McClean et al.

BMC Genomics 2010, 11:184

http://www.biomedcentral.com/1471-2164/11/184

RESEARCH ARTICLE Open Access

Synteny mapping between common bean and

soybean reveals extensive blocks of shared loci
Phillip E McClean1,2*, Sujan Mamidi1, Melody McConnell1, Shireen Chikara1, Rian Lee1,2

Abstract
Background: Understanding syntentic relationship between two species is critical to assessing the potential for
comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most
important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively.
Determining the syntentic relationship between these two species will allow researchers to leverage not only
genomic resources but also genetic data for important agronomic traits to improve both of these species.
Results: Genetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01
pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a
result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common
bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to
all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on
soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST
singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as
references points.
Conclusion: The collected evidence from this mapping strongly supports the duplicate history of soybean. It
further provides evidence that the soybean genome was fractionated and reassembled at some point following
the duplication event. These well mapped syntentic relationships between common bean and soybean will enable
researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both
species.

Background that aid the cloning of a gene in one species based on

Comparative genetics and genomics leverages knowledge
from companion species and attempts to define impor-
tant evolutionary relationships. Important to under-
standing these relationships is the physical and genetic
synteny between any two species. Physical synteny can
be used to explain the cytogenetic events that a genome
has undergone as it evolved along a lineage into its cur-
rent structural form. Associated with these genomic
events is the evolutionary repositioning of genes respon-
sible for phenotypes shared between the two species.
This repositioning places genes in different genomic
contexts that could alter the degree and timing of their
phenotypic effects. Understanding the overall position-
ing of genes in two related species can suggest strategies
* Correspondence: phillip.mcclean@ndsu.edu
1
Genomics and Bioinformatics Program, North Dakota State University, Fargo,
ND 58105, USA
its position in a reference species.
Synteny has been studied quite extensively in plants,
beginning with the early macro comparisons using RFLP
markers. Although these analyses used a limited number
of markers, they revealed major syntenic themes that
have informed much of the research in the field. Closely
related species, such as tomato and potato [1,2], have
highly conserved marker order that is only disturbed by
clearly defined events such as paracentric inversions. At
greater evolutionary distances, as evidenced by tomato
and pepper [3], inter- and intra-chromosomal transloca-
tions have redistributed loci such that only short synten-
tic blocks are observed while the chromosome number
remains unchanged. Finally, a one-to-two mapping of
loci, as seen with sorghum and maize [4], revealed the
effects of polyploidy on synteny. These types of studies,
involving multiple species and using collections of

