Mature pod color (PC) and pod size (PS) served as important characteristics are used in the soybean breeding programs. However, manual phenotyping of such complex traits is time-consuming, laborious, and expensive for breeders. Here, we collected pod images from two different populations, namely, a soybean association panel (SAP) consisting of 187 accessions and an inter-specific recombinant inbred line (RIL) population containing 284 RILs. An image-based phenotyping method was developed and used to extract the pod color- and size-related parameters from images. Genome-wide association study (GWAS) and linkage mapping were performed to decipher the genetic control of pod color- and size-related traits across 2 successive years. Both populations exhibited wide phenotypic variations and continuous distribution in pod color- and size-related traits, indicating quantitative polygenic inheritance of these traits. GWAS and linkage mapping approaches identified the two major quantitative trait loci (QTL) underlying the pod color parameters, i.e., qPC3 and qPC19, located to chromosomes 3 and 19, respectively, and 12 stable QTLs for pod size-related traits across nine chromosomes. Several genes residing within the genomic region of stable QTL were identified as potential candidates underlying these pod-related traits based on the gene annotation and expression profiling data. Our results provide the useful information for fine-mapping/map-based cloning of QTL and marker-assisted selection of elite varieties with desirable pod traits.

成熟豆荚颜色 (PC) 和豆荚大小 (PS) 作为重要特征用于大豆育种计划。然而，对育种者来说，对这种复杂性状进行手动表型分析既费时、费力、又昂贵。在这里，我们收集了两个不同群体的豆荚图像，即由 187 个种质组成的大豆关联组 (SAP) 和包含 284 个 RIL 的种间重组自交系 (RIL) 群体。开发了一种基于图像的表型分析方法，并用于从图像中提取与豆荚颜色和大小相关的参数。通过连续两年的全基因组关联研究（GWAS）和连锁图谱来破译荚果颜色和大小相关性状的遗传控制。两个种群都表现出广泛的表型变异以及豆荚颜色和大小相关性状的连续分布，表明这些性状的数量多基因遗传。GWAS 和连锁作图方法确定了荚果颜色参数背后的两个主要数量性状基因座 (QTL)，即qPC3和qPC19，分别位于 3 号和 19 号染色体上，以及跨 9 条染色体的 12 个与荚果大小相关性状的稳定 QTL。根据基因注释和表达谱数据，稳定 QTL 基因组区域内的几个基因被鉴定为这些荚果相关性状的潜在候选基因。我们的结果为QTL的精细作图/基于图谱的克隆和具有理想荚果性状的优良品种的标记辅助选择提供了有用的信息。