Among leguminous plants, the model legume Lotus japonicus (Regel) Larsen has many biological and genetic advantages. We have developed a genetic linkage map of L. japonicus based on amplified fragment length polymorphism (AFLP), simple sequence repeat polymorphism (SSRP) and derived cleaved amplified polymorphic sequence (dCAPS). The F2 mapping population used was derived from a cross between two L. japonicus accessions Gifu B-129 and Miyakojima MG-20. These parental accessions showed remarkable cytological differences, particularly with respect to size and morphology of chromosomes 1 and 2. Using fluorescence in situ hybridization (FISH) with BAC clones from Gifu B-129 and TAC (Transformation-competent Artificial Chromosome) clones from Miyakojima MG-20, a reciprocal translocation was found to be responsible for the cytological differences between chromosomes 1 and 2. The borders of the translocations were identified by FISH and by alignment toward the L. filicaulis x L. japonicus Gifu B-129 linkage map. The markers from the main translocated region were located on linkage groups 1 and 2 of the two accessions, Gifu B-129 and Miyakojima MG-20, respectively. The framework of the linkage map was constructed based on codominant markers, and then dominant markers were integrated separately in each linkage group of the parents. The resulting linkage groups correspond to the six pairs of chromosomes of L. japonicus and consist of 287 markers with 487.3 cM length in Gifu B-129 and 277 markers with 481.6 cM length in Miyakojima MG-20. The map and marker information is available through the World Wide Web at http://www.kazusa.or.jp/lotus/.

To apply genomic information of the model legume Lotus japonicus to soybean, the characteristics of the soybean genome in reference to the genome of L. japonicus were investigated. Macrosynteny between soybean and L. 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 consisted of mosaics of smaller segments syntenic with the L. japonicus genome. The presence of many homoeologous regions on different soybean linkage groups was suggested from the distribution of paralogs and orthologs. 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 the linkage groups D1b, B2 and H, respectively. We revealed a significantly high level of collinearity between these BAC clones and corresponding homologous genomic regions of L. japonicus. The information of L. japonicus could be used for the development of DNA markers, map-based cloning and assembling process of genome sequencing in soybean.

Soybean fasciation is controlled by a recessive gene affecting the shape of the aerial parts of the plant, which is characterized by flattened stem, infrequent branches and clustering of flowers and pods on shoot apices. Morphological feature of the fasciation mutation has been dissected, but molecular information is still limited. We developed three populations derived from the crosses between wild type cultivars and three Japanese fasciation varieties, Shakujodaizu, Taikadaizu and Shakujomame, respectively. The molecular mapping of the three F 2 populations revealed that the fasciation locus (F locus) was mapped on the chromosome 2 (LG D1b). Fine mapping experiment with a population consisting of 1536 seeds derived from the F 2 lines segregating for fasciation revealed that a DNA marker cosegregated with the fasciation phenotype. This DNA marker was dominant for wild type allele and the flanking region of this marker could not be amplified in Shakujodaizu as well as in the other two fasciation varieties, suggesting that some deletion or major rearrangement probably occurred at the f allele. Genomic information disclosed two predicted genes, Glyma02g36940 and Glyma02g36960, that were annotated in the vicinity of this DNA marker. The relationship between these candidate genes and the fasciation phenotype was discussed.