Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
School of Biology, Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK.
J Exp Bot. 2024 Oct 16;75(19):6167-6181. doi: 10.1093/jxb/erae371.
Winter dormancy is a key process in the phenology of temperate perennials. Climate change is severely impacting its course leading to economic losses in agriculture. A better understanding of the underlying mechanisms, as well as the genetic basis of the different responses, is necessary for the development of climate-resilient cultivars. This study aims to provide an insight into winter dormancy in red raspberry (Rubus idaeus L). We report the transcriptomic profiles during dormancy in two raspberry cultivars with contrasting responses. The cultivar 'Glen Ample' showed a typical perennial phenology, whereas 'Glen Dee' registered consistent dormancy dysregulation, exhibiting active growth and flowering out of season. RNA-seq combined with weighted gene co-expression network analysis identified gene clusters in both genotypes that exhibited time-dependent expression profiles. Functional analysis of 'Glen Ample' gene clusters highlighted the significance of the cell and structural development prior to dormancy entry as well the role of genetic and epigenetic processes such as RNAi and DNA methylation in regulating gene expression. Dormancy release in 'Glen Ample' was associated with up-regulation of transcripts associated with the resumption of metabolism, nucleic acid biogenesis, and processing signal response pathways. Many of the processes occurring in 'Glen Ample' were dysregulated in 'Glen Dee' and 28 transcripts exhibiting time-dependent expression in 'Glen Ample' that also had an Arabidopsis homologue were not found in 'Glen Dee'. These included a gene with homology to Arabidopsis VRN1 (RiVRN1.1) that exhibited a sharp decline in expression following dormancy induction in 'Glen Ample'. Characterization of the gene region in the 'Glen Dee' genome revealed two large insertions upstream of the ATG start codon. We propose that expression below detection level of a specific VRN1 homologue in 'Glen Dee' causes dormancy misregulation as a result of inappropriate expression of a subset of genes that are directly or indirectly regulated by RiVRN1.1.
冬季休眠是温带多年生植物物候学的一个关键过程。气候变化严重影响了它的进程，导致农业经济损失。更好地了解潜在机制以及不同响应的遗传基础，对于开发具有气候适应性的品种是必要的。本研究旨在深入了解红树莓（Rubus idaeus L）的冬季休眠。我们报告了两个具有不同休眠响应的树莓品种休眠过程中的转录组谱。品种“Glen Ample”表现出典型的多年生物候，而“Glen Dee”则表现出持续的休眠失调，表现出不合时宜的活跃生长和开花。RNA-seq 结合加权基因共表达网络分析确定了两个基因型中表现出时间依赖性表达谱的基因簇。“Glen Ample”基因簇的功能分析突出了休眠前细胞和结构发育的重要性，以及 RNAi 和 DNA 甲基化等遗传和表观遗传过程在调节基因表达中的作用。“Glen Ample”的休眠解除与与代谢恢复、核酸生物发生和加工信号反应途径相关的转录本的上调有关。“Glen Ample”中发生的许多过程在“Glen Dee”中失调，并且在“Glen Ample”中表现出时间依赖性表达的 28 个转录本在“Glen Dee”中没有发现其拟南芥同源物。其中包括一个与拟南芥 VRN1 具有同源性的基因（RiVRN1.1），在“Glen Ample”休眠诱导后其表达急剧下降。“Glen Dee”基因组中基因区域的特征分析显示，在 ATG 起始密码子上游有两个大的插入。我们提出，由于 RiVRN1.1 直接或间接调控的一组基因的表达不当，导致特定 VRN1 同源物的表达低于检测水平，从而导致休眠失调。
