Summary There is an increasing demand to boost photosynthesis in rice to increase yield potential. Chloroplasts are the site of photosynthesis, and increasing their number and size is a potential route to elevate photosynthetic activity. Notably, bundle sheath cells do not make a significant contribution to overall carbon fixation in rice, and thus, various attempts are being made to increase chloroplast content specifically in this cell type. In this study, we developed and applied a deep learning tool, Chloro‐Count, and used it to quantify chloroplast dimensions in bundle sheath cells of OsHAP3H gain‐ and loss‐of‐function mutants in rice. Loss of OsHAP3H increased chloroplast occupancy in bundle sheath cells by 50%. When grown in the field, mutants exhibited increased numbers of tillers and panicles. The implementation of Chloro‐Count enabled precise quantification of chloroplasts in loss‐ and gain‐of‐function OsHAP3H mutants and facilitated a comparison between 2D and 3D quantification methods. Collectively, our observations revealed that a mechanism operates in bundle sheath cells to restrict chloroplast occupancy as cell dimensions increase. That mechanism is unperturbed in Oshap3H mutants but loss of OsHAP3H function leads to an increase in chloroplast numbers. The use of Chloro‐Count also revealed that 2D quantification is compromised by the positioning of chloroplasts within the cell.

中文翻译：

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Chloro-Count 揭示了 ricehap3Hmutants 束鞘细胞中叶绿体占有率的增加：一种基于深度学习的新工具


摘要 促进水稻光合作用以提高产量潜力的需求越来越大。叶绿体是光合作用的场所，增加它们的数量和大小是提高光合作用活性的潜在途径。值得注意的是，束鞘细胞对水稻的整体碳固定没有显着贡献，因此，正在进行各种尝试来增加该细胞类型中的叶绿体含量。在这项研究中，我们开发并应用了一种深度学习工具 Chloro-Count，并使用它来量化水稻中 OsHAP3H 获得和功能丧失突变体的束鞘细胞中的叶绿体尺寸。OsHAP3H 的缺失使束鞘细胞中的叶绿体占有率增加了 50%。当在田间生长时，突变体表现出更多的分蘖和圆锥花序。Chloro-Count 的实施能够精确定量功能丧失和功能获得性 OsHAP3H 突变体中的叶绿体，并促进了 2D 和 3D 定量方法之间的比较。总的来说，我们的观察揭示了一种机制在束鞘细胞中起作用，以随着细胞尺寸的增加而限制叶绿体的占据。该机制在 Oshap3H 突变体中不受干扰，但 OsHAP3H 功能的丧失导致叶绿体数量的增加。Chloro-Count 的使用还揭示了 2D 定量会受到细胞内叶绿体定位的影响。