Acceleration of Soybean Genomics Using Large Collections of DNA Markers for Gene Discovery

Abstract

Legumes are known to provide nutritious proteins and vegetable oils while at the same time providing industrial products such as biodiesel. It is estimated that approximately 25% of world crop production is derived from legumes. Recently, knowledge of the molecular biology and genomics of legumes have been extended significantly using two model species, Lotus japonicus (http://www.kazusa.or.jp/lotus/) and Medicago truncatula (http://www.medicago.org/genome/). Genome sequencing of these two legumes will be completed soon and is expected to contribute to the identification and isolation of important genes involved in nitrogen fixation, seed productivity and so on. Many legume species possess the ability to establish symbiosis with nitrogen-fixing bacteria and key genes involved have been extensively studied through genomic approaches. Discovery of genes in legume plants is progressing rapidly and is yielding improved quantity and quality for industrial as well as agricultural uses (see http://intl.plantphysiol.org/cgi/collection/legume_biology). Soybean is undoubtedly the most important legume crop in the world. It is important in Japan for the production of traditional foods such as tofu, miso, shoyu and vegetable oil. Therefore, its agronomical characteristics have been analyzed at the molecular level to speed-up its breeding for various uses. In the past decade, plant genome analyses using model organisms have provided a large amount of genomic information and various categories of knowledge for gene functions: genome sequence, collection of expressed sequence tags (ESTs) and DNA markers are widely exploited for the discovery of genes. Soybean has a large genome of 1,115 Mbp with 2n = 40 that contains complex regional duplications. Several types of genome projects including linkage map production have been initiated to uncover its complex genomic structure and to help gene discovery. As for the EST collection, soybean has the sixth largest collection of more than 390,000 sequences (http://www.ncbi.nlm.gov/dbEST). Transcriptional maps with single nucleotide polymorphism (SNP) markers have been published using EST information. Recently, whole genome sequencing of soybean has started in the USA, using a shotgun sequencing strategy (http://soybeangenome.siu.edu, http://www.agbionetwork.org/∼soybeangenome/GSA.php). For the genetic and genomic analyses of the soybean genome, precise genetic and physical maps are important. Indeed, various types of physical maps have so far been reported using RFLP, RAPD, SSR and AFLP markers. Two important papers in this issue by Hisano et al. (doi:10.1093/dnares/dsm025) and by Xia et al. (doi:10.1093/dnares/dsm027) report on the collection of large numbers of soybean DNA markers and their precise map using a hybrid between the Japanese cultivar ‘Misuzudaizu’ and the Chinese line ‘Moshidou Gong 503’. Hisano et al. used microsatellite markers obtained from the public EST databases to generate a high-density linkage map of the soybean genome. They mapped 935 marker loci in 20 linkage groups. The method is efficient to produce a large number of DNA markers based on EST database. They found macrosynteny in various segments between soybean and L. japonicus. Their comparative analysis revealed the occurrence of significant genome shuffling during evolution after the separation of two species. Xia et al. reported an updated linkage map using AFLP, SSR, RFLP and STS markers and integrated the map with the previous one reported by the author's group. The updated map is expected to be useful for efficient positional cloning of agronomically important QTL genes. Sequencing of the soybean genome and the model legume species will provide us with a large amount of information for useful genes. Recently, a soybean genome sequence project was also started in Japan using a Japanese cultivar ‘Enrei’. More than 10,000 independent full-length cDNAs have been collected from various organs and stress-treated soybean. The reports in this issue will be useful for future functional analysis of genes involved in soybean productivity.