al
(1995). We would like to thank Christopher Lewis from AAFC Saskatoon Research Centre, who assisted with the
Blast analysis and provided Perl scripts for handling the data. We would also like to thank Drs Stephen Robinson
and Steve Barnes for critical reading of the manuscript.
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Arabidopsis/Brassica napus comparative map
Parkin et al.. 30
TABLE 1: Number of loci originating from each Arabidopsis chromosome, based on sequence
homology, for each B. napus linkage group. ND: Not determined.
C1 C2 C3 C4 C5 ND Total
N1 4 5 14 29 2 6 60
N11 3 6 13 27 7 7 63
N2 14 3 3 4 34 9 67
N12 12 4 4 7 41 2 70
N3 9 19 17 24 36 2 107
N13 19 16 25 17 42 11 130
N4 6 14 6 7 7 2 42
N14 13 33 10 6 13 6 81
N5 13 13 16 1 5 5 53
N15 36 3 16 2 7 4 68
N6 29 4 3 5 21 1 63
N17 17 11 9 23 18 4 82
N7 32 9 7 3 3 1 55
N16 17 0 3 0 3 1 24
N8 20 1 1 17 4 3 46
N18 31 7 12 7 8 7 72
N9 27 10 9 12 17 1 76
N19 10 4 5 8 57 7 91
N10 14 2 3 2 40 6 67
Total (%) 326 (26) 164 (13) 176 (13) 201 (16) 365 (30) 85 1317
Expecteda
313 209 240 187 281
Arabidopsis/Brassica napus comparative map
Parkin et al.. 31
a. Expected number of loci to originate from each Arabidopsis chromosome based on random
distribution of loci across five chromosomes with approximate sizes: C1 ­ 30 Mb; C2 ­ 20 Mb
(not including the NOR region); C3 ­ 23 Mb; C4 ­ 18 Mb (not including the NOR region) and C5
­ 27 Mb.
Arabidopsis/Brassica napus comparative map
Parkin et al.. 32
TABLE 2: Description of each conserved block found in Arabidopsis (refer to Figures 1 and 2).
Conserved
Blocka
No. of
times
replicated
No. of
comparative
markers in
Arabidopsis
(non-syntenous)b
No. of
comparative
loci in
B. napusc
Total cM
coverage in B.
napus
Length of
conserved
block (Mb) in
Arabidopsisd
C1A 7 31 (1) 88 192.1 6.68
C1B 7 22 (2) 54 64.7 5.32
C1C 7 14 (1) 28 38.1 4.12
C1D 4 10 (1) 18 24.1 2.49
C1E 4 23 (2) 42 106.6 6.07
C2A 5 12 (2) 19 42.1 8.71*
C2B 6 11 (1) 24 34.15 3.42
C2C 6 31 (3) 65 186 6.35
C3A 6 31 (1) 88 244.6 9.27
C3Be
5-8 7 13 24.75 1.66
C3Ce
1-4 6 8 4.35 3.07
C3D 6 18 (1) 34 36.85 4.7
C4A 6 11 31 25.65 7.09*
C4B' 6 8 18 5.85 1.45
C4B 6 35 (2) 106 244.85 8.96
C5A 6 44 (3) 142 245.7 7.55
C5B 6 7 25 55 1.98
C5C 4 7 (2) 11 27.55 3.54
C5D 6 16 (1) 26 45.05 2.42
Arabidopsis/Brassica napus comparative map
Parkin et al.. 33
C5E 6 18 (3) 52 45.35 4.32
C5F 5 6 (1) 14 13.15 1.99
Totals
(%)
115 (121) 368 (27) 906 1706.55
(86.7%)
101.16
(85.3%)
a. Conserved blocks are indicated in Figures 1 and 2, those blocks that are present in at least three
copies in each of the diploid Brassica genomes are indicated in bold text.
b. Number of comparative loci originating from the conserved block in Arabidopsis, that are
mapped in a conserved region within the A and/or C genomes of B. napus. Loci within the
conserved block that have not been mapped to a syntenous position in B. napus are indicated in
parentheses.
