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The mature soybean plants are of complex architecture with pods frequently touching each other, posing a challenge for in-situ segmentation of on-branch soybean pods. Deep learning-based methods can achieve accurate training and strong generalization capabilities, but it demands massive labeled data, which is often a limitation, especially for agricultural applications. As lacking the labeled data to train an in-situ segmentation model for on-branch soybean pods, we propose a transfer learning from synthetic in-vitro soybean pods. First, we present a novel automated image generation method to rapidly generate a synthetic in-vitro soybean pods dataset with plenty of annotated samples. The in-vitro soybean pods samples are overlapped to simulate the frequently physically touching of on-branch soybean pods. Then, we design a two-step transfer learning. In the first step, we finetune an instance segmentation network pretrained by a source domain (MS COCO dataset) with a synthetic target domain (in-vitro soybean pods dataset). In the second step, transferring from simulation to reality is performed by finetuning on a few real-world mature soybean plant samples. The experimental results show the effectiveness of the proposed two-step transfer learning method, such that AP$_{50}$ was 0.80 for the real-world mature soybean plant test dataset, which is higher than that of direct adaptation and its AP$_{50}$ was 0.77. Furthermore, the visualizations of in-situ segmentation results of on-branch soybean pods show that our method performs better than other methods, especially when soybean pods overlap densely.