蓝莓 CLC 基因家族的全基因组鉴定及盐胁迫表达分析

Genome-wide identification and expression analysis of the CLC gene family in blueberry (Vaccinium corymbosum) under salt stress

摘要

【目的】CLC蛋白在植物盐胁迫响应中发挥关键作用，然而蓝莓中 CLC家族成员的盐胁迫表达模式及分子调控网络尚不清楚。本研究在全基因组范围内鉴定蓝莓 CLC基因家族，系统分析其盐胁迫响应模式，旨在为揭示其介导Cl^–稳态、调控蓝莓耐盐性的分子机制奠定基础。【方法】利用生物信息学方法分析蓝莓 CLC家族的蛋白理化性质、基因结构、保守基序、支架定位、共线性关系、启动子区顺式作用元件及系统进化关系等，并利用转录组数据筛选差异表达基因，通过RT-qPCR分析其在盐胁迫下的表达模式。【结果】（1）从基因组中共筛选到19个编码 CLC家族的基因，不均匀分布于12个支架上。系统进化分析将其划分为4个亚家族，不同亚家族成员在基因结构与保守基序组成上差异显著。（2）启动子顺式作用元件和上游转录因子预测分析结果显示， VcCLCs启动子中含有多个与生长发育、植物激素和胁迫相关的调节元件，其表达可能受到ERF、NAC、WRKY等转录因子的调控。（3）基于盐胁迫下耐盐品种‘Duke’和盐敏感品种‘Sweetheart’的转录组数据，筛选到3个在两品种根中均差异表达的基因，命名为 VcCLCc1、 VcCLCc2和 VcCLCf2。RT-qPCR结果显示，上述3个基因在‘Duke’根中均受盐胁迫诱导显著上调，而在‘Sweetheart’根中显著下调，说明它们可能参与了蓝莓盐胁迫应答。【结论】本研究明确了蓝莓CLC家族的核心特征及盐胁迫响应关键基因，为解析盐胁迫下蓝莓Cl^–稳态维持的分子机制提供了候选基因和理论基础。

Abstract

[Objective] CLC proteins play pivotal roles in plant responses to salt stress; however, the salt stress expression patterns and molecular regulatory networks of the CLC family in blueberry (Vaccinium corymbosum) remain largely unknown. This study performed a genome-wide identification of the blueberry CLC gene family and systematically analyzed their expression profiles under salt stress, aiming to lay a foundation for elucidating the molecular mechanisms by which CLCs mediate Cl^– homeostasis and regulate salt tolerance in blueberry. [Method] Bioinformatics methods were used to analyze the physicochemical properties, gene structures, conserved motifs, scaffold locations, collinearity relationships, cis-acting elements in promoter regions, and phylogenetic relationships in VcCLCs family. Differentially expressed genes were screened based on transcriptome data, and RT-qPCR was used to analyze the expression patterns under salt stress. [Result] (1) 19 genes encoding CLC family members were identified from the genomic data and unevenly distributed across 12 scaffolds. Phylogenetic analysis classified them into four subfamilies, with significant variations in gene structure and conserved motif composition among the members of different subfamilies. (2) Analysis of promoter cis-acting elements and upstream transcription factor prediction revealed that VcCLCs promoters contain multiple regulatory elements related to growth and development, phytohormones, and stress responses. Their expression is likely regulated by transcription factors such as ERF, NAC, and WRKY. (3) Based on the salt-stress transcriptome analysis of roots from the salt-tolerant cultivar ‘Duke’ and the salt-sensitive cultivar ‘Sweetheart’, three common differentially expressed genes were identified and designated as VcCLCc1, VcCLCc2, and VcCLCf2. RT-qPCR results demonstrated that these three genes were significantly upregulated in ‘Duke’ roots under salt stress but were notably downregulated in ‘Sweetheart’ roots, indicating their potential involvement in blueberry salt-stress responses. [Conclusion] This study elucidates the core characteristics of the CLC gene family in blueberry and identifies key genes responsive to salt stress, providing candidate genes and a theoretical foundation for understanding the molecular mechanisms of Cl^– homeostasis maintenance under salt stress.

关键词

蓝莓 / CLC基因家族 / 全基因组鉴定 / 盐胁迫 / 表达分析 / 氯离子通道

Key words

Vaccinium corymbosum / CLC gene family / genome-wide identification / salt stress / expression profiling / chloride channel

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基金资助

山东省重点研发计划(2024LZGCQY025)

北京林业大学“5·5工程”科研创新团队项目(BLRC2023B08)