Abstract

Despite cold stress is a critical environmental condition that influences the growth and development of bell pepper (Capsicum annuum L.), the underlying molecular mechanism remains unclear. This study aimed to explore the genes associated with the low temperature stress response in bell pepper. Bell pepper ‘Zhongjiao NO.4’ (CRC, cold resistance cultivar) and ‘Zhong 30’ (WT, cold sensitive variety) was used in this study. CRC was grown under 4°C for 0 h (Low), 8 h (Low 8), 16 h (Low 16), and 24 h (Low 24), as well as WT was also grown under 4°C. The transcriptome profile of bell pepper was obtained through Illumina RNA-sequencing. The differentially expressed genes (DEGs) between Low and WT groups were explored, and DEGs between every two groups of Low, Low8, Low16, and Low24 were also screened. Time series clustering analysis of DEGs among Low groups was performed. Functional enrichment analysis of DEGs was conducted by using cluster Profiler package, followed by protein-protein interaction (PPI) analysis. The results showed that DEGs in CRC were involved in flavonoid biosynthesis and phenylalanine metabolism. Functional enrichment analysis of time-course related DEGs indicated that genes were mainly associated with metabolic process, photosynthesis, and lipid metabolic process. LOC107864131, LOC107857080, and LOC107855212 were considered as hub genes, and played vital role in cold stress in bell pepper. Meanwhile, the expression level of ribosomal proteins-related genes was significantly down-regulated during cold treatment. The dynamic expression changes revealed the regulatory role of genes in cold stress response of bell pepper. Our findings might shed light on the molecular mechanisms related to cold tolerance in bell pepper and provide useful candidate genes for genetic improvement.

中文翻译：

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转录组分析揭示了甜椒低温胁迫中涉及的候选基因

摘要

尽管低温胁迫是影响甜椒（辣椒（Capsicum annuum）L.），潜在的分子机制仍不清楚。这项研究旨在探索与甜椒低温胁迫反应相关的基因。在本研究中使用了甜椒“中交4号”（CRC，耐寒品种）和“中30号”（WT，冷敏感品种）。CRC在4°C下生长0小时（低），8小时（低8），16小时（低16）和24小时（低24），并且野生型也在4°C下生长。甜椒的转录组图谱通过Illumina RNA测序获得。探索了低和WT组之间的差异表达基因（DEG），并且还筛选了低，低8，低16和低24每两组之间的DEG。在低组之间对DEG进行时间序列聚类分析。通过使用Cluster Profiler软件包进行DEG的功能富集分析，然后进行蛋白质间相互作用（PPI）分析。结果表明，CRC中的DEG参与了类黄酮的生物合成和苯丙氨酸的代谢。时程相关DEG的功能富集分析表明，基因主要与代谢过程，光合作用和脂质代谢过程有关。LOC107864131，LOC107857080和LOC107855212被认为是中心基因，并且在甜椒的冷胁迫中起着至关重要的作用。同时，冷处理过程中核糖体蛋白相关基因的表达水平显着下调。动态表达变化揭示了基因在甜椒冷应激反应中的调节作用。我们的发现可能会阐明与灯笼椒耐寒性相关的分子机制，并为遗传改良提供有用的候选基因。