Flowering time (FT) and plant height (PH) are important agronomic traits in soybean. However, their genetic foundations are not fully understood. Thus, in this study, a total of 106,013 single nucleotide polymorphisms in 286 soybean accessions were used to associate with the first and full FT (FT1 and FT2) and PH in 4 environments and their BLUP values using 6 multi-locus genome-wide association study methods. As a result, 38, 43, and 27 stable quantitative trait nucleotides (QTNs) were identified, respectively, for FT1, FT2, and PH across at least 3 methods and/or environments. Among these QTNs for FT1, FT2, and PH, 31, 36, and 21 were found to have significant phenotype differences across 2 alleles; 22, 18, and 13 were consistent with the corresponding loci in previous studies; 13 and 8 genes, with more than average expression level, around 64 FT and 27 PH QTNs were predicted as their corresponding candidate genes. Among these candidate genes, GmPRR3b, and GmGIa for FT, and GmTFL1b for PH were known, while some were new, e.g., GmPHYA4, GmVRN5, GmFPA, and GmSPA1 for FT, and Glyma.02g300200, GmFPA, and Glyma.13g339800 for PH. All the validated QTNs were used to design the best cross-combinations in 2 FT directions. In each FT direction, the best 5 cross-combinations were predicted, such as Heihe 54 × Qincha 1 for early FT, and Yingdejiadou × Wuhuabayuehuang for late FT. This study provides solid foundations for genetic basis, molecular biology, and breeding by design of soybean FT and PH.

开花时间（FT）和株高（PH）是大豆重要的农艺性状。然而，它们的遗传基础尚未完全了解。因此，在本研究中，使用 6 个多位点全基因组关联，使用 286 个大豆品种中总共 106,013 个单核苷酸多态性与 4 个环境中的第一个和完整 FT（FT1 和 FT2）和 PH 及其 BLUP 值相关联研究方法。结果，在至少 3 种方法和/或环境中，分别鉴定了 FT1、FT2 和 PH 的 38、43 和 27 个稳定数量性状核苷酸 (QTN)。在 FT1、FT2 和 PH 的这些 QTN 中，发现 31、36 和 21 在 2 个等位基因上具有显着的表型差异；22、18、13与前期研究对应位点一致；13和8个基因的表达水平高于平均水平，大约64个FT和27个PH QTN被预测为其相应的候选基因。在这些候选基因中，FT的GmPRR3b和GmGIa以及PH的GmTFL1b是已知的，而一些候选基因是新的，例如FT的GmPHYA4 、 GmVRN5 、 GmFPA和GmSPA1，以及PH的Glyma.02g300200、GmFPA和Glyma.13g339800。所有经过验证的 QTN 均用于设计 2 个 FT 方向的最佳交叉组合。在每个FT方向上，预测了最好的5个杂交组合，如早期FT的黑河54×秦茶1，晚期FT的英德甲豆×五花八月黄。本研究通过大豆 FT 和 PH 的设计，为遗传基础、分子生物学和育种提供了坚实的基础。