Table 1_Comparative transcriptomics reveals key regulatory networks underlying cold stress adaptation in oil palm (Elaeis guineensis).xls

IntroductionClimate change has exacerbated cold stress, which severely impairs plant development. Oil palm (Elaeis guineensis), a tropical crop highly sensitive to low temperatures, exhibits stunted growth and yield reductions under such conditions.
MethodsTo investigate its cold stress response, oil palm seedlings were subjected to cold treatments, and their physiological and genetic adaptations were analyzed using fresh leaf samples. Key parameters, including antioxidant enzyme activity, reactive oxygen species (ROS) levels, photosynthetic pigment ratios, photosynthetic efficiency, and gene expression, were evaluated across exposure durations. Sequencing of the samples was performed using Illumina NovaSeq X Plus platform. Raw reads were processed using fastp (v0.18.0) to remove adapter-containing reads, exclude reads with >10% unidentified nucleotides (N), and eliminate reads where >50% of bases had Phred scores ≤20. The genome reference version is GCF_000442705.2 (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000442705.2/).
Results and discussionUnder cold stress, seedlings displayed a significant increase in superoxide dismutase (SOD, 546.08 U/g min FW) and peroxidase (POD, 153.27 U/g min FW) activities within 4 h compared with the control. Prolonged exposure (8 h) further elevated soluble sugar content (406.27 μg/g FW), malondialdehyde (MDA, 80.22 nmol/g), relative electrical conductivity (109.71%), and the carotenoid-to-chlorophyll ratio, indicating oxidative damage and membrane instability. RNA-seq analysis identified 144, 392, and 6,585 differentially expressed genes (DEGs) after 1, 4, and 8 h of cold exposure, respectively. KEGG pathway enrichment highlighted predominant associations with plant–pathogen interaction, plant hormone signal transduction, and the mitogen-activated protein kinase (MAPK) signaling pathway. Functional analysis revealed DEGs involved in four major hormone signaling pathways (auxin (AUX/IAA), jasmonic acid (JA), abscisic acid (ABA), and brassinosteroid (BR)), which also interact with the MAPK cascade to collectively regulate oil palm cold stress adaptation and growth adjustments. This study provides comprehensive insights into the genetic and molecular mechanisms underlying cold tolerance in oil palm, offering a basis for breeding cold-resistant cultivars.

引言
气候变化加剧了低温胁迫，严重损害植物的生长发育。油棕（Elaeis guineensis）作为一种对低温高度敏感的热带作物，在低温条件下会出现生长迟缓和产量下降的情况。

材料与方法
为探究油棕的低温胁迫响应机制，本研究对油棕幼苗施加低温处理，并利用新鲜叶片样本分析其生理与遗传适应性。针对不同低温暴露时长，我们评估了多项关键指标，包括抗氧化酶活性、活性氧（reactive oxygen species, ROS）水平、光合色素比率、光合效率以及基因表达。样本测序采用Illumina NovaSeq X Plus平台完成。原始读段（reads）使用fastp（v0.18.0）进行质控处理：移除带有接头的读段、排除含10%以上未知核苷酸（N）的读段，以及过滤掉超过50%碱基Phred分值≤20的读段。参考基因组版本为GCF_000442705.2（https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000442705.2/）。

结果与讨论
低温胁迫下，与对照组相比，油棕幼苗在低温暴露4小时内的超氧化物歧化酶（superoxide dismutase, SOD，546.08 U/g·min FW）和过氧化物酶（peroxidase, POD，153.27 U/g·min FW）活性显著升高。当低温暴露时长延长至8小时时，可溶性糖含量（406.27 μg/g FW）、丙二醛（malondialdehyde, MDA，80.22 nmol/g）、相对电导率（109.71%）以及类胡萝卜素与叶绿素的比率进一步上升，表明植株发生了氧化损伤与膜系统不稳定。RNA测序分析显示，低温暴露1、4和8小时后，分别鉴定出144、392和6585个差异表达基因（differentially expressed genes, DEGs）。KEGG通路富集分析结果表明，这些差异表达基因主要与植物-病原体互作、植物激素信号转导以及丝裂原活化蛋白激酶（mitogen-activated protein kinase, MAPK）信号通路相关。功能分析揭示，参与四大激素信号通路（生长素（auxin, AUX/IAA）、茉莉酸（jasmonic acid, JA）、脱落酸（abscisic acid, ABA）以及油菜素类固醇（brassinosteroid, BR））的差异表达基因，可与MAPK级联反应相互作用，共同调控油棕的低温胁迫适应与生长调节。本研究全面解析了油棕耐寒性背后的遗传与分子机制，为抗寒油棕品种的选育提供了理论基础。