Institute of Crop Science, NARO

Soybean Genomics

Soybean is one of the most important grain crops as a staple source of nutritious vegetable protein and oil for humans and livestock. Additionally, it provides industrial materials and biofuel. In Japan, soybean is an important source of traditional foods such as tofu, natto, miso and soy sauce. We have developed new strategies for effective soybean breeding through 1) analysis of the genome structure of Japanese (domestic) soybean, 2) development of DNA markers serving as landmarks of agronomically important traits, 3) development of research resources for the identifi cation of important genes in soybean, and 4) isolation of genes controlling traits of importance such as disease and pest resistance, productivity, and regional adaptability through maturity control.

  • Sequencing of the Japanese soybean cultivar 'Enrei'
  • Soybean genome database and resources
  • Identification of important soybean genes and development of new strategies for effective breeding
  • Sequencing of the Japanese soybean cultivar 'Enrei'

    To establish the basic research resources for whole genome analysis and domestic soybean breeding, we have sequenced the entire genome of a Japanese soybean cultivar 'Enrei' with a next-generation sequencer, Roche/454 GS-FLX Titanium. The sequenced genome size of soybean is 950 Mb. After sequencing and assembling the whole genome shotgun sequence data, we obtained an 'Enrei' data set with about 800 Mb total bases and 221,674 contigs with an average size is 3.6 kb. This sequence has a high quality score for each nucleotide, so it is appropriate to use in searching for differences in single nucleotide polymorphisms and insertions/deletions between genomes of 'Williams 82' and 'Enrei'. These sequence data, the derived SNPs and In/Dels, and additional data will be installed into the previously reported DaizuBase. DaizuBase includes "Unified map", which indicates the relationship between the linkage map and the physical map, and "Gbrowse", which exhibits aligned Enrei-BAC clones on the Glyma 1 assembly, and facilitates comparative genome analyses. It will show 'Enrei' draft genome sequence data. Next, we attempted to develop a method for comparative analysis among domestic soybeans. The fragmented DNAs prepared from domestic soybean were hybridized with synthetic oligonucleotides designed from end-sequences of mapped Enrei-BAC clones by the NimbleGen sequence capture method. Hybridized DNA was recovered and sequenced with Roche/454 GS-FLX Titanium. To validate this method, sequenced data were assembled and mapped by Blast searches of DaizuBase. Captured sequences corresponded well to the original BAC sequences (Fig. 1), suggesting that this method is suitable for genome-wide analysis of target regions in domestic soybeans.

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    Soybean genome database and resources

    We have developed DaizuBase as repository of the Enrei sequence data, genetic maps, SNPs and In/Dels, and other genome data. DaizuBase includes "Unified map", which indicates the relationship between the linkage map and the physical map, and "Gbrowse", which exhibits aligned Enrei-BAC clones on the Glyma 1 assembly, and facilitates comparative genome analyses. It will show 'Enrei' draft genome sequence data. Next, we attempted to develop a method for comparative analysis among domestic soybeans. The fragmented DNAs prepared from domestic soybean were hybridized with synthetic oligonucleotides designed from end-sequences of mapped Enrei-BAC clones by the NimbleGen sequence capture method. Hybridized DNA was recovered and sequenced with Roche/454 GS-FLX Titanium. To validate this method, sequenced data were assembled and mapped by Blast searches of DaizuBase. Captured sequences corresponded well to the original BAC sequences, suggesting that this method is suitable for genome-wide analysis of target regions in domestic soybeans.

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    Identification of important soybean genes and development of new strategies for effective breeding

    Flowering represents the transition from the vegetative to reproductive phase in plants. Various external cues, for example photoperiod and temperature, are known to initiate plant flowering under the appropriate seasonal conditions. Of these cues, photoperiod sensitivity is one of the important keys that enable crops to adapt to a wide range of latitudes. In soybean, several maturity genes designated as E genes have been identified. Out of these maturity genes, one flowering quantitative trait locus, FT2, corresponding to the maturity locus E2, was detected in recombinant inbred lines (RIL) derived from cultivars 'Misuzudaizu' (e2/e2) and 'Moshidou Gong 503' (E2/E2). A map-based cloning strategy using the progeny of a residual heterozygous line (RHL), showing a simple segregation pattern for a target QTL, was employed to isolate the gene responsible for this QTL. A fine mapping experiment based on one RHL containing 888 plants showed that the E2 locus was delimited in a single BAC clone covering a 94-Kbp region on chromosome 10 (Gm10). In this physical region, a GIGANTEA ortholog, GmGIa (Glyma10g36600), was identified as a candidate gene. Phylogenic analysis showed that soybean GI proteins displayed a high level of similarity (71% to 91%) to GI proteins from dicots and monocots. The comparison of donors for dominant and recessive alleles indicates a common premature stop codon at the tenth exon was present in the Misuzudaizu allele and in other NILs originating from 'Harosoy' (e2/e2). Furthermore, a mutant line harboring another premature stop codon showed an earlier flowering phenotype than the original variety, 'Bay' (E2/E2). The e2/e2 genotype exhibited elevated expression of GmFT2a, one of the florigen genes that lead to early flowering. The effects of the E2 gene on flowering time were similar among NILs (4.0-5.0 days) and stable under high (43oN) and middle (36oN) latitudinal regions in Japan. These results indicate that GmGIa is the gene responsible for the E2 locus and that a null mutation in GmGIa may contribute to the geographic adaptation of soybean.

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