c. Total number of mapped loci within B. napus which originate from the conserved block and are
found in a syntenous position.
d. Physical length of the designated conserved block in Arabidopsis as shown in Figure 2. The
complete block may not be represented in each of the duplicate copies. * indicates blocks which
include centromeric regions in Arabidopsis.
e. Limited marker data in the region flanking the centromere on Arabidopsis chromosome three
makes it difficult to accurately identify these regions within the B. napus genome
Arabidopsis/Brassica napus comparative map
Parkin et al.. 34
FIGURE LEGENDS
FIGURE 1: Genetic linkage map of Brassica napus. Linkage groups are arranged according to
the regions of primary homology between the A (N1-N10) and C (N11-N19) genomes (Parkin et
al., 2003), with cM distances indicated to the left of each group. Each genetic locus is coloured
according to the presumed Arabidopsis homologue: light blue - chromosome 1; orange -
chromosome 2; dark blue - chromosome 3; green - chromosome 4 and red - chromosome 5. Loci
in italics were found within conserved blocks based on secondary or tertiary hits within the
Arabidopsis genome. Loci duplicated within a B. napus linkage group are indicated by vertical
lines to the right of the group. Identified genome blocks showing conservation of marker content
and marker order between the Arabidopsis and B. napus genomes are shown to the left of each
linkage group. Each block is coloured and labelled according to the identified homologous
region in Arabidopsis (see Figure 2). Inversions identified in Brassica relative to Arabidopsis
are indicated by arrows. Regions of the B. napus genome which have been tentatively aligned
with Arabidopsis centromeric regions are indicated by hashed blocks.
FIGURE 2: A representation of the Arabidopsis genome based on the primary location of each
sequenced B. napus RFLP marker on the Arabidopsis pseudochromosomes (Mb distances are
indicated to the right of the chromosomes). Duplicate marker locations are indicated in
parentheses. Blocks of markers found to be genetically linked in B. napus are indicated by
shading and capital letters (A-F). In the majority of cases C4B is conserved as a complete block,
but in two instances, on N4 and N14, a small section of the block was observed and is
represented by C4B'.
Arabidopsis/Brassica napus comparative map
Parkin et al.. 35
FIGURE 3: Distribution of the physical distance in Arabidopsis compared to the genetic
distance in B. napus for each pair of linked comparative markers found with the conserved
blocks.
FIGURE 4: Alignment of segment of B. napus linkage group N19 with both Arabidopsis
chromosome 1 and chromosome 5, highlighting the difficulty in identifying the most related
Arabidopsis region where there are ancient duplications in the model genome.
IB12e pW157a
CA36e
0.0
mi431b4.5
pW239a6.7
pW225c8.4
CA53a11.7
pW145e IC06c13.4
CA112c15.4
pN206a pO52X3
mi330d ID11a
es2659a pN107a
es1153c pW105b
23.5
CA142c26.8
pN67a pW179a
pC2a28.5
pO17b31.0
pR36b IG12a
fca1 IC01a33.5
pN97b35.2
pO29c pN152a
CA138V1 T14233c
38.5
es3665a pN173a
pW203c
es2298a
IA04h mi138j
T45996d
43.4
pW108a es4671g
pR114a CA119a45.5
pW136f47.6
pN148a49.7
IF08d51.8
IH08f53.5
IA02a56.8
IC01b60.1
pW201d63.9
T44979a CA144a
pO12e
77.1
es1847c pW136b
pW172a85.5
pN13b88.8
mi74a pR85a92.1
IE05i93.8
N1
IB12f0.0
pW157b CA36a
pN186c
3.4
CA100b pW239b
CA53b pW145a
8.5
pO173E111.0
pO43E1 IC06d
CA87V3
13.5
pN206b_72 pN52e19.9
pO52b21.0
IF08e22.0
mi330c22.8
ID11b es2659c23.6
pN107c pW105E1
N96493e28.6
CA142e33.6
pW179c35.3
pC2b37.8
pO17a pR36a
IG12b40.3
IF05RI345.3
IC01c pN97d
pN152E1 pO118E1
pN47E3 pW120b
pW101d
48.6
CA138V2 T14233d50.8
mi137b53.0
pN173d_72 pO70e
pR36f pN53f
pN129a_72
55.2
pO168E1 mi138f
pN180n pW108c
CA73e CA119b
56.9
IA02e IC01RI7
N65549b70.6
pW201c81.3
T44979c CA144b86.1
pN121E290.9
CA120j93.1
pO12c97.6
pW136c99.3
pW172b pN13c101.0
pR85b104.9
N11 N2
B B
A
A
A
E
E
B
D
B
Figure 1_Parkin et al.
