Genetic and Molecular Analysis of Soybean Genome
Harada K.1, A. Kaga1, Y. Katayose1, Y. Tsubokura1, S. Sato2, S. Watanabe1, Z. Xia1, M. Hayashi1,
H. Kanamori3, T. Shimizu3, K. Machita3, H. Ikawa3, T. Ito3, K. Kurita3, K. Ito3, J. Wu1, T, Matsumoto1,
S. Tabata2, T. Sasaki1
1

National Institute of Agrobiological Sciences (NIAS ) Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
Kazusa DNA Research Institute , Kazusa Kamatari 2-6-7, Kisarazu, Chiba 292-0818, Japan.
3
Institute of Society for Techno-Innovation of Agriculture, Forestry and Fisheries , Kamiyokoba Ippaizuka
446-1,Tsukuba,Ibaraki 305-0854, Japan.
Corresponding author: Kyuya Harada. Kannondai 2-1-2, Tsukuba 305-8602, Ibaraki, Japan. Tel: 81-298-38-7452,
Fax: 81-298-38-7452,
E-mail: haradaq@nifty.com
2

Abstract
To obtain precise marker information for soybean genetic maps, we are currently constructing
a high-density linkage map using a single F2 mapping population from the cross between Enrei and
Peking. Enrei which is an elite cultivar with a high quality for food processing is being sequenced as arepresentative cultivar in Japan, while Peking is resistant to many diseases and displays an outstanding
stress resistance under wet conditions. New 948 SSR markers were designed to large scaffolds(>100kb) of U.S. cultivar Williams 82, Glyma 0, and were incorporated into the map in order toobtain a precise assembly of the genome sequences in the Japanese soybean genetic background.
Currently, 1,860 markers have been located on the map. The marker location on the linkage map wascompared with that of the chromosome-scale assembly of the soybean genome, Glyma 1.0 (http://
www.phytozome.org/soybean.php), updated in December 2008. In total, 1,837 markers (98%)
were anchored on the genome assembly. Generally, the marker order on the linkage map revealed aclose agreement with that of physical data. Currently, the causes of the large differences are being
determined; reverse orientation of marker order on the Gm05, Gm11, Gm13, Gm14, Gm19 and otherminor differences between Williams 82 and Enrei × Peking. This map will provide information to
identify regions in the sequence assembly where additional information is required to resolve themarker order.
In order to develop new breeding strategies for soybean production, we launched acomprehensive analysis of the soybean genome using the Japanese cultivar Enrei. BAC libraries
were constructed and the end-sequences of approximately 100,000 BAC clones were analyzed andused for the construction of a physical map of the genome. To increase the saturation of the map,
BLAST analysis between the BAC-end sequences and the genome assembly of another soybean
cultivar, Williams 82 (Glyma1.0 assembly) was also carried out. This physical map will be used
for characterizing the genome structure of Japanese soybean cultivars in order to accelerate theisolation of agronomically important genes and to develop new breeding strategies for increasing
the production of local cultivars. We are also constructing a soybean genome database to facilitatecomparative genome analysis.
To elucidate the characteristics of the soybean genome in reference to the genome of L.
japonicus , synteny between the genomes was investigated. Macrosynteny between soybean andL. japonicus was analyzed by mapping the same cDNA clones on the maps of both species by the
RFLP method, and by identifying the positions of orthologs on the L. japonicus map for cDNA
markers located on the soybean map. Relatively large synteny blocks were observed between a few
linkage groups of L. japonicus and soybean. The major parts of the soybean linkage groups consistedof mosaics of smaller segments syntenic with the L. japonicus genome. The presence of manyhomoeologous regions on different soybean linkage groups was suggested from the distribution ofparalogs and orthologs. To investigate the microsynteny between soybean and L. japonicus , threesoybean BAC clones were selected for the GmNFR1a , GmNFR1b and Nts1 genes mapped on themacrosyntenic regions of the linkage groups D1b, B2 and H, respectively. We revealed a significantly
high level of collinearity between these BAC clones and corresponding homologous genomic regionsof L. japonicus .

