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Journal of Integrative Agriculture  2022, Vol. 21 Issue (11): 3216-3229    DOI: 10.1016/j.jia.2022.07.051
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions
DUAN Yao-ke1, HAN Rong1, SU Yan1, WANG Ai-ying2, LI Shuang2, SUN Hao2, GONG Hai-jun1

1 Shaanxi Engineering Research Center for Vegetables/College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, P.R. China

2 Henan Key Laboratory of Ion-Beam Bioengineering, College of Agricultural Sciences, Zhengzhou University, Zhengzhou 450000, Henan, P. R. China

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摘要  番茄是研究果实发育和逆境响应的模式植物,基因表达分析是番茄研究中一项重要内容。定量PCR是一种应用广泛的基因表达分析技术,其中内参基因的选择可能会影响结果乃至结论的准确性。虽然番茄中已经有一些常用的参考基因,但研究表明,其中一些基因在不同组织或环境条件下的表达并不稳定。此外,目前从基因组水平鉴定和筛选番茄中内参基因的研究还很少。本研究从公开的转录测序数据中筛选出15个候选内参基因,并在胁迫和激素处理下分析了这些候选基因和7个传统使用的内参基因的表达稳定性。结果表明:一半以上的候选内参基因是番茄中的管家基因;不同的处理下最稳定表达的基因有所不同,在候选和传统使用的内参基因中,除了两个传统使用的Solyc04g009030和Solyc07g066610之外,大多数基因至少被推荐为首选内参基因一次。本研究不仅提供了番茄中的一些新的内参基因,而且还提供了不同环境条件下的首选内参基因,这有助于今后番茄的基因表达研究。我们的研究同时还表明,从转录组测序数据中挖掘稳定表达的基因是筛选qPCR分析内参基因的可靠方法。


Tomato (Solanum lycopersicum) is a model plant for research on fruit development and stress response, in which gene expression analysis is frequently conducted.  Quantitative PCR (qPCR) is a widely used technique for gene expression analysis, and the selection of reference genes may affect the accuracy of results and even conclusions.  Although there have been some frequently used reference genes in tomato, it has been shown that the expressions of some of these genes are not constant in different tissues and environmental conditions.  Moreover, little information on genomic identification of reference genes is available in tomato.  Here, we mined the publicly available transcriptional sequencing data and screened out fifteen candidate reference genes, and the expression stability of these candidate genes and seven traditionally used ones were evaluated under stress and hormone treatment.  The results showed that over half of the selected candidate references were housekeeping genes in tomato cells.  Among the candidate reference genes and the traditionally used ones, the most stably expressed genes varied under different treatments, and most of these genes were recommended as preferred reference genes at least once except Solyc04g009030 and Solyc07g066610, two traditionally used reference genes.  This study provides some novel reference genes in tomato, and the preferred reference genes under different environmental stimuli, which may be useful for future research.  Our study suggests that excavating stably expressed genes from transcriptome sequencing data is a reliable approach to screening reference genes for qPCR analysis.  

Keywords:  tomato (Solanum lycopersicum)       gene expression       quantitative polymerase chain reaction (qPCR)       reference gene       expression stability  
Received: 10 February 2022   Accepted: 21 April 2022

This work was supported by the National Key Research and Development Program of China (2018YFD1000800), the National Natural Science Foundation of China (32072561) and the Natural Science Foundation of Henan, China (222300420282).

About author:  DUAN Yao-ke, E-mail:; Correspondence SUN Hao, Tel: +86-371-67785095, E-mail:; GONG Hai-jun, Tel: +86-29-87082613, E-mail:

Cite this article: 

DUAN Yao-ke, HAN Rong, SU Yan, WANG Ai-ying, LI Shuang, SUN Hao, GONG Hai-jun. 2022. Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions. Journal of Integrative Agriculture, 21(11): 3216-3229.

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