Yang Ming, Wang Yixing
Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, United States.
PeerJ. 2025 Jul 7;13:e19599. doi: 10.7717/peerj.19599. eCollection 2025.
Maternal auxin signaling inhibits seed germination in , but little is known about the gene network that mediates the inhibition of seed germination by auxin. Based on publicly available data, we first determined the expression patterns of () genes in the funiculus (FUN)-chalazal seed coat (CSC) continuum. We found that , , and exhibited a down-expression gradient and , , and an up-expression gradient from FUN to CSC, and members in each of the two groups were linearly correlated in expression in FUN, CSC, and the distal seed coat (DSC). We then searched for auxin-regulated genes that exhibited one of the two expression gradients. We found 118 such genes that were assigned into four groups based on their response mode to auxin and expression gradient direction. The four groups were further broken down into 12 subgroups based on the linear correlation coefficient values. Only three of the 12 subgroups, including a total of 30 genes with 21 of them being known or highly likely to function in the seed germination process. To explore whether additional genes of the remaining nine play roles in seed germination, we tested mutants of five of them in a germination assay and found all of them exhibited either delayed or hastened germination. The experimental results support the validity of our approach for predicting the involvement of these genes in seed germination. Based on publicly available data and data from this investigation, we constructed a gene network, which should provide a valuable framework and new clues for future studies of the molecular mechanism controlling seed germination.
母体生长素信号传导抑制种子萌发，但对于介导生长素对种子萌发抑制作用的基因网络了解甚少。基于公开可用的数据，我们首先确定了（）基因在珠柄（FUN）-合点种皮（CSC）连续体中的表达模式。我们发现，从FUN到CSC，、和呈现出表达下调梯度，而、和呈现出表达上调梯度，并且两组中的每一组成员在FUN、CSC和远端种皮（DSC）中的表达呈线性相关。然后，我们搜索了呈现出这两种表达梯度之一的生长素调节基因。我们发现了118个这样的基因，根据它们对生长素的反应模式和表达梯度方向将其分为四组。这四组又根据线性相关系数值进一步细分为12个亚组。12个亚组中只有3个，总共包含30个基因，其中21个已知或极有可能在种子萌发过程中发挥作用。为了探究其余9个亚组中的其他基因是否在种子萌发中起作用，我们在萌发试验中测试了其中5个基因的突变体，发现它们都表现出萌发延迟或加速。实验结果支持了我们预测这些基因参与种子萌发的方法的有效性。基于公开可用的数据和本研究的数据，我们构建了一个基因网络，这应该为未来控制种子萌发分子机制的研究提供一个有价值的框架和新线索。