INTRODUCTION
The Fabaceae family is the third largest family of angiosperm plants including around 20,000
species of legumes. The subfamily Papilionoideae
includes agriculturally important species such as soybean, pea, common bean, mungbean, and cowpea,
and model legumes, Lotus japonicus and Medicago
truncatula .
Soybean is currently the most important legume in the world, because its seeds contain large

amounts of edible protein and oil, and it is widelyused for food, livestock feed, industrial materials andbiofuel.
The genome size of soybean (n =20) is estimated at 1.12Gb (Arumunganathan and Earle 1991),
a value about 2.0 times higher than that of Vigna
species. It was suggested that the soybean genome
is the product of a diploid ancestor (n =11), which
underwent aneuploid loss (n =10), and subsequent
polyploidization (Lackey 1980). The occurrence of- 23 -

two rounds of genome duplication or hybridization
and rearrangements was estimated by many researchers (Shoemaker et al . 1996, Shoemaker et al . 2002,
Blanc and Wolfe 2004, Schlueter et al . 2004).
A linkage map of soybean was constructed
mainly based on restriction fragment length polymorphism (RFLP) using random genomic clones asprobes (Keim et al . 1990, Lark et al . 1993, Shoemaker and Specht 1995, Mansur et al . 1996). However,
the relatively low degree of polymorphism in addition to the large genome size and complex genome
structure has slowed the construction of a linkage
map covering a large region of the soybean genome.
Simple sequence repeat (SSR) markers were integrated into RFLP linkage maps (Akkaya et al . 1995).
Cregan et al . (1999) integrated soybean linkage
maps into 20 homologous linkage groups using SSR
markers based on their correspondence with someknown linkage maps. Five maps were integrated
with the map of Cregan et al . (1999) using JoinMap,
and a composite map with 1015 SSR, 709 RFLP, 73
RAPD, 6 AFLP, 10 isozyme markers, 24 classicalmarkers and 12 other markers has been developed(Song et al 2004). Choi et al . (2007) located 1,141
genes onto one or more of the three maps based on
single nucleotide polymorphism (SNP). A high-density integrated map of 1,810 SSR or sequence-taggedsite (STS) markers using three recombinant inbred
populations was developed (Hwang et al . 2009). A
genetic map composed of 509 RFLP, 318 SSR, 318
AFLP, 97 AFLP-derived STS, 29 BAC-end or ESTderived STS, 1RAPD and five morphological markers using a single F2 population was constructed (Xiaet al . 2008).
Genome-wide integrated physical and genetic
maps will provide powerful tools for research into
various aspects of the soybean genome, including
large-scale genome sequencing, target marker development, high-throughput EST mapping and efficient
positional cloning. Integrated genetic and physicalmapping of Forrest (http://soybeangenome.siu.edu/)
and Williams 82 (http://soybase.agron.iastate.edu/)
was conducted using restriction enzyme fragment
fingerprints of BAC clones.
A high level of synteny on entire linkage
groups was observed between mungbean (Vigna
radiata ) and cowpea (Vigna unguiculata ) (Menanciohautea et al . 1993). Though comparable levelsof synteny were identified between mungbean andcommon bean (Phaseolus vulgaris ), synteny blocks
were more limited between these species and soybean (Boutin et al . 1995). Lee et al . (2001) observed
a high level of conservation between chromosomesof mungbean and common bean, and the chromosome segments of soybean. Choi et al . (2004) reported genome-wide macrosynteny among legumes(M. truncatula , M. sativa , L. japonicus , Pisum sativum , Cicer arietinum , mungbean, common bean andsoybean), using a large set of cross-species genespecific markers. Though the length of the synteny
blocks was reduced by chromosome rearrangements
in some regions, chromosomes from a variety of
Papilionoid species could be aligned, based on thechromosomes of M. truncatula . However, only small
synteny blocks were observed between M. truncatulaand soybean.
The order and orientation of at least six genes
were found to be conserved in a 70kb region, including apyrase genes from soybean and M. truncatula(Cannon et al . 2003). Choi et al . (2004) examined
two BAC clones from the region containing the cyst
nematode resistance gene, rhg1 , of soybean and homologous BAC clones of M. truncatula , and revealed
that the order and orientation of fourteen genes wereconserved between these genomes. They also analyzed ten homologous pairs of BAC clones from M.
truncatula and TAC clones from L. japonicus andfound that 72 genes (82%) were syntenic between
the genomes. Mudge et al . (2005) uncovered twolarge soybean regions surrounding the cyst nematoderesistance genes, rhg 1 and Rhg 4, that exhibited a
synteny with M. truncatula .
Microsynteny analysis between homoeologous regions surrounding the N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes (Schlueter et al .
2006), fatty acid desaturase 2 (FAD2) genes (Schlueter et al . 2007a), and LysM kinase genes (Zhang etal . 2007) has been performed.
Construction of a soybean linkage map based on asingle F2 mapping population derived from Enrei
×Peking
The marker order on the integrated maps fromseveral different population is sometimes obscure. To
obtain precise marker information for soybean genetic maps, we are currently constructing a high density
linkage map using a single F2 mapping populationfrom the cross between Enrei and Peking. Enrei isan elite cultivar with a high quality for food processing. On the other hand, Peking displays many useful characteristics such as cyst nematode resistance,soybean mosaic virus resistance, Phytophthora rot
resistance and a high stress resistance in germination
under wet conditions.
Initially, genomic SSR markers developed by
Cregan et al . (http://soybase.org/resources/ssr.php),- 24 -