© 2010 McClean et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative
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reproduction in any medium, provided the original work is properly cited.
McClean et al. BMC Genomics 2010, 11:184
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shared probes, have revealed major evolutionary rela-
tionships within lineages such as the grasses [5] and
legumes [6]. For the grasses, using 30 segments of the
rice genome as a reference, the genomes of ten other
species could be reconstructed [5].
More recently, Brassicaceae evolution was studied in
depth with a high density set of markers. Using the gen-
ome of the amphidiploid B. napus as a reference, the
duplication history of its two parents, B. rapa and B.
oleracea, revealed earlier rounds of duplication shared
between these two diploid genomes and suggested that
a progenitor with fewer chromosomes was responsible
for the lineage [7]. Finally, a comparison of a dense
genetic map of B. napus, consisting of > 1000 loci
orthologous to Arabidopsis genes, and the genomic
sequence of Arabidopsis, revealed that 90% of the
B. napus genome could be reconstructed from 21 ortho-
logous blocks of Arabidopsis genome while a number of
the Arabidopsis segments were duplicated in the
B. napus genome [8].
With the wide-spread availability of whole genome,
BAC, and EST sequencing, and new approaches to high
density mapping, further aspects of comparative evolu-
tion were revealed. Early comparisons of the genomic
sequence data from Arabidopsis and tomato, two species
whose divergent evolution began 94 MYA at the time of
the Asterid/Rosid divergence [9], revealed a pattern of
segmental duplication followed by local gene loss [10].
A similar pattern, but not to the same degree, was
4.9
Mya
5.6
Mya
18.0
Mya
23.0
Mya
25.5
Mya
Figure 1 Phylogeny of economically important Phaseoleae legumes. The phylogeny is condensed from that presented in Stefanovic et al.
(2009). The nodal dates are the minimum date of the range based on 32.1 million years ago (MYA) date of “A” node representing the
divergence of the Phaseoleae legumes from Apios americana. The haploid chromosome number and C-value [in piocgrams (pg)] are from the
Plant C-Value Database http://data.kew.org/cvalues/; verified May 5, 2009).
Page 2 of 10
observed between Arabidopsis and B. oleracea, two spe-
cies that diverged ~20 MYA [11]. The length of the
shared block appears to depend upon the divergence
time. The rice/wheat synteny appears to vary, with some
regions showing extensive microcolinearity [12,13] while
other regions exhibit a history of cytological events that
has reduced the extent of local syntenty [14,15]. Maize
and sorghum are recently related evolutionarily through
a common ancestor that gave rise to sorghum and the
two progeneitors of maize [16]. The species diverged
only 12 MYA [17], yet the synteny between sorghum
and maize appears to be less extensive than that
between sorghum and rice that diverged ~40 MYA
[18,19].
Here we investigate the syntenic relationship between
two important legumes, common bean (Phaseolus vul-
garis L.) and soybean (Glycine max). These two species
are the two most important economically important
legumes, soybean for its many human and animal
usages, and common bean as an important nutritional
crop for many economically poorer countries [20].
These two legume species are members of the Phaseo-
leae (Figure 1), a clade within the economically impor-
tant Papilionoideae legumes. This clade diverged from
the IRLC clade, the other economically important Papi-
lionoideae clade, 54.3 MYA [21,22].
Common bean and soybean diverged 19 MYA [21,22].
Determining those genomic events that followed the
divergence is important as investigators attempt to
Phaseolus vulgaris (n=11; 0.60 pg)
Vigna unguiculata (n=11; 0.60 pg)
Dolichos lablab (n=11; 0.38 pg)
Glycine max (n=20; 1.13 pg)
Erythrina sousae (n=21; 1.55 pg)
Cajunus cajan (n=11; 0.88 pg)
McClean et al. BMC Genomics 2010, 11:184
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leverage the recently released soybean genome sequence
[23] as a tool for research within the clade. RFLP map-
ping [24] and EST Ks analysis [25] provide strong evi-
dence that soybean under went a major duplication
event dated at 11 MYA [[25], Mamidi S, Lee RK, Terp-
strea J, Lavin M, Schlueter JA, Shoemaker RC, McClean
PE: Whole genome duplications in the evolutionary his-
tory of legumes, submitted]. Most likely this was an
autopolyploid event [22,26]. By contrast, molecular mar-
ker data [27] show that common bean is a diploid while
EST Ks analysis suggests that its genome has only
undergone localized segmental duplications. Given their
close relationship within the Phaseoleae, common bean
is considered a diploid model for soybean [20]. Low-
density RFLP mapping [28] found that the two species
share a high degree of sequence homology but synteny
is only found only over shorts blocks of the genomes.
This is in contrast to the long stretches of synteny
shared between common bean and mung bean (Vigna
radiate), another member of the Phaseoleae clade.
These two species diverged between 4.9 and 8.0 MYA
[21,22].
To better understand the structural relationships
between the common bean and soybean genome, we
compared the organization of an extensive gene-based
map of common bean with the complete sequence of
the soybean genome. We discovered overwhelming evi-
dence of a one-to-two relationship between common
bean and soybean sequences. In addition, we were able
to trace many of the gene rich regions of all soybean
chromosomes back to specific regions of the common
bean genetic map. Evidence is also provided that, rela-
tive to common bean, soybean is segmentally rear-
ranged. Using this genetic/physical synteny, we have
also been able to electronically map an additional 20,000
common bean EST contigs and singletons relative to
soybean. This result is a major first step in understand-
ing the evolution of the soybean genome relative to a
diploid species within the Phaseoleae clade while provid-
ing a framework for the comparative genetics and geno-
mics of these two species.
Results and Discussion
A few limited studies have investigated the relationship
between the common bean and soybean genomes. Bou-
tin et al. [28] utilized shared RFLP markers and discov-
ered a number of shared common bean/soybean
syntentic markers blocks. In addition, individual markers
showed a more complex pattern of syntenty between the
two species suggesting a pattern of fragmentation in the
evolutionary history of soybean relative to common
bean. Subsequently, Lee et al. [29] built upon these
results and were the first to show a clear one-to-two
relationship between the common bean and soybean
Page 3 of 10
genomes. Although these results are compelling, they
only provided a limited description of the genomic rela-
tionships between these two species. With a richer array
of sequenced-based resources, including an increasing
number of ESTs in common bean and an extensive
draft sequence of the soybean genome, it is now possible
to investigate the syntentic relationships between these
two species at a greater depth.
Common bean and soybean orthologous loci
Our first analysis of common bean and soybean syn-
teny was based on 300 gene-based loci [McConnell M,
Chikara S, Mamidi S, Rossi M, Lee R, McClean PE.
A gene-based linkage map of common bean (Phaseolus
vulgaris), submitted.] that were genetically mapped
using the community-wide P. vulgaris BAT93 × Jalo
EEP558 mapping population and 59 gene-containing
RFLP probes [30,31]. These loci were compared to the
first public release of the soybean genome, consisting
of 20 pseudochromosomes, using the blastn algorithm.
We first limited the hits to those with an E-value < 1
× 10 -10 . This decision was motivated by our decision
to compare the two genomes by uncovering those soy-
bean loci with some degree of orthology to the com-
mon bean query sequences. A total of 1065 hits were
detected that met this criterion, and the median E-
value for these hits was 2.0 × 10-61. These hits were to
loci on all 20 soybean pseudochromosomes.
Since another goal of this analysis was to determine
the genomic relationships between common bean and
soybean genomes, we next limited the analysis to the
best two soybean hits for each common bean sequence.
This decision was based on the assumption that soybean
underwent a whole genome duplication event since it
divergence from common bean, an assumption sup-
ported by a number of lines of evidence [24,25]. There-
fore, absent a major reduction in newly duplicated
soybean genes, there should be a one-to-two locus cor-
respondence between common bean and soybean.
Under this criterion, a total of 720 hits were observed,
and the median E-value was 3.5 × 10-91. Again, hits to
loci on all 20 pseudochromosomes were observed.
A common bean centric display of the synteny is found
in Figure 2.
Conserved common bean and soybean genomic blocks
A conserved syntenic block was defined as one that
shared three loci between common bean and soybean
and covered a minimum of 4 cM of the common bean
genetic map. A total of 55 syntenic blocks were
observed between the two species. On average, each
block consisted of 7 loci. From a common bean genetic
perspective, the mean size of each syntenic block was
32 cM (with a median of 29 cM). 75% of the blocks
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Pv1 Pv2 Pv3 Pv4 Pv5

