马铃薯GGPS基因家族的全基因组鉴定及其对非生物胁迫的响应分析

Genome-Wide Identification of the Potato GGPS Gene Family and Analysis of Its Response to Abiotic Stress.

作者信息

Fu Changqing, Li Wei, Chen Xiaotian, Gao Shunjuan, Jia Mingfei, Zhang Shuqing, Cui Jianghui

机构信息

College of Agronomy, Hebei Agticultural University, Baoding 071000, China.

Hebei Key Laboratory of Crop Germplasm Resources, Hebei Agticultural University, Baoding 071000, China.

出版信息

Genes (Basel). 2025 May 28;16(6):646. doi: 10.3390/genes16060646.

DOI:10.3390/genes16060646

PMID:40565539

Abstract

BACKGROUND

Geranylgeranyl pyrophosphate synthase (GGPS) is a pivotal enzyme in terpene biosynthesis, influencing the production of carotenoids, chlorophylls, and diverse phytohormones. This study aimed to identify and characterize the gene family in potato () to elucidate its involvement in carotenoid synthesis and responses to abiotic stresses.

METHODS

Employing bioinformatics approaches, including HMMER, SMART, and Pfam, we conducted a genome-wide identification of StGGPS genes. Subsequent phylogenetic analysis, gene structure characterization, conserved motif detection, and synteny analysis were performed to investigate evolutionary relationships within the family. The expression patterns of StGGPS genes were then analyzed using RNA-seq data and quantitative real-time PCR (qRT-PCR) in potato tubers exhibiting different pigmentation and under drought and salt stress conditions.

RESULTS

Eleven genes were identified, unevenly distributed across seven chromosomes, and classified into three subfamilies based on phylogenetic and structural analyses. Synteny analysis revealed one intra-genomic duplicate pair (/) and conserved orthologs with other Solanaceae species. Promoter analysis identified cis-elements related to light response and abiotic stress (e.g., ABRE and CGTCA-motif). Expression data showed differential regulation of StGGPS genes in colored tubers, with yellow and red tubers exhibiting higher expression of carotenoid-related genes. Under drought stress, was significantly upregulated (5.2-fold, < 0.001), while showed salt-responsive induction (3.8-fold, < 0.001), linking them to ABA signaling and cytoskeletal dynamics, respectively.

CONCLUSIONS

This study provides a comprehensive overview of the StGGPS gene family, highlighting their roles in carotenoid biosynthesis and abiotic stress responses. The stress-specific expression patterns of and offer potential targets for genetic improvement of potato stress resilience.

摘要

背景

香叶基香叶基焦磷酸合酶（GGPS）是萜类生物合成中的关键酶，影响类胡萝卜素、叶绿素和多种植物激素的产生。本研究旨在鉴定和表征马铃薯（Solanum tuberosum）中的该基因家族，以阐明其在类胡萝卜素合成和对非生物胁迫响应中的作用。

方法

利用生物信息学方法，包括HMMER、SMART和Pfam，对StGGPS基因进行全基因组鉴定。随后进行系统发育分析、基因结构表征、保守基序检测和共线性分析，以研究该家族内部的进化关系。然后利用RNA测序数据和定量实时PCR（qRT-PCR）分析马铃薯块茎在不同色素沉着以及干旱和盐胁迫条件下StGGPS基因的表达模式。

结果

鉴定出11个StGGPS基因，它们不均匀地分布在7条染色体上，根据系统发育和结构分析分为3个亚家族。共线性分析揭示了一对基因组内重复基因对（StGGPS1/StGGPS2）以及与其他茄科物种的保守直系同源基因。启动子分析确定了与光响应和非生物胁迫相关的顺式作用元件（如ABRE和CGTCA-motif）。表达数据显示，彩色块茎中StGGPS基因存在差异调控，黄色和红色块茎中类胡萝卜素相关基因的表达较高。在干旱胁迫下，StGGPS1显著上调（5.2倍，P < 0.001），而StGGPS2表现出盐响应诱导（3.8倍，P < 0.001），分别将它们与脱落酸信号传导和细胞骨架动力学联系起来。