Characterization of soybean genome based on synteny analysis with Lotus japonicus

Abstract

To apply genomic information of the model legume Lotus japonicus to soybean, the characteristics of thesoybean genome in reference to the genome of L. japonicus were investigated. Macrosynteny between soy-bean and L. japonicus was analyzed by mapping the same cDNA clones on the maps of both species by theRFLP method, and by identifying the positions of orthologs on the L. japonicus map for cDNA markers lo-cated on the soybean map. Relatively large synteny blocks were observed between a few linkage groups ofL. japonicus and soybean. The major parts of the soybean linkage groups consisted of mosaics of smallersegments syntenic with the L. japonicus genome. The presence of many homoeologous regions on differentsoybean linkage groups was suggested from the distribution of paralogs and orthologs. To investigate themicrosynteny 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, re-spectively. We revealed a significantly high level of collinearity between these BAC clones and correspond-ing homologous genomic regions of L. japonicus. The information of L. japonicus could be used for thedevelopment of DNA markers, map-based cloning and assembling process of genome sequencing in soybean.Key Words: Glycine max (L) Merrill, Lotus japonicus (Regel) Larsen, macrosynteny, microsynteny,homoeologous region, genome duplication, paralog.IntroductionThe Fabaceae family is the third largest family of an-giosperm plants including around 20000 species of legumes.The subfamily Papilionoideae incl udes agriculturally impor-tant species such as soybean, pea and common bean, andmodel legumes, Lotus japonicus and Medicago truncatula.Additionally, legumes are able to fix nitrogen through sym-biotic infection with rhizobium bacteria and are character-istized by a high protein conten t in their seeds. The genomicsof legumes enables to identify agriculturally useful genesfor efficient breeding as well as accumulation of academicknowledge.L. japonicus is a model plant for the genomics of thefamily Fabaceae, as well as M. truncatula. It displays appro-priate features as a model plant (Handberg and Stougaard1992), including diploidy, self-fertility, small genome size(432 Mb, Pedrosa et al. 2002, 442 Mb, Ito et al. 2000, 494Mb, Kawasaki and Murakami 2000), short life cycle (ap-proximately 3 months), small number of chromosomes ( n= 6)and high transformability with Agrobacterium tumefaciense.The genome resources of L. japonicus, such as thesequence and positional information of TAC/BAC clones(http://www.kazusa.or.jp/lotus/index.html), EST libraries(http://www.kazusa.or.jp/en/plant/lotus/EST/index.html), andthe complete sequence data of chloroplast and symbioticrhizobium bacteria Mesorhizobium loti (http://www.kazusa.or.jp/rhizobase/Mesorhizobium/index.html) has beenexploited. In addition to the linkage map of TAC/BACclones (http://www.kazusa.or.jp/lotus), another linkage mapof L. japonicus was also constructed using AFLP, SSR anddCAPS markers (Hayashi et al. 2001).Soybean is the most important leguminous crop in theworld. The genome size of soybean is estimated at 1.12 Gb(Arumunganathan and Earle 1991), a value approximately2.5 times larger than that of L. japonicus. It was suggestedthat the soybean genome is the product of a diploid ancestor(n = 11), whichunderwent aneuploid loss (n = 10), and sub-sequent polyploidization (Lackey 1980). The occurrence oftwo rounds of genome duplications orhybridizations andrearrangements was estimated by many researchers(Shoemaker et al. 1996, Shoemaker et al. 2002, Blanc andWolfe 2004, Schlueter et al. 2004).The rapid accumulation of genome sequence informa-tion for L. japonicus and M. truncatula provides a unique