In yam (Dioscorea spp) species, bulbils at leaf axils are the most striking species-specific axillary structure and exhibit important ecological niches. Genetic regulation underlying bulbil growth remains largely unclear so far. Here, we characterize yam (Dioscorea alata L.) bulbil development using histological analysis, and perform full transcriptional profiling on key developmental stages together with phytohormone analyses. Using the stage-specific scoring algorithm, we have identified 3451 stage-specifically expressed genes that exhibit a tight link between major transcriptional changes and stages. Co-expressed gene clusters revealed an obvious over-representation of genes associated with cell division and expansion at the initiation stage of bulbils (T1). Transcriptional changes of hormone-related genes highly coincided with hormone levels, indicating that bulbil initiation and growth are coordinately controlled by multiple phytohormones. In particular, localized auxin is transiently required to trigger bulbil initiation, and be further depleted or exported from bulbils to promote growth by up-regulation of genes involved in auxinconjugation and efflux. The sharp increase in supply of sucrose and an enhanced trehalose-6-phophate pathway at T1 were observed, suggesting that sucrose probably functions as a key signal and promotes bulbil initiation. Analysis of the expression of transcription factors (TFs) predicated 149 TFs as stage-specifically expressed; several T1-specific TFs (from Aux/IAA, E2F, MYB, and bHLH families) have been shown to play key roles in triggering bulbil formation. Together, our work provides a crucial angle for in-depth understanding of the molecular programs underlying yam’s unique bulbil development processes. Stage-specific gene sets can be queried to obtain key candidates regulating bulbil growth, serving as valuable resources for further functional research.

中文翻译：

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形态学和阶段特异性转录组分析揭示了山药（Dioscorea alata L.）珠芽生长的不同调控程序。


在山药（薯蓣属）物种中，叶腋处的珠芽是最引人注目的物种特异性腋窝结构，并表现出重要的生态位。迄今为止，珠芽生长背后的基因调控在很大程度上仍不清楚。在这里，我们使用组织学分析来表征山药（Dioscorea alata L.）珠芽的发育，并在关键发育阶段进行完整的转录分析以及植物激素分析。使用阶段特异性评分算法，我们鉴定了 3451 个阶段特异性表达基因，这些基因在主要转录变化和阶段之间表现出紧密的联系。共表达基因簇揭示了与珠芽起始阶段（T1）细胞分裂和扩张相关的基因明显过度表达。激素相关基因的转录变化与激素水平高度一致，表明珠芽的起始和生长受到多种植物激素的协调控制。特别是，局部生长素短暂地需要触发珠芽起始，并进一步耗尽或从珠芽中输出，以通过上调参与生长素结合和流出的基因来促进生长。在 T1 观察到蔗糖供应的急剧增加和海藻糖-6-磷酸途径的增强，表明蔗糖可能作为关键信号发挥作用并促进珠芽的形成。转录因子 (TF) 表达分析表明 149 个 TF 为阶段特异性表达；一些 T1 特异性转录因子（来自 Aux/IAA、E2F、MYB 和 bHLH 家族）已被证明在触发珠芽形成中发挥关键作用。我们的工作共同为深入了解山药独特的珠芽发育过程背后的分子程序提供了一个关键的角度。 可以查询特定阶段的基因集以获得调节珠芽生长的关键候选基因，作为进一步功能研究的宝贵资源。