日本作物科学研究所Masao Ishimoto团队取得一项新突破。他们研究出日本和全球大豆甘氨酸max品种基因水平结构变异的基因组景观。2025年3月3日出版的《自然—遗传学》发表了这项成果。

为了研究它们独特的基因组特征，包括基因组结构变异（SVs），该课题组人员构建了11个基于纳米孔的日本大豆和其他大豆品系基因组参考。他们基于组装的比较方法Asm2sv全面鉴定了基因水平的SV，使全球462个栽培品种和品种的全基因组分析成为可能。在此基础上，研究人员确定了日本和美国大豆之间的选择性扫描，其中一个是抗豆荚基因PDH1。

全基因组关联研究进一步确定了几个数量性状位点，这些位点可以解释日本大豆系的大种子表型，其中一些位点也接近选择性扫描的区域，包括PDH1。值得注意的是，等位基因的特定组合，包括SVs，被发现增加了一些日本地方品种的种子大小。除了种植环境的差异外，不同的食品加工方式也可能导致日本大豆基因组的变化。

据悉，传统上，日本种植大豆是为了生产豆腐、味噌和煮大豆等大豆食品。

附：英文原文

Title: The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars

Author: Yano, Ryoichi, Li, Feng, Hiraga, Susumu, Takeshima, Ryoma, Kobayashi, Michie, Toda, Kyoko, Umehara, Yosuke, Kajiya-Kanegae, Hiromi, Iwata, Hiroyoshi, Kaga, Akito, Ishimoto, Masao

Issue&Volume: 2025-03-03

Abstract: Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated ‘Asm2sv’, identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.

DOI: 10.1038/s41588-025-02113-5

Source: https://www.nature.com/articles/s41588-025-02113-5