F
pO147b0.0
CA120e3.8
CA149f9.4
mi97a15.0
CA71c17.7
mi174c pN121a20.4
pR64a22.1
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CA4a pN102d
23.8
IE05j25.5
pN91g pN180m
IC04d IG01a
IB06a
32.2
IH06b37.3
mi138h pW102b
CA39b pR29a
pR30a_72 IG04b
IA09i pN63h
pR115a
47.5
IG07c pO85c51.5
IC10e pW154a
CA117b
57.5
pW161a pW150d65.9
pO85g69.2
pO86a_72 CA76f
pO3b IA04a
pW207a
70.9
ID02b CA37d
pW180b
72.6
pR4b pN181a
IH02a Z17798a
74.3
T43968h CA111c
pW194e IC01d
ATTS2094e
77.6
es1732b79.3
IB01a81.0
pR72a82.7
crrp5a89.4
mi271c92.6
IB06RI793.0
mi125b pW176b
pO120a96.1
CA72c CA69b
mi219b101.1
pO119a104.4
pW191e109.6At C1
At C2
At C3
At C4
At C5
N12 N3 N13
A
A
A
E
E
E
E
B
B
D
C
B
A
A
B
A
C
B
A
B
B
?
C
Figure 1_Parkin et al.
F
B
CA120f pW116E10.0
pW109a9.2
CA71d18.3
pN13E2 pN121q30.3
CA4c pN102e
IE05k COd
pN91e CA40c
pN180d pN174E2
35.3
pO136E1 IC04a40.2
IG01b IB06e
IH06c R89998c
pR86E1
41.9
pW102g mi90c
CA39e IA04RV943.6
IA10h pR29b
IG04c45.3
pN63b45.9
pR115c46.5
pO17E147.0
H36913a48.7
IG07d pR34E2
pO85a
50.4
pW154b IG02c
IC10fT41629b
52.1
CA117a pW161b54.6
pN105e IA04b
pW207b
57.0
ID02c CA37c
pW180c pR4a
IH02b es4424b
pW148E2 pW177E3
pW218a IB08b
pW135E2 Z17798c
60.3
pO153E263.6
IB01RI3 pO125E2
pR72b pO59f
66.9
pO5b_7270.2
pR20E1 pW167E1
IB06B6 pO120c
71.9
CA72V5d pW141E173.6
pO119e84.2
pW191b91.2
CA120a0.0
pN3d3.9
H36821d Z33873d
N96493b pW153a
CA71a
8.4
pN151g CA155b
pN121b11.8
pR64g13.4
CA130V115.1
pW153b15.7
CA110c16.3
IE05l pN102c_72
pW189a
16.8
pO160c pN105a18.5
pN180b IB06b
IG01c R89998g
pW152c IA10j
IG04d pW214a
pW144b IA09j
21.8
IC11H2pO155b
pW102c H36913e
CA131b
23.5
pN22a26.8
ID05a34.7
IC12a38.6
CA58f IB01RI4
IA10i pN120d
pW133a_72 IE03a
43.6
ID01B245.3
pC3c47.0
CA2b pN167d
IF05j N95848a
48.7
es4671b CA15b
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55.4
pN167e57.1
pN213g pW148a
CA55c IH02e
ID01i pO79c
pO87c pR85e
58.7
IE05m pW172d60.4
pO12b63.7
es2533a ID05d
es1847a
67.0
Z26226a T44979d
pN102i
68.7
pN215b pW142a_72
pW181b pN148f
pS2d IH08a
70.4
CA73c73.8
pN22d76.3
IG02d IA05a
IF01a pW188a
78.8
T20808e pN154a84.6
pN97c90.4
pO59a pO29d
IC07a92.1
