Table_8_Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress.XLSX

Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis–antenna proteins, plant–pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.

花生是一种全球广泛种植、具有重要经济价值的油料作物，其地上开花、地下结果。当果针穿透土壤后，会进入黑暗环境并承受来自土壤的机械胁迫，进而发育为正常荚果；若新发育的荚果露出土壤，则会变绿并停止生长。已有研究表明，黑暗环境与机械胁迫均为荚果正常发育所必需。本研究针对果针穿透土壤的逆向过程——即挖出Pattee 3期荚果引发的发育停滞——开展基因表达变化分析：通过套袋地上荚果模拟机械胁迫缺失，直接暴露地上荚果则模拟机械胁迫与黑暗环境同时缺失。在失去机械胁迫与黑暗环境后，差异表达基因（Differentially Expressed Genes, DEGs）显著富集于光合作用、光合作用-天线蛋白、植物-病原体互作、DNA复制以及昼夜节律通路。其中DNA复制通路由下调基因富集而成，其余四条通路则由上调基因富集而成。上调基因同时显著富集于蛋白质泛素化与钙调蛋白相关基因，凸显了泛素化与钙信号通路在荚果发育中的重要作用。对差异表达基因的进一步分析显示，光敏色素A（Phy A）、生长素响应因子9（IAA9）以及机械敏感离子通道蛋白在地下结实（geocarpy）过程中发挥重要作用，地下荚果中这些基因的表达量上调，而地上荚果中则下调。基于本研究中鉴定到的大量叶绿体相关基因、钙调蛋白、激酶以及泛素相关蛋白，我们提出了两条参与花生地下结实的潜在信号转导通路：一条始于叶绿体，通过磷酸化向下传递信号；另一条始于非生物胁迫，通过钙信号通路、磷酸化与泛素化向下传递信号。本研究为花生荚果发育的潜在调控基因提供了宝贵信息，有助于进一步理解地下结实这一生物学现象。