Abstract Low-temperature (LT) stress is known to restrain sugarcane productivity in sub-tropical regions significantly. Many researchers have prioritized their work towards developing climate-resilient sugarcane varieties incorporating genome of stress-tolerant sugarcane related wild-type species in the pre-breeding programs. However, the lack of genomic resources for wild-type sugarcane limits the identification and utilization of stress-related genes in molecular breeding. In this study, for the first time, we generated ∼182 million RNA-seq paired-end reads for Saccharum spontaneum roots grown under low temperature (10 °C) at different time intervals (0 h, 3 h, 6 h, 12 h, 24 h, and 48 h), to identify LT stress responsive genes and pathways. These data were assembled into 141,409 unigenes and subsequently used to identify 2715 upregulated and 1710 downregulated transcripts under LT stress. Combining evidences from GO enrichment, KEGG pathways, histological studies, biochemical assays, and physiological analysis, our results revealed several key genes and pathways involved in cold acclimatization in the S. spontaneum roots. Transcription profiling of roots during LT stress revealed cold stress sensors (i.e., proline, MDA, calcium-dependent kinase, G-coupled proteins, and histidine kinase) that trigger and activate signal transduction through transcription factors (i.e., MYB, ERF, ARF2, DREB, CAMTA, and C2H2) resulting in upregulation of LT stress responsive genes (i.e, annexin, LEA, germins, LT dehydrins, osmotins, and COR) thereby enhancing cold tolerance. Also, transcriptomic analysis envisaged cold responsive metabolic pathways such as phenylpropanoid and sugar metabolism stimulate the synthesis of flavonoid, sucrose, galactose, raffinose, and fructose, antioxidants, phytohormones, and secondary metabolites, and thus trigger cold-responsive transcriptional regulation. Together, this study provides insights into cold tolerance of wild sugarcane roots to LT stress, thus providing a foundation for developing climate-resilient sugarcane varieties.

中文翻译：

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自发甘蔗根转录组分析揭示应对低温胁迫的关键基因和途径

摘要 低温（LT）胁迫对亚热带地区的甘蔗生产力有显着抑制作用。许多研究人员将他们的工作重点放在开发具有气候适应性的甘蔗品种上，这些甘蔗品种在预育计划中结合了抗压甘蔗相关野生型物种的基因组。然而，野生型甘蔗基因组资源的缺乏限制了胁迫相关基因在分子育种中的鉴定和利用。在这项研究中，我们首次为在不同时间间隔（0 小时、3 小时、6 小时、12 小时）在低温（10°C）下生长的甘蔗自发根生成了约 1.82 亿个 RNA-seq 配对末端读数。 、24 小时和 48 小时），以确定 LT 应激反应基因和途径。这些数据被组装成 141，409 个 unigenes，随后用于鉴定 LT 胁迫下 2715 个上调和 1710 个下调的转录本。结合来自 GO 富集、KEGG 通路、组织学研究、生化分析和生理分析的证据，我们的结果揭示了参与 S. spontaneum 根冷驯化的几个关键基因和通路。LT 胁迫期间根的转录分析显示冷胁迫传感器（即脯氨酸、MDA、钙依赖性激酶、G 偶联蛋白和组氨酸激酶）通过转录因子（即 MYB、ERF、ARF2、 DREB、CAMTA 和 C2H2) 导致 LT 应激反应基因（即膜联蛋白、LEA、生发素、LT 脱水蛋白、渗透素和 COR）的上调，从而增强耐寒性。还，转录组学分析设想冷响应代谢途径如苯丙烷和糖代谢刺激黄酮类化合物、蔗糖、半乳糖、棉子糖和果糖、抗氧化剂、植物激素和次级代谢物的合成，从而触发冷响应转录调控。总之，这项研究为野生甘蔗根系对 LT 胁迫的耐寒性提供了见解，从而为开发具有气候适应性的甘蔗品种奠定了基础。