0 D1080
6.0 0 g1795 41.0 52.8 0 g1686 4.2 0 DROI16a 0 g2467 0.7 12 g564
0 DFR 6 D1619 15 DDiap_1
13 g797 7 DROF10b 11.6 16 50.1

11
g1188

1
7 g1645 27 D1151

15 12
8
16 NRAMP 32 g2274 5.6 14 g1375 19 DROD20b 47.1
13 g2145 14.1 24 g2596
14

29 g511 9.2 39 g2108 39.0

17
20 g1092 51.3 2.8 19 g2303 36.1 32 g2410
47 g1830 40 g1968 33.0

2
30 g2266 42 g34

19
57 g1805 27 Bng71
45 g1410 45 D1595 65 D1377 43 g174
44 g1086 3.2

13
14.3 73 g964 36 D1298 45 D1301

13
24.9 51 g822 54.7 64 g1515 0.8
54 g934 27.5 69 80 g1520 63 g483 47 g1333

15
ChS 50 g1689
83 DROF10a

11
58 D1327 76 DROS3c 86 g417,g1656 2.9 72 DRbcs 55 g2308

1
65 g2647 36.7 81 DROG19b 61 D1251
87 g1801 7.8 77 g2685 7.3 43.7 66 g1883 0.7
86 g2490 53.7 93 g1556 1.5 90 Z_AM10S 69 g1664
37.3 96 g2476 79 G_AP3 72
102 g1737 33.5 95 g457 7.7 Bng162
101 g125 79 G_U14S 79 DROC18a
108 g1771 102 g1148 42.1 104 g1925
115 g849

2
79 G_AP7
5
110 g1959 106 g2371

17
123 g1784 41.8
113 g724 107 DROF7c 84 g128
19

32.3 126 g2113 4.7

117 g1176 108 g117
3

2.1 119 g2409 104 D1325

119 g1954 133 g893 125 g686

5
136 D0166 123 Bng224
132 g2162 36.6 10.7 4.0 129 g1808
143 g1247
5

8
147 g1952 148 g1132 143 g2341
37.0 11.1 150 g665 149 g968
155 g2504 151 D1287 18.7
4.4 156 g2213
44.7 166 g1404 47.2 153 D1367

2
189 Bng171a 41.2 161 g1194 1.2 164 g2558,g2218 27.6

16
199 Bng122 2.6 164 g2577 5.1 171 g664
166 g680 27.8
36.3 202 g1224 g774 8
5

203 g499 169170 g693

206 gCV54201 173 g2427
207 TGA1.1 39.9 181 g2127 5.0
18
11

210 g1367 198 S2

214 g2562 208 DROS3b
218 g683
225 g523
39.0 232 g2132 0.2

Pv6 Pv7 Pv8 Pv9

0 DROJ9c 0 g503 0 g1588 62.2 4.6 0 D1831
8.1 6 g544
41.4 14 g2538 50.4 10 CHI_INT3 15 g2543 9 D1096_2
2

4
8.4 20 g2311 12 g791
23 g2553 14.6 21 g2298 34.2 22 g89 2.4 13 IRT3 3.4
27 DROF1b 23.5 17 g2178
31 g2551 24 g2393 5.6 24 g1884
8