pO52X1 ID11c93.8
pN107d94.9
pW105a96.0
CA142a pN181h97.2
pW179b_72102.2
pC2e105.5
pW144c pR36d110.5
IG12c112.2
CA112b pO43a
pW145f CA53c
pW225d IC09a
T42294b
118.9
IC07b122.9
CA120k pW116E2
pN3e pW200E2
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0.0
pW153c2.3
CA155c ATTS2506d
CA71b5.7
CA30V37.8
pN121s pR64b
CA144g CA130V2
pO111E1 CA110a
pN102E1 pW189c
9.9
pO160d11.6
pN105d CA40d
pN180e IG01d
13.3
IB06RI1 pW111E115.8
R89998a pW152a
IA09f pW214b
pW144a pO155a
18.3
H36913b CA131a
pR34E3 pO98E2
pN22b CA58c
25.0
IB01RI6 pW112c
pN120e pW133E2
pO171E2 IE03b
CA58j
31.7
IF05h33.4
pO85e33.5
mi138g36.1
F20108a40.7
N95848b41.3
pW143E341.9
es4671e pN167c
pN53g N96078a
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42.5
pO79e pN102h
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pW148E1
45.0
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pW172f IE05n
46.7
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pO12a es2533b48.4
SLR1b ID05b50.1
Z26226b51.8
IH08b pW142E1
pW181a pW201b
pN148e IA02b
IA10b
55.1
pN207a pN20E1
pW188b CA73b
IG02e IF01b
56.8
CA157f IA05b58.5
pO10E3 pN154b
pW102E1
61.8
pO142E3 pR116b63.5
IE05a IC10a
pS2a mi438b
71.9
es2298f pO172E1
pR6a pO119g
pN99e pR64d
pO123b IG09a
pW146E1 pN47E2
IG10a IA01b
pO87E1 IA10c
75.2
CA152V2 CA58g
pW115f
83.6
pN96b85.3
CA115a IB12a87.0
pN107X588.7
pW130h pO52E1
CA36c
90.4
CA100c93.7
flower97.1
T46721a107.9
IF05i118.7
pW225E1 CA112d120.4
pO43E1123.7
es4619f Z30800d
pR54a128.7
pR116a133.7
IA10RI70.0
pW205c3.9
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pW130e pN91d
T14233a IF01d
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14.0
pN202c pW239e15.7
CA13a pW122d
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IC07e
22.3
R90150a pN99d25.6
IA04e IC06b27.3
pN167b pN44c
pN151c
32.3
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pW239c38.1
CA111d pN59f38.9
T43968a CA58l42.2
pO98a pN66d43.9
pW139b IC12RV248.9
IB01d52.3
CA58d pR113a
T45845c57.1
pN97g60.3
IF05RI463.5
ID01a65.7
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N4
N14 N5
A
C
C
B
B
C
B
C
D
D
D
B
C
Figure 1_Parkin et al.
