Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences Institute of Qinghai University, Xining 810016, China.
College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China.
Cells. 2023 Mar 26;12(7):1015. doi: 10.3390/cells12071015.
Plant-specific transcription factors such as the TCP family play crucial roles in light responses and lateral branching. The commercial development of has been influenced by the ease with which its lateral branches can be germinated, especially under greenhouse cultivation during the winter with supplemented LED light. The present study examined the TCP family genes in using bioinformatics analysis (whole-genome sequencing and RNA-seq) to explore the response of this family to different light treatments. Forty-one TCP genes were identified through a genome-wide search; phylogenetic analysis revealed that the CYC/TB1, CIN and Class I subclusters contained 16 SmTCP, 11 SmTCP and 14 SmTCP proteins, respectively. Structural and conserved sequence analysis of SmTCPs indicated that the motifs in the same subcluster were highly similar in structure and the gene structure of SmTCPs was simpler than that in 40 of the 41 SmTCPs were localized to 12 chromosomes. In , 17 tandem repeat sequences and 17 pairs of SmTCP genes were found. We identified eight TCPs that were significantly differentially expressed (DETCPs) under blue light (B) and red light (R), using RNA-seq. The regulatory network of eight DETCPs was preliminarily constructed. All three subclusters responded to red and blue light treatment. To explore the implications of regulatory TCPs in different light treatments for each species, the TCP regulatory gene networks and GO annotations for and were compared. The regulatory mechanisms suggest that the signaling pathways downstream of the TCPs may be partially conserved between the two species. In addition to the response to light, functional regulation was mostly enriched with auxin response, hypocotyl elongation, and lateral branch genesis. In summary, our findings provide a basis for further analysis of the TCP gene family in other crops and broaden the functional insights into TCP genes regarding light responses.
植物特异性转录因子如 TCP 家族在光响应和侧枝发育中起着关键作用。 的商业开发受到其侧枝易于萌发的影响，尤其是在冬季温室栽培中，补充 LED 光时。本研究利用生物信息学分析（全基因组测序和 RNA-seq）研究了 TCP 家族在 中的基因，以探讨该家族对不同光处理的反应。通过全基因组搜索鉴定出 41 个 TCP 基因；系统发育分析表明，CYC/TB1、CIN 和 I 类亚群分别包含 16 个 SmTCP、11 个 SmTCP 和 14 个 SmTCP 蛋白。SmTCPs 的结构和保守序列分析表明，同一亚群中的基序在结构上高度相似，SmTCPs 的基因结构比 40 个简单。41 个 SmTCP 中的 40 个被定位到 12 条染色体上。在 中，发现了 17 个串联重复序列和 17 对 SmTCP 基因。我们使用 RNA-seq 鉴定出在蓝光（B）和红光（R）下差异表达的 8 个 TCP（DETCPs）。初步构建了 8 个 DETCPs 的调控网络。三个亚群都对红蓝光处理有反应。为了探讨不同光处理下调控 TCP 对两种植物的意义，比较了 和 的 TCP 调控基因网络和 GO 注释。调控机制表明，两种植物的 TCP 下游信号通路可能部分保守。除了对光的响应外，功能调控主要富集在生长素反应、下胚轴伸长和侧枝发育上。总之，我们的研究结果为进一步分析其他作物中的 TCP 基因家族提供了基础，并拓宽了关于光响应的 TCP 基因的功能见解。
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