Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon 34141, Republic of Korea.
Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea.
G3 (Bethesda). 2024 Aug 7;14(8). doi: 10.1093/g3journal/jkae118.
Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts.
大豆是一种重要的农业作物，以其高蛋白和高油含量而闻名，对人类的营养和健康有重要的益处。大豆在中国已有 5000 多年的栽培历史，现已适应了不同的环境，并在世界各地广泛种植。本研究旨在调查来自中国、韩国、日本、欧洲、北美和南美等不同地理区域的 2317 个公开可用的大豆全基因组序列的基因组特征和群体结构。我们使用大规模全基因组测序数据进行高分辨率分析，以揭示大豆品系的遗传特征。来自中国和韩国的大豆品系具有地方品种的特征，表明其具有更高的遗传多样性和对当地环境的适应性。另一方面，来自日本、欧盟和南美洲的大豆品系由于人工选择和农艺性状的选育，遗传多样性较低。我们还确定了与适应不同环境相关的关键变异和基因。在韩国大豆品系中，我们观察到异黄酮合成的强烈选择信号，这是一个适应特征，通过减轻环境压力，对提高大豆的适应性、生存能力和繁殖成功率至关重要。观察到与异黄酮合成相关的基因 HIDH、CYP73A11、IFS1 和 CYP81E11 等基因的独特选择模式的特定基因组区域，为潜在的适应机制提供了有价值的见解。我们的研究极大地提高了我们对遗传水平上大豆多样性的理解。我们已经确定了影响适应性的关键遗传变异和基因，为基于基因组学的育种计划和作物改良工作的未来进展奠定了基础。