30 DBng199 29 g2498

6
4
33 D0096
8

34 AGT1 33 g1615 22.5 29 g1879 32 g993

18

10

37 g1639 36 g501 36 g1119 7.3 34 g1107 6.8

40 gTC1436 40 g129 42.6 37 WagG_W17 38 g732
20

43 g739 44 Bng060 45.9 44 g792 9.9

44.7 44 g139 45 Phs 38 g2567 46 Bng102
47 g471 44 DJ1kscar 47 Bng228

18
50 g1192 4.8 46 D1861 49 g708
54 g1233 54 g696,g2462

6
54 D1086 52 g2516
9

4
59 DROC11b 48.6 61 g2531 55 g1206
19

61 g2329 64 g1378 40.1 58 g131 58 g1126

66 g1361 49.5 44.0 66 g487
2.7 69 g1852 11.2 70 61 g549 66 g2510 16.2
76 g1748 Bng204
9

0.4 5.2 65 g1031 41.1 89 g1671

82 g1159
10

73 g415 23.5 45.5 69 g1990

32.3 99 g861 4.4 74 g2416
108 DP2062 78 P_U3 17.8 73 g776,C_AP2S
Pv10 Pv11
13
15

113 g2192 93 g1175

7
13

114 Bng94 103 g2459 15.5 75 g1539

117 g1998 6.2
10 10

120 g2208 112 g1065 0 g2521 0 g811 2.3

7.2 116 g1357 25.6 77 g440,Bng205
12.7 8.7 3 g785
122 g1818 121 g1853 30.1 39.0 3 DROE9a
20

34.7 130 g1280 35.4 7 g2273

7
14.3 135 130 g1380 77 g1758 5 BIP_J17S 13 g1731

11
g1757 23.7 16 g1932

12
80 g2514 9 g1383
8

14.8 136 g1190 3.8 29.6 133 g290 6.6 20 g1438

g1174 32.5 86 g140 25 g2285
143 28 g2331
12

146 g1947 46.0 109 g1713 1.8 17.4 31 g835

4.3 33 g1994

16
146 Bng104 31.8 118 g2264 4.9 44 L_L4S 33 DRON9b
2

125 g1181 0.5 34 g1168 25.4

14

47 g2600 15.2
134 A1CAO 52 g2560 35 DROJ9a
7

50.9 159 DROS3a 0.8 55 g2268 36 D1630

8
58 g1341 38 DROG5b
62 g2260 54 g2135
183 g2316 1. 2 66 g1661 17.3 61 DH20sT
70 DROF1a 67 g1983
73 g1215

Figure 2 Syntentic relationships of soybean relative to the common bean genetic map. A common bean genetic map anchors
corresponding syntenic regions of the soybean 1.01 genome build. The location (in megabase pairs) of each soybean fragment straddling the
common bean linkage is noted at the beginning and end of the homology.

were > 20 cM in length. Conversely, the mean physical DNA has a much lower gene density than euchromatic
distance relative to soybean was 4.9 Mb (with a median regions at the ends of the chromosomes. Finally, these
of 2.6 Mb). 63% of the blocks were > 2 Mb in length. regions have a much lower recombination rate than the
By comparing the location of these blocks, it is very euchromatic region. All of these features appear to be
clear that nearly all segments of the common bean gen- common for eudicot genomes.
ome mapped to two segments of the soybean genome. As Figure 3 shows, 35 of the 40 of the soybean chro-
69.3% of the genetic distance of the common bean map mosome arms exhibit a signature of conserved synteny
mapped to some region of the soybean genome. Much between the two species. Much of the synteny that we
of the uncovered regions in common bean fell in larges observed here was to orthologous loci in the euchro-
gaps on the linkage map. Conversely, these blocks con- matic regions of the soybean genome. Only a few soy-
sisted of 271 Mb or 27.9% of the soybean genome bean chromosomes, specifically 10, 12, 14, 17, 18, and
sequence. To better understand the difference in gen- 20, contain extensive blocks of common bean loci that
ome coverage, we needed to integrate additional soy- map to soybean pericentromeric DNA. If we exclude
bean genomic information into our analysis. the pericentromeric DNA from our calculations, of the
As displayed graphically at Soybase http://soybase.org 271 Mb of the soybean that were syntentic to common
and Phyotzome http://www.phytozome.org/soybean, and bean, 200 Mb mapped to the euchromatic arms. There-
captured in Figure 3, much of the soybean genome con- fore, using this limited set of common bean loci, we
sists of pericentromeric DNA. Several features of this were able to determine the ancestry of 42.7% of the
class of DNA are important for this analysis here. First, gene rich euchromatic region of soybean. Further, 30 of
this DNA is centered around the centromeres and the 33 duplicated blocks of soybean genome anchored
encompasses 56% of the soybean genome. Further, this to the common bean genetic map were also defined as
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Gm1 Gm2 Gm3 Gm4 Gm5 Gm6 Gm7 Gm8 Gm9 Gm10
0 66 161 82