including markers that have been used for MAS
and mapping by breeders and researchers wereanchored on the linkage map to cover the genome
widely. Subsequently, newly developed EST-SSR
markers by Hisano et al . (http://www.kazusa.or.jp/
soymarker/) were integrated into the map. The
genome sequence of a U.S. cultivar Williams 82,
Glyma 0, has been available since January 2008
and chromosome-scale assembly of the soybean
genome, Glyma 1.0, updated in December 2008
(Soybean Genome Project, DoE Joint Genome Institute, http://www.phytozome.net/soybean.php).
New SSR markers were designed to large scaffolds(>100kb) of Glyma 0 or to Glyma 1.0 and havebeen incorporated into the map in order to obtaina precise assembly of the genome sequences in theJapanese soybean genetic background. Additionally, SNP markers from 5,551 STS containing SNPs
developed by Choi et al . (http://bfgl.anri.barc.usda.
gov/soybean/) are being integrated. Currently, 1,860
markers (282 USDA SSR markers, 383 EST-SSR
markers, 247 SNP markers and 948 newly designed
SSR markers) have been located on the map (Fig.1,
left white bar). This map spans a total length of
2913 cM with an average marker distance of 1.6

cM and maximum distance of 6.3 cM. Severe segregation distortion (P<0.001) was observed on the
Gm06 and Gm11 (Fig.1, blue line). The map length
is longer (21%) than that of the soybean consensus
map 3.0 developed by Cregan et al . (http://soybase.
org/LG2Xsome.php).
The marker location on the linkage map(Fig.1, left white bar) was compared with that of
the chromosome-scale assembly of the soybean genome, Glyma 1.0 (Fig.1, black right bar). In total,
1,837 markers (98%) were anchored on the genome
assembly. The other 23 markers were localized
either on the unexpected chromosome due to duplicated loci (8), or unassigned scaffolds (9) or no hit(6). Generally, the marker order on the linkage map
revealed a close agreement with that of physicaldata. Although the relationship between the genetic
distance and physical distance appears to be ~360
kb/cM, assuming a genome size of approximately
1.1 Gb, positional biases (50kb-7M/cM) were
found. In each chromosome, a genomic region witha highly suppressed recombination between markers, possibly the pericentromeric region, was observed and the extent differed among chromosomes(Fig.1). The ratio of genetic and physical distanceFig.1. A genetic linkage map constructed based on an F2 population derived from the crossbetween Enrei and Peking (left). Physical map of Williams 82, Glyma 1.0, was aligned(right) and marker locations are connected by black lines. In each chromosome, thephysical map revealed a region of highly suppressed recombination between markers on
the linkage map. These regions which are shown on the same scale at the right side may
correspond to the pericentromeric regions. Chromosomal regions in which the order of
DNA markers is different from sequence in the physical map are highlighted in red boxes.

