Abstract
Glycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.
Highlights
CACis the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio-temporal interactions (CAC,R3HDM2 and DNAJ)
In G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and coefficients varied from 0.9887 (CS) were recommended for developmental stages
The E value of the selected candidate reference genes from RNA-Seq data ranged from 90.63% (CAC) to 107.58% (CYP) and correlation coefficients varied from 0.9887 (CS) to 0.9963 (COPS3) (Table 1), and all these primers are suitable for Reverse transcription quantitative real-time PCR (RT-qPCR) analysis[32]
Summary
Two-year-old licorice plants (G. uralensis and G. inflata) were grown in the test field at the Northwest Biological Agricultural Center, Chinese Academy of Sciences (Ningxia, China). Rhizomes and leaves were collected in April (returning green), May (rapid growth and flowering), July (seed setting), and October (aging) (Fig. 1). All samples were flash frozen in liquid nitrogen, shipped to Guangzhou in dry ice and stored at -80 °C for RNA extraction. All experiments were carried out with three biological replicates.
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