156 (Pv3) 9
13
3
119
129 17 33 181
6 69
171 (Pv3)
0
24 9 2 126 7 74
73
15 (Pv8) 38 112
20 (Pv8)
34 9 44
10 143
148
116
10 39 60
3 0 16
73 75
5 24
69 8 73 10
135 (Pv6)
136 (Pv6)
47
20 66
8 29
24

Mb 133
30
126
95 7
143 121
86 2 148
181
40
1 89 161 14
37
166 9 6 44 8 69 66
109 44
8 7
50 29 10
159
2 0
87
64
Gm11 Gm12 Gm13 Gm14 Gm15 Gm16 Gm17 Gm18 Gm19 Gm20
0 64 159 66 44 232 0
93
29 0
8 5 44 3 33
86 1 4
2 0 11 14 118 136
199
96
4 0
6 3 6 77
10
3 77 1
69
11 50
31
150
20
73
34
7 51 130
116
164 0 7
30 171 121
Mb 99
3
40 6 130 21
202
1 5 32 65
232
40
24
5 1 0 64
54
66 1 7
24 166
50 5 16

8
60
77

Figure 3 Syntentic relationships of common bean relative to pseudochromosomes defined in build 1.01 of the soybean genome.
Painted on each soybean pseudochromosome are syntenic common bean fragments. The genetic location (in cM) of the fragment are noted.
The extent to which each fragment was electronically extended (see text for procedure) beyond the genetic mapping distance is noted as the
distance beyond the genetic boundaries of the syntenic common bean fragment. The gray bar represents the heterochromatic region, and the
black dot is the location of the centromere. This information was collected from the Soybean Genome Browser at SoyBase.org http://soybase.
org/gbrowse/cgi-bin/gbrowse/gmax1.01/.

