Lotus japonicus is a model legume used by researchers worldwide to study nodulation and other aspects of legume biology. We investigated 15 morphological traits in a large collection of wild L. japonicus accessions collected in Japan, and also analyzed the genetic diversity among them, in order to develop a core collection based on genome-wide SSR polymorphisms. We found a wide diversity of morphological traits among the accessions. A total of 321 putative alleles were detected using 25 SSR primer pairs. The average observed and expected heterozygosity scores for individual loci were 0.014 and 0.772, respectively, indicating a high degree of homozygosity. The accessions were divided into 9 clusters based on G ST ' and STRUCTURE analyses. In addition, we selected 20 accessions to serve as the representative core collection based on SSR analysis. The range of morphological traits in the core collection was representative of that found in the entire collection. This core collection will be useful for genome-wide studies and data obtained for this model species should lead to numerous practical applications for crop legumes. All accessions from the entire collection are available from Legume Base (http://www.legumebase.brc.miyazaki-u.ac.jp/), a section of the National BioResource Project in Japan.

Summary Lotus is a leguminous and cosmopolitan genus in the Loteae tribe consisting of more than 200 species. The number of chromosomes has been reported for many Lotus species; however, molecular studies have focused only on a few important species of this genus. The present study was conducted to estimate the genome size and ploidy levels of 28 Lotus accessions, and to identify their genetic diversity using inter-simple sequence repeat (ISSR) analysis. The chromosome number of 16 accessions agreed with previous reports (except for Lotus salsuginosus), while that in 11 accessions were reported here for the first time. The smallest nuclear DNA content was identified in the diploid, Lotus unifoliolatus (0.28 0.01 pg C 1 ). In contrast, the tetraploid, Lotus australis, had a genome size of 1.28 0.03 pg C 1 , representing a five-fold difference in genome size among the Lotus species. When expressed as a per Cx value, Lotus species genome sizes ranged from 0.28 pg Cx 1 in L. unifoliolatus to 0.71 pg Cx 1 in Lotus wrightii, representing a 2.5-fold difference. There was no relationship between genome size and chromosome number or ploidy level; thus, genome size is species specific in the Lotus species. On ISSR analysis, a total of 379 fragments were generated with 12 primers, and all accessions were grouped into four clusters by phylogenetic analysis. The results of this investigation will be useful for plant breeders attempting to expand the genetic variation found in this species by crossbreeding using these resources.