- 25 -

Gm02

Gm06
18 0

1 60

Gm02

16 0

Gm06

1 40

14 0

1 20
12 0
1 00

(cM)

(cM)

10 0
80

80

60

60

40

40
20

20

0
0

0
0

10

20

30

40

50

10

20

60

(Mb)
Gm05

40

50

60

160

1 60

Gm05

1 40

Gm11

140

120

1 20

100

(cM)

1 00

(cM)

30

Gm11
(Mb)

80

80

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60

40

40

20

20

0

0
0

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50

(Mb)

10

20

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(Mb)

Fig.2. Variation in genetic/physical distance ratio. X and Y axes show the physicaldistance and genetic distance, respectively. Small dots indicate marker
locations. Blue arrows designate reverse orientation of marker order on theGm05 and Gm11 and red arrows indicate the regions where the orders ofmarker positions are being determined.
varied considerably depending on the chromosomal region (Fig.2). Currently the causes of the large differences are being determined; reverse orientation of marker
order on the Gm05, Gm11, Gm13, Gm14, Gm19 (Fig.1,
red) and the other minor differences between Williams
82 and Enrei × Peking. This map will provide information to identify regions in the sequence assembly where
additional information is required to resolve the marker
order.
Construction of soybean BAC-based physical map
and database
To develop the basic resources for analyses of thewhole genome, we have constructed two bacterial artificial chromosome (BAC) libraries from the Japanesesoybean cultivar Enrei using the restriction enzymes
Hin dIII and Mbo I. We have sequenced Enrei BAC end
sequences since 2007 to develop a BAC-based physical map and database by using the Williams 82 genome
assembly. We sequenced about 80,000 clones from a
Hin dIII-library and about 20,000 clones from a Mbo Ilibrary. To construct a BAC-based physical map of the
Enrei genome, BLASTn analysis between the BAC-end
sequences of Enrei and genome assembly of Williams
82 (Glyma1 assembly, http://www.phytozome.org/soybean.php) was carried out. This physical map will be
used for characterizing the genome structure of Japanese- 26 -

soybean cultivars in order to accelerate the isolationof agronomically important genes and to develop new
breeding strategies for increasing the yield of Japanesecultivars. We are also constructing a soybean genome
database, “DaizuBase”, to facilitate comparative genome analysis. Unified map of DaizuBase indicates therelationship between the linkage map and physical maps
(Fig. 3). GBrowse shows aligned Enrei BAC clones on
Glyma1 assembly (Fig. 4). Although presently, only participants in the DD-project (Genomics for Agricultural
Innovation of MAFF) can utilize DaizuBase, consultation will be opened by the end of 2009. We introduced
a next generation sequencer GS-FLX (Roche/454) todecode the Enrei genome for the characterization of the
genome structure of Japanese (domestic) soybean. The
high sequencing ability will enable us to conduct a comparative analysis of the soybean genome structure.
Characterization of soybean genome by synteny
analysis with Lotus japonicus
The rapid accumulation of genome sequence information for L. japonicus and M. truncatula provides aunique opportunity for comparative studies between themodel legume and leguminous crops.
Macrosynteny between soybean and L. japonicus
was analyzed by mapping the same cDNA clones on themaps of both species by the RFLP method, and by iden-

Fig.3. Screen shot of UnifiedMap on DaizuBase. This shot offers information about DNA
markers, BAC clones and the relationship between the linkage map and physicalmaps.

tifying the positions of orthologs on the L. japonicus
map for the cDNA markers located on the soybean map.
Relatively large synteny blocks were observed between L. japonicus LGs (Lj LGs) 1, 3 and 4 and soybean
LGs (Gm LGs) L, H and A1, respectively (Fig. 5). However, the major parts of Gm LGs consisted of mosaicsof smaller segments syntenic with L. japonicus . On theother hand, the L-G synteny map indicated that each of
the Lj LGs harbored syntenic regions with two or more
Gm LGs (Fig. 5). In particular, each region of Lj LGs
often overlapped with syntenic segments of different
Gm LGs, suggesting that such overlapped segments of
Gm LGs reflected the homoeologous duplicated regions.
Such possible duplications were observed between A1
and A2, A1 and D2, A1 and K, A2 and M, B1 and B2,
B1 and C2, B1 and D1b, B2 and G, C1 and C2, C2 andB1, D1a and D1b, E and K, F and M, G and L, G and

M, I and L, I and O, L and O, and N and O (Fig. 5). In
fact, the same DNA markers or paralogs were located at
two or three positions mostly on different chromosomes.
They are indicated in Fig. 5 and include the putative
Nod-factor receptor gene and its paralog, GmNFR1a(D1b) and GmNFR1b (B2), and the autoregulation gene
Nts1 (H) and its paralog GmCLV1A (B1).
To investigate the microsynteny between soybean
and L. japonicus , three soybean BAC clones were selected for the GmNFR1a , GmNFR1b and Nts1 genes,
mapped on the macrosyntenic regions of Gm LGs D1a,
B2 and H, respectively (Fig. 5). Nucleotide sequences of
the BAC clones WBb76L15 (GmNFR1a ), WBb98N11(GmNFR1b ) and WBb225L1 (Nts1 ) were determinedby the shotgun method with a 5-time redundancy, andassembled sequences of 124,649 bp, 132,374 bp and
129,251 bp were obtained, respectively. The nucleotide- 27 -