soybean-to-soybean duplicates based on dot blot analysis
of the full genome sequence of soybean [[23]; see Figure
S5 there].
We next compared the ratio of the physical distance
to genetic distance in common bean. To calculate the
physical distance per cM, we used the physical distance
in soybean relative to the genetic distance in common
bean. This same approach was used when the A. thali-
ana and B. napus genomes were compared [8]. The
physical distance per cM was calculated for a total of
245 comparisons of neighboring loci. The average dis-
tance was 290,441 bp/cM. The median ratio was
119,405 bp/cM, and 42% of the comparisons were less
than 100,000 bp/cM. These later values were very simi-
lar to those observed when A. thaliana and B. napus
were compared.
Next, a comparison of the physical to genetic distances
between duplicate blocks from the soybean genome that
were syntentic to the same common bean genetic block
was made. The average difference between these block
was 33,571 bp/cM, while the median was 18,056 bp/cM.
The range of difference spread from 76 to 203,002 bp/cM.
This largest difference was between duplicates on soybean
chromosomes 8 and 18 that were syntenic to a Pv6 block
bounded by markers g2553 and g139 in the interval from
23-47 cM. The ratio for these two blocks (Gm8 = 119,914
bp/cM; Gm198 = 351,548 bp/cM) was much greater than
the genome-wide average. These two soybean blocks ter-
minate in the low recombination region, and the Gm18
blocks goes further into the pericentromeric region. This
probably accounts for the differences in the physical to
genetic distance ratio.
McClean et al. BMC Genomics 2010, 11:184
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Electronic mapping of common bean sequences
Given the extensive synteny observed between common
bean and soybean, we considered the possibility of map-
ping other common bean sequences relative to the
observed duplicate syntentic blocks. The underlying
concept is that duplicate soybean blocks could serve as
a reference that would point to the most likely genetic
position for any given common bean sequence. This
concept is analogous to the binning of ESTs in wheat
[32] except rather relying on the physical deletion land-
marks it relies upon the comparative genomic structure
between two species within the same evolutionary line-
age. These electronically mapped loci might also 1)
reveal additional details about the degree of synteny and
the chromosomal history of these two species, and 2)
point to duplication blocks in the soybean genome itself.
To test this concept, we collected all available com-
mon bean sequences for a blastn analysis. This analysis
consisted of 11,043 EST contigs and 9,847 EST single-
tons that were constructed here using the procedure
described by Childs et al. [33]; 85,102 repeat masked
BES [34]; and 694 CDSs from common bean. Several
criteria were used before a sequence was included in
our set of electronically mapped sequences. First, the
sequence must have two hits against different segments
of the soybean genome. Secondly, the e-value for all hits
must be less than 1 × 10 -30 . Next, the length of the
match of the query to the soybean must be 150 nt or
greater. And finally, to ensure that the homology was
against two different sequences, the distance between
the 3’ end of one sequence and the 5’ beginning of is
neighboring sequence must be greater than 50 nucleo-
tides. Using these criteria an additional 15,091 common
bean sequences were electronically mapped. This con-
sisted of 549 gene-based sequences, 2,548 BES, 4,522
EST singletons, and 7,472 EST contigs. Of these, 316
were previously mapped genetically. This gives a total of
14,775 newly mapped loci. The median distance
between any two sequences, based on their soybean
orthologous location, was 11,068 nucleotides.
In addition to its usefulness for studying common
bean and soybean synteny, this large collection of elec-
tronically mapped common bean sequences greatly
increases the marker set available for common bean
genetics. For this to be the case, it was essential to
determine if the electronic map position of each of
these sequences corresponds to its predicted genetic
position. To test this concept, we focused on a 43 cM
region of Pv7 between markers g2298 and g1378. We
selected this region because although QTL for common
bacterial blight [35] and white mold resistance [36] are
known to map to this location, useful markers have not
yet been developed for marker assisted selection. Pri-
mers were designed to 15 EST contig or singleton
Page 6 of 10
sequence loci within the interval, and the amplification
products from BAT93 and Jalo EEP558 were sequenced.
Of these we detected 7 polymorphic loci. CAPs markers
were developed, and the loci were mapped on the
BAT93 × Jalo EEP558 community mapping population.
All 7 of the loci mapped within the interval that was
selected for study. Five of the seven mapped exactly as
predicted. The positions of the remaining two loci were
inverted relative to the positions of the two soybean