pW177E10.0
pN13f1.7
pN97f_72 pN174b
IF05a T45845b11.8
pN194a pR94E2
pC3b16.7
CA12V2b20.9
pW143E225.1
pO147d30.1
pO171a30.4
pN95a30.7
pN120a31.0
ATTS2506b31.3
pN53i31.6
pW137a33.3
IC12c35.0
pR64E438.3
IB08c41.6
T43968f pN64b
pN66b
43.3
pR113e IG04f
CA58b45.0
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pN151b_72 pN44b_72
T46379c pN173b
IB08B4 es1153a
pW108f pW218c
pO145E2 pO106E1
pO9c
51.7
pW120E2 pW136E2
pW205E2 pW188E2
53.4
HS1a pN180i58.4
IH10a pW130a_72
pO87a pN91E1
T14233b pN202a
60.1
IF01c IG02f63.4
pW122c CA137e70.1
pR54d IA10d
IC07c IA04c75.1
pN167a_72 pN44e
pN151d
76.8
CA111b78.5
pN59c T43968b
CA58i pO98b
pN66c pW139a
pW133b_72
80.2
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IB01b88.6
pR113c CA58e
T45845a93.9
pC3d pO126E3
pW143E1 IF05b
102.0
pN13h107.3
es3665c0.0
pN13e3.6
pN174a8.0
IF05c17.0
CA12a pN194b_7222.0
pN99c_7223.7
pO171b_7227.0
pN95b_7228.7
pN120b30.4
pW137b IC12e
mi330b ID05c
33.7
IB08d43.8
T43968e45.5
pN66a47.2
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CA58a APSb
50.5
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es3665b
52.2
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pW217a Z30800c
IB06f
53.9
pO46b54.3
es4619c54.7
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pW115e es4671f
CA73a pR114b55.5
pW114c58.8
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pN53d
62.1
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F20108e66.0
N96307a66.5
IC01e67.1
pN215a73.8
CA144d75.8
pO123c92.8
CA67a es1847f96.1
pN113c pN2d_72
pW172e
99.4
IE05b104.5
C
C
B'
B'
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es2060d pN23E3
pO92E15.0
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pN52a25.3
pO152E1 pN101g
pO105E1 pW224a_72
28.6
pW197E1 Z17993c
CA149c CA42c
IF08a pN123E2
pW123E1
31.9
pW145d36.9
CA25c T22090a
T46145a pN216e
ID08f
41.9
pW164E145.2
pO159b pW138E146.9
CA39c51.1
CA155e pN91E2
pO143a55.3
pO131E157.0
CA42e57.5
es5209a58.1
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IG10c IA01d
CA101e
58.6
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pO136E2 T75662d
es4619b61.9
pR54e65.3
es2298b CA73d
pW114a
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pN148d pO128E173.6
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pW197d N96307b87.7
pN215c pO153E1
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92.2
pN59E2 pN91f97.2
pO123a CA67b102.2
pO12d pN113a
pN2c105.5
es1847d pN113b110.5
pW172c114.7
IE05c121.1
pR85c128.4
N15 N17
A
A
B A
B
C
B
A
B
E
F
D
B
D
Figure 1_Parkin et al.
N6
B
B
pW115b0.0
pW217b pO46a1.7
es4619a6.4
pO9a13.5
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pN199a20.1
pN52b pO152b
pW199a pO105a
pO165e
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pN199b27.7
pN101e pW224b28.5
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CA42a pN123X2
es1230g
31.8
pW145c CA25e
T22090b T46145b
pN216f ID08e
pO159c pO143b_72
45.5
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es5209b53.0
pO119d60.7
pR6b IA09h
IC10c pO9d
pN180o
69.2
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es3092a pW102d70.8
CA72a CA69d72.9
pN101a pO120b79.2
pW167a80.9
pW137c_72 IA05c82.6
Z18443b es1230c84.3
pR43b87.6
IB01c IC01h90.9
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es1732c101.1
IC01f pR3a107.8
pN86a111.1
ID11e112.8
pO112a116.6
IB08e IB12b
pW218d
124.6
pO87E20.0
pO104E1 pW194b
pW186a IE05d1.7
CA87V17.1
es4619g9.8
IA05e pN59d_72
pW162E1 pO79a
CA157c pR36g
11.8
pO142E2 pW108b_72
pR93E115.1
pW197f pO70c
pW162b_72 IG02g16.8
IA01e IG10d
es1230e IG09d
CA76a pO131E2
pO85b
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pR36e pO169E125.2
pN53h26.9
pN184b29.4
pN86b pR3b
pN20E2 pR113d
IC01g
31.9
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pR43a_7241.5
es1230b pO5a
Z18443a IA05d
45.3
pW137e pN216E2
pW167b pO120d
pN64E2
55.4
pN101c CA72f
es4930a57.1
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es1230a pO59c
pW104E1 pW174E1
T41662a
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pO29a pN97e
pO52a
77.4
pO118E379.9
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pN107b84.1
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pN181g86.7
pW179d87.5
pR36c pC2f
pW101c pW120a
IG12g
89.2
CA112a pO43c
pW225a
102.9
IF05e CA36d
CA115b
106.2
IB12c T42294a111.3
B
C
C
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pW186b4.3
CA87V46.3
IA05f8.3
CA157b10.3
pO79b12.3
pW162a_72 pW108d14.0
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IA01H7 IG10e
es1230d IB09b
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pW191f pW180g
pW130d
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pN59g
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CA15a
CA2a
CA16a CA37a
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31.1
pR94a pR60a_72
pO86d_72 pW134a_7236.1
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N7 N8 N18
C
C
B
A
E
B
D
B
B
A
D
Figure 1_Parkin et al.