Fig.4. Screen shot of GBrowse of DaizuBase. BAC contigs are shown on each chromosome of the Williams 82 genome assembly.

sequences obtained were subjected to manual assignment of protein-encoding genes, and as a result,a total of 44 complete gene structures and 9 partial
and pseudo-gene structures could be identified. The
average gene density of each clone ranged from one
gene every 8.3 kb to 9.6kb. This density was lower
than that in previous estimates (Young et al . 2003,
Triwitayakorn et al . 2005, Mudge et al . 2005) but
slightly higher than that in a recent report surveyed
by 17 BAC sequences (Schlueter et al . 2007b).
Sequence comparison of WBb225L1 (Nts1 )and corresponding HAR1 genomic region of L.
japonicus revealed a highly conserved microsynteny(Fig. 6A). Among 14 predicted genes, including
partially predicted and pseudo-genes in the HAR1

region of the L. japonicus genome, 11 (78%) genes
had homologs on WBb225L1 (Fig. 6A). On theother hand, 69% (11/16) of the genes of WBb225L1
predicted in the overlapped region shared homologs
in the HAR1 region of the L. japonicus genome.
Similarly, a highly conserved microsynteny was
identified based on a comparison between the NFR1
genomic region of L. japonicus and homoeologous
regions of soybean NFR1 , WBb76L15 (GmNFR1a )and WBb98N11 (GmNFR1b ) (Fig. 6B). Among the
19 predicted genes, including partially predicted andpseudo-genes in the NFR1 region of the L. japonicus
genome, 14 (74%) genes showed homologs in the
GmNFR1 genomic regions (Fig. 6B). On the other
hand, 73% (11/15) and 79% (15/19) of the predicted- 28 -

genes on WBb76L15 and WBb98N11, respectively,
displayed homologs in the NFR1 region of the L.
japonicus genome. The level of gene conservation
between the homoeologous regions of GmNFR1a/
GmNFR1b/NFR1 was even higher compared withthat in the Nts1/HAR1 region. In 89% (25 out of 28)
of the predicted genes in the overlapped regions, theorder and orientation were conserved. In most cases,
genes with complete structures were identified inboth regions (ie, homoeologs). In such cases, most of
the homoeologs showed a 90% or higher nucleotide
sequence identity in exons and even introns.
We are currently constructing a synteny map
based on the sequences of soybean and Lotus japoni-Fig. 5. L-G synteny map of six Lj LGs accompanied by macrosyntenic segments Gm LGs. The anchoring marker pairs were connected by strait lines. Nts1 , HAR1 : autoregulation genes for nodule
number. NFR1 : Nod-factor receptor gene. GmNFR1a , GmNFR1b : putative Nod-factor genes.

- 29 -

(A)G. max : WBb225L1 (LG H)
Nts1
WBb225L1

CM0216(LjT09E02)

HAR1

L. japonicus : CM0216 (chr3 75.6 cM)

10kb

(B)
G. max : WBb76L15 (LG. B2), WBb98N11 (LG. D1b)
GmNFR1b

WBb76L15

GmNFR1a

WBb98N11

NFR1

CM0545
LjT02D13

LjT05B16

LjT211O12

L. japonicus : CM0545 (chr2 68.1 cM)

LjT26K22

10kb

Fig. 6. Microsynteny of (A) Nts1 /HAR1 orthologous and (B) NFR1 orthologous regions
in soybean and L. japonicus . Each block arrow on the horizontal lines represents
a gene and each dotted line connects homologs. Shaded and dotted arrows indicate the truncated or mutated genes and retrotransposons, respectively.

cus genomes.
Acknowledgements
This research was supported by a grant from
the Ministry of Agriculture, Forestry and Fisheries
of Japan (Genomics for Agriculture Innovation, DD1010, DD-1020) and by Grant-in-Aid for Scientific
Research on Priority Areas “Comparative Genomics”(18017004) and (A) (18208001).
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