164 RILs (those of crosses between Mis-
uzudaizu and Mashidou Gong 503), 96 RILs
(MxS lines, those of crosses between TK780
and B01167), 21 mutants, 39 strains of Edam-
ame, and 37,890 clones of full-length cDNA.
23.2 Integrated Databases
23.2.1 PlantGDB
PlantGDB (http://www.plantgdb.org) is an inte-
grated database for plant genomics, in which 16
dicots and 7 monocots have been registered. For
Fabaceae, the genome and gene models ofL.
japonicus, M. truncatula,andG. max, spliced
alignment of EST, cDNA, PUT (assembled
unique transcript) against genome sequences are
available in LjGDB, MtGDB, and GmGDB.
23.2.2 The Gene Index Project
The Gene Index Project (http://compbio.dfci.
harvard.edu/tgi/) encompasses tentative consen-
sus (TC) contigs assembled from expressed
sequence tag (EST) data for plants, animals,
protest, and fungi. For plants, EST and TC
sequences have been provided for 60 species. As
for Fabaceae, bean (Phaseolus vulgaris), cowpea
(Vigna unguiculata),L. japonicus,M. truncatula,
scarlet bean (Phaseolus coccineus), and soybean
(G. max) have been registered in the database.
23.2.3 Phytozome
Phytozome (http://www.phytozome.net) contains
releases of the nodes, clusters and consensus
sequences, and annotation of transcripts for 41
plant species. The source data for the database
were constructed using the BioMart framework
(http://www.biomart.org). The source data were
subsequently integrated with physical map posi-
tions and displayed using GBrowse (http://gmod.
org/wiki/GBrowse). For Fabaceae, bean
(P. vulgaris),M. truncatulaand soybean (G.
max) have been registered in the database.23.2.4 PGDBj (Plant Genome DataBase
Japan)PGDBj (http://pgdbj.jp/?ln=en) is a portal site
integrating the databases related to plant omics
studies (Asamizu et al. 2014 ). The information
related to DNA markers and QTL for 55 plant
species has been collected from the literature by
manual curation. Information for the following
leguminous species has been collected—L. japo-
nicus(1,073 SSR markers and 82 dCAPS mark-
ers),G. max(7,020 SSR markers),M. truncatula
(65 SNP markers, 544 SSR markers, 246 QTL,
827 other markers (CAPS, RFLP, etc.)), red clo-
ver (Trifolium pratense) (7,468 SSR markers, 314
other markers (RFLP etc.)), and white clover (T.
repens) (1,993 SSR markers). PGDBj contains
cross-links to other databases, such as SABRE2
(http://sabre.epd.brc.riken.jp/SABRE2.html) for
plant resources ofL. japonicusandG. max, and
KNApSAcK (http://kanaya.naist.jp/KNApSAcK/
) for species-metabolite relationships inL. japo-
nicus,G. max,M. truncatula,T. pratense, andT.
repens.23.3 Database for Legume Genome
Information23.3.1 Soybean (G. max)SoyBase (http://www.soybase.org) was estab-
lished to publish the integrated information on
the genetics, genome information, and molecular
biology of soybean. The database contains
ontologies, metabolic pathways (SoyCyc), and
microarray data (SoyChip developed by Af-
fymetrix®). Genetic maps and physical maps can
be browsed by CMap and GBrowse from the
menus,“Maps”and“Genome,”respectively. The
database also contains genomic sequence, gene
predictions, potential SSRs, and ESTs. On the260 H. Hirakawa et al.