A
B
B
A
pR54b0.0
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pN168b IB08a
CA22b3.4
pO52e T14233e
T46721b pO29e
mi330a pO113b
mi291c ACYLb
es2659f ID11h
5.1
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pW225b_72 CA100a12.0
IG12f CA36b
pC2c
23.8
IB12d CA115c28.8
pN96a35.5
pR85g38.0
IG10f IA01g40.5
CA76e IG09f42.2
IB09a CA152V343.9
pO143e pO159d50.6
CA25b52.3
ID08c pN216c54.0
pN34a59.0
pO165c IG04a65.7
pW177a CA86b
CA20c pN170b_72
es2298d
73.1
pO123e pO113E1
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pN120E1
0.0
pN53e pW121E1
pR54E4 pN170c
1.7
pN87a pN23c3.4
pN168a IB08g8.4
pN59b10.1
pN184c pO113a_72
pO29b CA22d
11.8
IG04k mi291a13.5
pO52d pN129E221.9
ID11g23.6
IG12e pR36E1
pC2d
25.3
pO142E130.3
T13648c35.1
CA58h pN216a
pO165d39.9
CA25a pO159a
pR86E2 pW138E2
43.7
pW207E345.4
CA76d47.4
pO143d49.5
IB09f53.7
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CA101d pO131a
IF08c
57.1
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IA09e pW130b
T45996b pW104E262.1
CA103a63.8
pW188c67.1
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pR97a H36320d
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68.8
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pO143c79.8
ID08b82.1
pN216b_72 CA58k
pW123E282.2
pN123b IF08g86.2
pN34E192.2
pO152E2 pO92E2
pN173E1 pN23E193.9
pN21E197.2
pW120E40.0
pR54E1 pO9b4.2
pN180E44.8
pR64E26.0
pW221E18.1
pW103E19.5
pW228E111.3
pO10e13.1
pR94b15.5
pO128E2 pO104E317.9
pW197E219.7
pW134E122.7
pO104E235.8
pO10E263.2
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pW217c
pO46c
pW115a
pW130f
pO3e
C
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pW150a
pR60b pO86b
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A
B
D
A
B
D
B
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A
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A
A
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B
A
D
Figure 1_Parkin et al.
