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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形态学和特定阶段的转录组分析揭示了山药（Dioscorea alata L.）球茎生长的不同调控程序。

在山药（Dioscorea spp）物种中，叶腋的鳞茎是最引人注目的物种特有的腋生结构，并表现出重要的生态位。迄今为止，关于鳞茎生长的遗传调控仍不清楚。在这里，我们使用组织学分析表征山药（Dioscorea alata L.）鳞茎发育，并在关键发育阶段进行完整的转录谱分析，并进行植物激素分析。使用阶段特定的评分算法，我们已经确定了3451个阶段特定表达的基因，它们在主要的转录变化和阶段之间表现出紧密的联系。共表达的基因簇揭示了在胚芽（T1）起始阶段与细胞分裂和扩增相关的基因的过度表达。激素相关基因的转录变化与激素水平高度吻合，表明鳞茎的起始和生长受多种植物激素协调控制。特别地，短暂地需要局部生长素来触发球茎启动，并且通过上调生长素结合和外排的基因上调来进一步减少球茎中的生长素或将其从球茎中输出以促进生长。观察到蔗糖供应的急剧增加和T1处海藻糖-6磷酸途径的增强，这表明蔗糖可能起关键信号的作用并促进了鳞茎的起始。分析转录因子（TFs）的表达可预测有149个TFs为阶段特异性表达；几个T1特异的TF（来自Aux / IAA，E2F，MYB和bHLH家族）已显示在触发球茎形成中起关键作用。一起，我们的工作为深入了解山药独特的球茎发育过程的分子程序提供了一个至关重要的角度。可以查询特定阶段的基因集，以获得调节球茎生长的关键候选基因，为进一步的功能研究提供宝贵的资源。