植物，一種不具備自由移動能力的生物，不時會面對來自外在環境的各種生物性與非生物性刺激。受逆境刺激而反應的基因，是植物適應環境變遷的重要機制之一。此篇研究的主要重點在於藉由綜合轉錄體資料分析，揭露環境逆境下，植物的共通性與特殊性基因轉錄調控。
在此利用過去已經公開發表的水稻轉錄體資料進行研究，其為水稻根部組織受三種根際毒性物質（鉻、汞及阿魏酸）處理，探討轉錄體的迅速與延遲性反應。在共通性基因中，有 102 個迅速且短暫表現的基因、182 個迅速且持續表現的基因，以及 30 個延遲性表現基因。依據基因網絡分析，PP2C68、MPK5、LRR-RLK 及 NPR1 為最顯著的核心訊息基因。在基因結構分析中，迅速與延遲性基因分別具有特別顯著的啟動子辨識區域，以及不同比例的 CpG 位點分佈。此外，共通性迅速且持續性基因的高 Ka/Ks 比例，表示它們可能有較快的演化速率。
青花菜花球形成在高溫環境下會顯著減少。在此研究中，以耐熱（HT）與熱敏感（HS）兩種青花菜品系，試圖找出溫度如何影響花球發育。首先將 HT 及 HS 青花菜品系種植於 15 至 27°C 的環境中 50 天，接著分析轉錄體差異。鈣離子訊息傳遞途徑、有絲分裂活化蛋白質酵素及轉譯出耐熱蛋白質等基因在 HT 與 HS 青花菜品系中明顯受高溫誘導，特別的是，在 22 °C 下，這些基因在 HS 品系中的表現量高於 HT 品系。此外，硫代葡萄糖苷新陳代謝相關基因在 HT 品系中則有較高的表現量。在分析 BoFLC1 啟動子序列時，發現 HT 品系的 BoFLC1 啟動子有較少的 AT-rich 區域，以及缺少一個 EcoRI 限制酵素辨識位點。
綜合這些研究結果，可以使我們對於水稻如何利用共通性調控基因因應環境逆境有較多的認識，同時亦對於青花菜不同品系在高溫下的早期生物反應途徑有較多 瞭解。此外，BoFLC1 啟動子的特殊結構亦能應用於耐熱青花菜品系的育種選拔。

As sessile organisms, plants were constantly challenged with biotic and abiotic stresses. Transcriptional regulation of stress-responsive genes is a crucial part of the plant adaptation to environmental changes. The aims of this study are to discover the common and uniquely transcriptinoal regulatory genes under environmental stresses via integrating transcriptomic data.
Early- and delayed-response of rice roots to three rhizotoxic perturbations: chromium, mercury, and frulic acid, were analyzed using published microarray data. There were 102 common early-transient, 182 common early-constant, and 30 common delayed genes upregulated under all three treatments. According to the network analysis, PP2C68, MPK5, LRR-RLK, and NPR1 are the most highly connect signalling hub genes. Gene architecture analysis shown that early and delayed genes were enriched with different conserved promoter motifs and different ratio of CpG island distribution. The higher Ka/Ks ratio of early-constant genes demonstrated an increased evolutionary rate compared to early-transient, delayed, and the genome median.
The development of the curd of broccoli is dramatically reduced under high temperature stress. Here, heat-tolerant (HT) and head-sensitive (HS) broccoli genotypes were used to determine the effects of temperature on curd development. HT and HS broccoli genotypes were exposed within a temperatures range of 15 - 27°C for 50 days. Comparative transcriptomic analysis indicated that high temperature activated calcium signalling pathways, mitogen-activated protein kinase cascades, and gene coding for heat-shock proteins in both HT and HS. Interestingly, the genes involved in these pathways were expressed at a lower level in HT than HS under 22°C condition. The distinct upregulation of glucosinolated metabolic associated genes were found in HT. The analysis of BoFLC1 promoter architecture had shown less AT-rich regions in HT than HS, and revealed a distinct EcoRI restriction site in HS.
These results provide insight into the common activation of transcriptional regulators in rice under environmental stresses and the early activation of biological pathways in broccoli genotypes under high temperature. Furthermore, the identification of specific BoFLC1 promoter architecture may facilitate breeding of heat-tolerant broccoli.

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