Table 3_Comparative transcriptomics reveals key regulatory networks underlying cold stress adaptation in oil palm (Elaeis guineensis).xlsx

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，严重损害植物生长发育。油棕（Elaeis guineensis）作为对低温高度敏感的热带作物，在低温条件下会出现生长受阻与产量下降的现象。

方法：为探究油棕的低温胁迫响应机制，本研究对油棕幼苗进行低温处理，并利用新鲜叶片样本分析其生理与遗传适应性。研究评估了不同处理时长下的多项关键参数，包括抗氧化酶活性、活性氧（ROS）水平、光合色素比值、光合效率以及基因表达水平。样本测序采用Illumina NovaSeq X Plus平台完成。原始测序读段（raw reads）使用fastp（v0.18.0）进行质控过滤：去除含接头的读段、排除未知核苷酸（N）占比超过10%的读段，以及剔除超过50%碱基的Phred质量值≤20的读段。本研究使用的参考基因组版本为GCF_000442705.2（https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000442705.2/）。

结果与讨论：与对照组相比，低温胁迫处理4小时内，油棕幼苗的超氧化物歧化酶（SOD，546.08 U/g min FW）与过氧化物酶（POD，153.27 U/g min FW）活性显著升高。延长处理至8小时后，可溶性糖含量（406.27 μg/g FW）、丙二醛（MDA，80.22 nmol/g）、相对电导率（109.71%）以及类胡萝卜素/叶绿素比值进一步升高，表明植株出现氧化损伤与膜稳定性下降。RNA测序（RNA-seq）分析显示，低温处理1、4、8小时后分别鉴定出144、392和6585个差异表达基因（DEGs）。KEGG通路富集分析结果显示，这些差异表达基因主要富集于植物-病原体互作、植物激素信号转导以及丝裂原活化蛋白激酶（MAPK）信号通路。功能分析表明，参与生长素（AUX/IAA）、茉莉酸（JA）、脱落酸（ABA）以及油菜素内酯（BR）四大激素信号通路的差异表达基因，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过程。本研究全面解析了油棕耐寒性的遗传与分子机制，为耐寒品种的选育提供了理论基础。