orthologs. This result strongly suggests that the electro-
nic mapping approach provides extensive physical and
genetic position information not previously available for
common bean.
These results allowed us to systematically extend the
distance of the common bean syntenic block (Figure 3).
The principle we applied is to search for a common
bean genetic block shared by two soybean regions and
extend the borders in either or both directions until
sequence colinearity between the two soybean blocks is
broken. For example, the Pv 9 block from 44-89 cM is
shared with both Gm4, from positions 41.1 to 45.9 Mb,
and Gm6, from positions 11.9 and 16.2 Mbp. By apply-
ing the principle described above, we see an unbroken
block in the same orientation from 36.0-49.0 Mbp on
Gm4 and from position 8.6-19.5 Mbp on Gm6. By
applying this concept, we were able to extend the degree
of synteny relative to this one Pv9 block from 9.1 Mbp
to 23.1 Mbp. We reexamined the synteny between the
two species and applied the same principle we used
with the Pv9 to the entire genome. Using this newly
derived information, we can account for an additional
187 Mbp of syntentic regions between common bean
and soybean. All of our approaches here allow us to
trace the ancestry of 456 Mbp of the soybean genome
relative to the diploid common bean genome.
Duplication history of soybean
Given that soybean has undergone a major duplication
event in its history, it is reasonable to expect that many
common bean sequences should map to two locations
in soybean. Our extensive Blastn analysis using all avail-
able common bean sequences clearly showed this to be
the case. Given that common bean is a diploid relative
of soybean, the common bean sequences can then be
used as a reference point that links two duplicate
regions in soybean. This approach does have limitations,
although not serious. First, any sequence or sequence
block unique to the soybean lineage will not have a
common bean sequence signal, and any duplication
associated with those sequences will not be uncovered.
Also, given that 83% of the sequences we were able to
map electronically were gene-based, and that most
genes are found in the euchromatic regions near the
ends of eukaryotic chromosomes, the strongest evidence
McClean et al. BMC Genomics 2010, 11:184 Page 7 of 10
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regarding the duplication history will come from those blocks. These blocks are interrupted by a duplicate
gene-rich regions. block from Gm7. Two of the blocks on both Gm5 and
To investigate the duplication history of each soybean Gm8 are syntenic to common bean Pv2. Furthermore,
chromosome relative to the remainder of the soybean of the two chromosomes, Gm8 shares duplications with
chromosome set, we first ordered all of the common more Gm chromosomes which in turn trace back to five
bean sequences relative to their soybean ortholog on a different common bean linkage groups.
chromosome-by-chromosome basis. That ordering was Using both the Pv/Gm syntentic data as well the
cross-referenced to the duplicate with the lowest E-value duplications found in Gm using the large data set from
on a second soybean chromosome. These defined blocks Pv, several conclusions can be drawn regarding the
of loci that mapped to the same duplicate chromosome. chromosomal history of soybean. First, the one-to-two
It was required that each block consist of ten common mapping of Pv to Gm sequences provides further com-
bean loci, and that the loci must be in consecutive order. pelling evidence that a major duplication event is part of
Figure 4 summarizes the duplicated block data for the history of the soybean genome [25]. The modular
chromosomes Gm5 and Gm8 in graphical form. These nature of the both the Pv/Gm synteny and soybean
two were chosen because they are representative of the duplications suggest that either coincident with the
other chromosomes, and because they share synteny to duplication, or shortly after, the duplicated chromo-
the same regions on common bean Pv2. The most somes were fractionated or new chromosomes were
apparent observation is the modular nature of each reassembled. A dramatic example is found by comparing
chromosome with regards to their duplicate blocks. the Gm15 duplicates to Gm8. Here we see three dupli-
Gm5 shares duplication blocks with three other soybean cate blocks from the end of Gm15 organized non-con-
chromosomes (Gm8, Gm17, Gm19) while Gm8 shares tiguously. These are right next to a block from the
duplication blocks with Gm5, Gm7, Gm12, Gm15, and beginning of the same chromosome. A chromosome-
Gm18. Furthermore, the modular blocks from the dupli- wide analysis suggests that at least 19 blocks rearranged
cate chromosome are not contiguous. For example, to form Gm8. Because of a lack of significant sequences
beginning at position 0 on Gm8, there is about 12 Mbp homologous much of the pericentromeric region, we
of sequences duplicated on Gm5 in three non-contigous could not determine the modular nature of that region.

