BACKGROUND Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.

中文翻译：

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根据基于全基因组序列的选择特征对大豆群体进行剖析。

背景技术驯化和改良过程，伴随着选择和适应，已经在大豆群体中产生了全基因组的分化和分层。同时，由不同亚种群组成的大豆种群已经形成了自己的适应性特征，增强了适应性、抗性、农艺性状和形态特征。这些特性背后的遗传性状在改善其他大豆种群方面发挥着重要作用。结果本研究的重点是确定大豆群体的选择特征和适应性特征。从 4,234 个大豆种质中选出的 245 个核心种质（112 个野生型、79 个地方品种和 54 个改良大豆）被重新测序。根据驯化和改良对它们的基因组结构进行了检查，然后根据各种种群分析将材料分为 3 个野生型、2 个地方品种和 2 个改良亚组。选择和基因集富集分析表明，地方品种亚群分别具有大豆胞囊线虫HG 0型和种子发育与萌发的选择信号，改良亚群分别具有植物活力发育和种子发育与胚胎发育的选择信号。大豆胞囊线虫的适应性特征部分受到多种抗性材料的支持，与种子发育相关的特征得到了我们对种子重量的表型发现的支持。此外，它们的适应性特征也被证实为基于基因组的证据，并且揭示了 13 个候选基因表现出不同选择和选择性扫描模式的独特基因组区域。结论 尽管我们的研究结果需要进一步的生物学验证，但它们提供了有关大豆育种策略的宝贵信息，并为寻求供体系以改善大豆种群的育种者提供了新的选择。