Soybean (Glycine max), in Japanese word 'Daizu', is one of the most important crops in the world. Its production is strongly associated with food security concerns as it is utilized not only as a material for oil production but also as a source of livestock feed. In Japan, there are several well-known traditional soyfoods such as Miso, Tofu, Natto, and Edamame. Herein, large seed size, round seed shape, as well as high protein content have been important breeding target in JP soybean cultivars. The NARO institute has been working on genomics research of some JP standard cultivars such as 'Enrei' and 'Fukuyutaka'. In 2015, the contig dataset of the cv. 'Enrei' was published based on Roche 454 platform (Enrei V2). To further promote data-driven breeding as well as functional genomics research of soybean, we completely renewed the 'Enrei' genome reference by combining long read Oxford Nanopore, BioNano, and Hi-C. This reference designated 'Enrei V3' contains 59K protein-coding genes with the complete protein BUSCO5 values of 99.8%. The main purpose of this 'Daizu-net' web database is to provide information of the Enrei V3 reference (e.g. sequence information of each gene, evidence of the consensus gene ID). Currently, several web applications are available as listed below.
[Contact] naro_soybean_resource [-at-] ml.affrc.go.jp
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News! Our paper has been published. Please cite the following paper:
- Yano et al. (2025) The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars. DOI: 10.1038/s41588-025-02113-5
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updated
[18th Jan, 2024] Added EST alignment to Enrei v3.31 (GFF=3.32) and Wm82 508v4.
[8th June, 2023] Dotplot view is available for 41 genome assemblies including 7 NARO genomes [based on Enrei v3.31 (GFF=3.32)].
*Example of dotplot view between Enrei_ver3.31 and Wm82 508v4.
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[12th June, 2023] Published resequencing dataset of 208 lines including NARO core collection is available.
[12th June, 2023] Published resequencing dataset of 491 lines including NARO core collection and US cultivars is available.
*Depth data is inserted only for Enrei v3.31 reference.
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updated
[9th Jan, 2024] Haplotype analysis function has been added.
[12th June, 2023] Published resequencing dataset of 208 lines including NARO core collection is available.
[12th June, 2023] Published resequencing dataset of 491 lines including NARO core collection and US cultivars is available.
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[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
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[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
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[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
[24th Jul, 2023] Short read mapper : Multi-reference serach mode has been implemented.
[19th Jul, 2023] BLAST : Gene ID query mode is enabled for several soybean genomes or other plant species including Arabidopsis and rice.
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updated
[9th Jab, 2024] Bugs fixed and updated datasets based on Enrei v3.31 (GFF=3.32).
[18th Aug, 2023] Updated gene-level synteny view function.
[8th July, 2023] Updated multi-genome synteny view function.
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*preview version, distict research project (external server)
[13th Apr, 2023] Co-expression dataset of 44 RNA-seq (22 tissues, Enrei and Williams82) based on Enrei v3.31 (GFF=3.32).
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