Pv3 Pv2 Pv2 Pv2

51 - 41 84-112 65-60 27-47
10.2 - 9.5
6.5 - 6.2

6.6 - 6.8

0.8 - 0.1
0.2 - 0.6

0.7 - 1.2

8.4 - 6.8 10.2 - 13.1 Gm 5 15.9 - 13.2 11.7 - 23.7 9.4 - 1.3

13 91 136 20 39 19 24 65 535 57 394

Pv2 Pv2 Pv2 Pv5 Pv10 Pv8 Pv6

47-27 84-112 65-60 15-24 62-80 29-25 124-102
37.4 - 38.1

36.0 - 35.1

49.8 - 50.4
37.4 - 37.5
49.7 - 49.1
48.9 - 46.9

32.6 - 32.5

62.2 - 61.6
38.1- 46.3
4.4 - 3.6

0.5 - 1.6
0.3 - 0.5
2.7 - 1.6
0.3 - 0.1
0.1 - 0.2

41.9 - 38.1 30.6 - 37.3 59.1 - 60.7 Gm 8 24.6 - 6.1

57 394 74 466 24 10 31 58 62 16 104 13 95 56 14 89 245 50 36

0 10 20 30 40 50

5 7 8 12 15 17 18 19

Gm chromosome code
Figure 4 Duplicated blocks along soybean chromosomes Gm5 and Gm8 based on reference ordering of common bean sequences.
Each chromosome consists of a series of duplicate blocks that are color coded. White blocks have no reference common bean sequence. The
physical position (in Mbp) of the duplicate block on its home chromosome is given. The position is given in either direct or inverted order
based on its position relative to the reference chromosome. Above some blocks is the genetic location of the corresponding syntentic common
bean blocks. Below each block is the number of common bean sequences used to establish the block. The thin bars represent the location of
the pericentromeric regions of the chromosomomes. The physical distance scale at the bottom is in Mbp.
McClean et al. BMC Genomics 2010, 11:184
http://www.biomedcentral.com/1471-2164/11/184
Conclusions
We have used the first public release of the soybean
genome to evaluate the syntentic relationship between
this important economic species and common bean,
another member of the Phaseoleae legumes. It appears
that extensive regions of synteny exist between these
two species. These relationships further suggest that the
soybean genome has undergone a whole genome dupli-
cation based on the fact that nearly all of the common
bean sequences that map to a single location, have two
copies in the soybean genome. Furthermore, soybean
appears to have undergone extensive chromosome
breakage and rearrangement. This conclusion is based
on the observation that most soybean chromosomes
consist of fragments from multiple common bean chro-
mosomes. Whether these rearrangements occurred prior
to, coincident with, or following the duplication event is
unclear at this time. From an applied perspective, these
results suggest that a comparative genomics approach to
gene discovery is feasible for these two evolutionarily
related species.
Methods
EST contiging and BAC-end sequence processing
The 83,448 Phaseolus vulgaris sequences in the National
Center for Biotechnology Information (NCBI) EST data-
base available on August 1, 2008 were downloaded from
http://www.ncbi.nlm.nih.gov/sites/entrez?db=nucest.
EST contigs and singletons were defined using the pro-
cedures described in Childs et al. [33]. The procedure
was performed using the following stand-alone software:
SeqClean (http://www.tigr.org/tdb/tgi/software; default
parameters), Megablast [[37]; http://www.ncbi.nlm.nih.
gov/blast/megablast.shtml; default parameters], and
CAP3 [[38]; default parameters]. All 89,017 BAC-end
sequences (BES) were downloaded from the NCBI GSS
database http://www.ncbi.nlm.nih.gov/sites/entrez?
db=nucgss on August 1, 2008. We limited our analysis
to those 85,102 BES representing sequences from both
ends of 42,551 sBACs. Prior to the blastn analyis, these
BES were analyzed using RepeatMasker (http://www.
repeatmasker.org; default parameters, v. 3.15) with the
Fabaceae repeats database obtained from Plant Repeat
Database [[39]; http://plantrepeats.plantbiology.msu.edu/
; file: TIGR_Fabaceae_Repeats.v2_0_0.fsa.txt]. A fasta file
containing the singletons and EST contigs is available
upon request from the corresponding author.
Blastn analysis
The 20 pseudochromosomes from the version 1.01
release of the soybean assembly were downloaded from
ftp://ftp.jgi-psf.org/pub/JGI_data/Glycine_max/Glyma1/
assembly/sequences/ and used as a database for all
Page 8 of 10
blastn analyses. First, 300 EST or singletons, originally
developed by Ramirez et al. [40], using a set of 21,026
EST, and 15 other sequences, all mapped onto the 11
common bean linkage groups at a LOD value of 2
[McConnell M, Chikara S, Mamidi S, Rossi M, Lee R,
McClean PE. A gene-based linkage map of common
bean (Phaseolus vulgaris), submitted.], were used as a
query. Subsequently, blastn analyses were performed
using the new set of ESTs (11,043) and singletons
(9,847) as one query, and the 85,102 BES as a second
query. A final query consisted of 694 complete P. vul-
garis coding sequences (CDS) downloaded from NCBI
http://www.ncbi.nlm.nih.gov/ on August 8, 2008.
Because we were looking for significant levels of orthol-
ogy between common bean and soybean sequences, we
initially limited all blastn analysis to hits with E-values
less than 1 × 10-10 and overlaps of at least 150 nt. The
results reported here are based on the first high scoring
pair. See Additional File 1 for all of the common bean
sequences that met these criteria.
High density mapping of linkage group Pv7
Primers were developed for 15 contig or singletons that
electronically mapped between markers g2298 and
g1378 on linkage group Pv7. A 3’-primer was designed
to a sequence within 150 nt of the putative stop, and
the corresponding 5’ primer was located about 500 nt
upstream of the 3’-primer site. Subsequent PCR amplifi-
cation and sequencing followed the procedures
described in McClean et al. [41]. Based on sequence
polymorphism, either CAPs or SNP diagnostic markers
were developed. These markers were used to score poly-
morphisms among members of the community-wide
BAT93 × Jalo EEP558 RI population. These marker loci
were then mapped using the MAPMAKER software
[42]. The final order was verified using the “ripple” com-
mand with a LOD value of 3.0.
List of abbreviations
BAC: bacterial artificial chromosome; BES: BAC end
sequence; bp: base pairs; CAPs: cleaved amplified poly-
morphic sequence; CDS: coding sequence; cM: centi-
morgans; EST: expressed sequence tags; Gm: Glycine
max; LOD: logarithm of (base 10) of odds; Mb: mega-
bases; MYA: million years ago; RFLP: restriction frag-
ment length polymorphism.
Additional file 1: Electronically mapped common bean loci based
on synteny to the soybean genome sequence. List of P. vulgaris loci
which met the following selection criteria for electronic mapping: e-value
less than 1 × 10-30, hits to two soybean chromosomes, query length
greater than 149 nt, and soybean position for the end of one soybean
locus and the beginning of the next locus was less than 50 nt.
McClean et al. BMC Genomics 2010, 11:184
http://www.biomedcentral.com/1471-2164/11/184
Acknowledgements
This research was funded in part by the United States Department of
Agriculture Cooperative State Research, Education and Extension Service
National Research Initiative as part of their Plant Genome program. The
grant was awarded to PEM, and the award number is 2005-00757. Partial
support for SM was made possible by NIH grant number P20 RR016741
from the INBRE program of the National Center for Research Resources.
These soybean sequence data were produced by the US Department of
Energy Joint Genome Institute http://www.jgi.doe.gov/ in collaboration with
the user community.
Author details
1
Genomics and Bioinformatics Program, North Dakota State University, Fargo,
ND 58105, USA. 2Department of Plant Sciences, Loftsgard Hall, North Dakota
State University, Fargo, ND 58105, USA.
Authors’ contributions
PEM conceived the project and was the principal author of the manuscript.
MM performed all of the molecular marker analysis for common bean and
analyzed the initial syntenty between the two species. RL and SM jointly
developed the common bean contigs, and performed all of the
bioinformatic analysis of blast analyses between the common bean
sequences and the soybean 1.01 build. SC remapped the common bean
molecular segregation data as new data became available. MM, RL, SM, and
SC each reviewed the manuscript.
Received: 26 August 2009 Accepted: 18 March 2010
Published: 18 March 2010
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doi:10.1186/1471-2164-11-184
Cite this article as: McClean et al.: Synteny mapping between common
bean and soybean reveals extensive blocks of shared loci. BMC
Genomics 2010 11:184.

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