D
A
ID01g0.0
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pR116c pN52f
pN213b
10.3
pW157e12.0
pO125E115.3
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pW167E218.7
pN101h23.7
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pO106E349.2
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pO145E1 T20808d
pN173E2 pW122b
pW194d pW180h
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52.6
pW203b56.0
pW233a pW135E1
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67.4
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pN181E1 pR34E1
IG07b76.3
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H36913c77.5
pO127E178.0
pO168E2 pR115d79.7
pO155c pW240b
mi138b pW102i
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pW212a
88.1
pO119i91.4
mi219a mi322b
pN105b pN91b
pO160b pW189b
pW106E1 pW155E1
pW195a IE05g
COb pN102f
CA4d
98.2
CA40a CA110b101.5
ATTS2524a103.2
pO111E2106.5
CA144h pR64E1111.5
pO7b pO118b116.5
ATTS2506f pN47E4119.8
ID05f123.2
N96493d Z33873b
H36821c pW239E1
pN3c pW200a
124.9
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pW109e132.7
CA120c139.1
es5147b147.1
ID01b pW101a_720.0
es2298c2.8
R30624b pN170a11.7
CA9a19.8
T21447a20.6
mi291b21.2
pN21b IG12d
es2060r pN53b_72
pO92b pR34b
pN23f CA20a
CA22c ess40a
IB08f
21.8
IG07a Z17993a23.5
mi138a pN199c
pR115b pO155d
pW240a IG04i
pW102a IA09c
28.5
pW152b29.0
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IA10f30.1
CA39a38.5
CA30b39.3
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IG01e IC04b
mi219c mi322a
mi438a pN180h
40.2
CA40b41.0
pN105c pN91a
pO160a_72 pW189d
41.9
IE05f COa48.6
pN102a50.3
CA110d54.8
IF05fATTS2524b
CA144f57.0
pO7a pO118a61.8
CA155d CA71e64.7
N96493a Z33873a
H36821b pN3f
pW200b
75.5
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pW109d82.3
pO147e es5147d84.0
D
pW157d0.0
pW109f2.9
ID01c15.9
pN52g24.0
CA55b24.9
pN213e pR64f
pR116e pW157c25.7
CA72e31.4
es4930c CA69c34.2
IC10b T45996f36.0
IB12X852.6
pW122a61.7
pN173c pW203a
pO150a pW180a
R30624d
65.0
pW233b66.7
T75662c pN184a
pR30a CA142b
pR36h pN181b_72
68.4
IH02c ID11d70.1
CA129a71.8
es4671a es4424c
T04362a pW235a
73.5
ACYLd75.2
CA101b IA01c
IG10b pW146a
80.2
IG09b R30025a
pN105f
81.9
pO59e pW191d_7285.2
IDO5h pN52c_7286.9
pW130c CA103b
IA09g90.2
ID01d91.9
pW205b93.6
pW101b_72 pR97b
IA10e IF05d95.3
es5147a103.7
IA04d IC06a
CA16c CA137d
es1230f
106.4
IC07d CA86a108.2
ID08g110.0
IF08f113.7
pN216d pN123X3
pN34c
115.5
pO165a117.2
pO152a IG04RV8118.9
pW239g120.5
pN23b es2060a122.2
pN21e_72127.2
F
A
ID01
pW177(2)
pN170
CA20 pN21
es2060
pN23 pO92
T04135
IG04(2)
pO152 pW199 pO105
pO165
pO145 pN199
pW224
pN34
Z17993
CA42(2) pN123
pW123
pW145(2)
CA25 ID08T22090 T46145 pN216
pW164
pO159
pW138
pO143
pO131
CA42
pO85
es5209
CA76(2) IG09
es1230
pW146
pN47
IG10 IA01
CA101
N95848
pO87
pW162 IA10 IE03 pN96
ACYL
pO136
pW235 T04362N65549 es4424(2)
ess40
CA22
IB08
pN95
pN168
pW217
Z30800
IB06 pO46
es4619
pR54
T13648 pW115
pW221
pW228
T20808
pN173
pW122
