Phosphorus (P) is essential for the growth and development of plants, playing crucial roles in energy acquisition, storage and utilization, regulation of enzyme activities, and yield formation. Therefore, P deficiency in soil is a main factor restricting crop production. The main reason is that crop yields depend on photosynthesis which is vulnerable to low P stress. Thus, it is important to study the relationship between photosynthesis and P efficiency. In this study, we evaluated the P efficiency by using the photosynthesis-related traits in 219 diverse soybean accessions across three different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). In total, 30 significant SNPs distributed in 14 genomic regions were identified to be associated with three photosynthesis-related traits under different P levels. Among the 14 associated regions, two regions (qP13 and qP19) were both found in two environments and explained 14.01% and 16.75% of the phenotypic variation, respectively. Furthermore, seven candidate genes underlying qP13 and qP19 were considered promising candidates involved in both soybean photosynthetic and low P tolerance. In all, we uncover two novel environmentally stable major genomic regions of P efficiency by using photosynthesis-related traits, which may provide more information for marker-assisted breeding in soybean and laying the foundation for simultaneously improving P efficiency and photosynthetic capacity.

磷（P）对于植物的生长和发育至关重要，在能量获取，存储和利用，酶活性的调节以及产量形成中起着至关重要的作用。因此，土壤中的磷缺乏是限制作物产量的主要因素。主要原因是农作物的产量取决于光合作用，而光合作用容易受到低磷胁迫的影响。因此，研究光合作用与磷效率之间的关系很重要。在这项研究中，我们通过在三个不同环境中使用219种不同大豆种质的光合作用相关性状，评估了磷的效率，并使用高分辨率全基因组关联研究（GWAS）剖析了其潜在机制。总共，确定了分布在14个基因组区域的30个重要SNP与不同P水平下的三个与光合作用相关的性状相关。在14个相关区域中，有两个区域（qP13和qP19）均在两种环境中发现，分别解释了表型变异的14.01％和16.75％。此外，qP13和qP19的7个候选基因被认为与大豆光合作用和低P耐性有关。总之，我们利用光合作用相关性状揭示了两个新的环境稳定的P效率环境稳定的主要基因组区域，它们可能为大豆的标记辅助育种提供更多信息，并为同时提高P效率和光合能力奠定基础。