pW203 pO150
pO145(2)
H36320
T42294
CA137 pO106
pO9
CA117 pN2 pW161
T41629
pW150
pO86 pW134
IC10(4)
IG10(2) IA01(2)
CA76 pR60
pO3
IA04
pO104 H77224
pW207
pR94
IH08
CA149
ID07 CA37 ID02
pO10
pW180
5
10
15
20
25
30
At C1
pO142
es1732
CA129
pO79
pW162(4)
pN154
pO153
pN59(2)
CA157
IF05
pW186 CA87
pN52
pW194
CA86
IC07
CA137(2) R90150
IC06
pN167 F20108
CA15
pN44_pN151 T46379
pO59 CA111
pO98
IC11
pN67 pN66
pR64(2)
pN22
IE03(2) IA10(3)
pW139
ID05(3)
IC12
IB01(3) pW112
pN120 pW133
pO170_O171
CA2
HS1(BLASTX)
pR113
T45845
pO85(2)
pN194 CA9
pC3
CA12
pR97
ID01(4) IF08
pW143 pN174
pN97(2)
pN13
CA16(2) es3665
5
10
15
At C2
pR85 IE05(2)
pW155
pW172
pN113 pR85(3)
CA67
pO12
IE05(3)
es2533
CA120
pO123
ID05(2)
CA144 Z26226T44979
pO153(2) pN215
pW142
pW181 pW201
es1847 N96307
IA02
pO128
pN148
IH08(2)
CA119
pR114
CA73
es4671
pW108
IG02(2)
IA05(2)
pR72
IB01
pO125 pR43
pO5
es1230(3)
pN207
pN53
IC10(3)
pR6
T45966 pW191(2)
R30025
pN59
pW104
pW174
ID05
pN99
T20671
IA09(4) pW130
CA103
pW188
IH10 CA2(2)
HS1(2:BLASTX)
pW205
pW101_pW120
ID01(5)
CA16
5
10
15
20
At C3
Figure 2_ Parkin et al
A
B
C
D
E
A
B
C
A
B
C
D
IC10(2)
es2298(3)
pO172
es5147
pO147
CA120
pW109 pW116
CA54
pW200 pN3
H36821 Z33873
N97067
pW153(2)
CA71 CA155
ATTS2506
CA149(2)
pO118
pO7
T75662
pN121
pR64 CA144(2)
CA130
pO111 pW153
ATTS2524CA110
CA4
pN102
IE05
CONSTANS
pW155(2) pW189
pO160
pN91 pN105
CA40 N96493
pW212
pN180
IG01 IB06
IH06
CA30
R89998
pW152
pR86
IA09(3)
CA69
es4930
CA72
pN64
pW167
pO120
pN101
pO113
pN202
pW122(2)
IA05
Z18443(2) R30624
T20808
CA137
pW103
pW218 IB12 IB08(2) pW135
pW233
T43968
pO112
ID11(2) Z18443
pO169 pN184 ATTS2094 pN86
IC01(2) pR3
pN20
pW176
pR20
pW154
pR34
CA131
IG07
H36913
pO127
pO17(2)
pO168
pR115
pN63 pO155 IC04
pW240
pW144
pW214
pW102(2) IA09
IG04
pR29
pW141
IC10
pO119
Z17798
es3092
pW102
T45966
pW191
5
10
15
20
25
At C5
pR116
pR4
ID01(2)
pN213
pW148 pW177
CA55
es4424
pW235(2)
IH02
pN181
pR54(2)
T14233
IG02 IF01
es4671(2)
IB06(3)
CA138
pN152
pO29
FCA
pN97
T41662
IC01
pO52
ID11
pN206 es2659
pN107
T46721
es1153
pW105
CA142
pN181(2)
pW130(2)
pW179
pC2
pO17
pR36 IG12
CA112
pO43
pO173
pW145
CA13_CA53
pW225
CA100
pW157
IC09
CA36
es2298
pW157(3)
IB09
CA115
5
10
15
At C4
Figure 2_ Parkin et al
A
B
A
B
C
E
F
B'
pW239_W240
D
Arabidopsis/Brassica napus comparative map
Parkin et al..
FIGURE 3.
0
50
100
150
200
250
300
100000200000300000400000500000600000700000800000900000100000020000003000000
>3000000
Physical distance (bp) in Arabidopsis equivalent to
1cM in B. napus
Numberofintervals
T13648
pW115
pW221
T20808
pN173
pW122
pW203 pO150
pO145 pN199
H36320
pW224
CA42 CA137
pO106
pO9
20
D
C
CA13V2 CA87V243.4
pO106E349.2
CA137b50.9
pO145E1 T20808d
pN173E2 pW122b
pW194d pW180h
CA149e
52.6
pW203b56.0
pW233a pW135E1
T43968c
67.4
IA10g69.6
D
pO120
pN101
IB01
pO113
pN202
IA05
Z18443 R30624 pO5
T20808
CA137 pO106
pW103
pW218 IB12 IB08 pW135
pW233
T43968
pO112
ID11 Z18443
pN184 ATTS2094 pN86
IC01 pR3
pN20
pW176
15
C
At C1 At C5N19
Figure 4_Parkin et al