Shoukai Lin^1,2,#, Shichang Xu^1,#, Liyan Huang¹, Fuxiang Qiu¹, Yihong Zheng¹, Qionghao Liu¹, Shiwei Ma^1,2, Bisha Wu^1,2, Jincheng Wu^1,2,*

Phyton-International Journal of Experimental Botany, Vol.92, No.4, pp. 1185-1201, 2023, DOI:10.32604/phyton.2023.026752 - 06 January 2023

Abstract Loquat (Eriobotrya japonica Lindl.) is a subtropical evergreen fruit tree that produces fruits with abundant nutrients and medicinal components. Confirming suitable reference genes for a set of loquat samples before qRT-PCR experiments is essential for the accurate quantification of gene expression. In this study, eight candidate reference genes were selected from our previously published RNA-seq data, and primers for each candidate reference gene were designed and evaluated. The Cq values of the candidate reference genes were calculated by RT-qPCR in 31 different loquat samples, including 12 subgroups of developing or abiotic-stressed tissues. Different combinations of stable… More >

FENGLIN BAI^1,2,#, BIANXIA BAI^1,2,#, TINGTING JIN^1,2, GUIPING ZHANG^1,2, JIAHONG REN^1,2,*

BIOCELL, Vol.47, No.3, pp. 647-656, 2023, DOI:10.32604/biocell.2023.024758 - 03 January 2023

Abstract Background: Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacteria isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula; nonetheless, until now, no validated reference genes from the genus Serratia have been reported that can be used for the normalization of quantitative real-time polymerase chain reaction (RT–qPCR) data. Methods: To screen stable reference genes of S. ureilytica DW2, the expression of its eight candidate reference genes (16S rRNA, ftsZ, ftsA, mreB, recA, slyD, thiC, and zipA) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT–qPCR. The expression stability of these genes was analyzed using… More >

Zhipeng Sheng, Yuting Luan, Cong Xu, Jun Tao^*, Daqiu Zhao^*

Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 801-814, 2023, DOI:10.32604/phyton.2023.024953 - 29 November 2022

Abstract Herbaceous peony (Paeonia lactiflora Pall.), as a high-end cut flower in the international market, has high ornamental and medicinal values. But in Northern China, drought is a major environmental factor influencing the growth and development of P. lactiflora. Quantitative real-time polymerase chain reaction (qRT-PCR) can evaluate gene expression levels under different stress conditions, and stable internal reference is the key for qRT-PCR. At present, there is no systematic screening of internal reference for correcting gene expressions of P. lactiflora in response to drought stress. In this study, 10 candidate genes [ubiquitin (UBQ2), UBQ1, elongation factor 1-α (EF-1α), Histidine (His), eukaryotic… More >

Qiang Ai, Cuijing Liu^*, Mei Han^*, Limin Yang

Phyton-International Journal of Experimental Botany, Vol.91, No.11, pp. 2537-2548, 2022, DOI:10.32604/phyton.2022.021889 - 12 July 2022

Abstract Iris domestica is a plant of the Iridaceae family and is drought-tolerant, but its drought-resistance mechanism is not yet clear. Analysing the gene expression changes of I. domestica by qRT-PCR is an important mean to understand its drought resistance characteristics. Nevertheless, a lack of reference genes greatly hinders investigation and research on the adaptation of I. domestica to drought at the molecular and genetic levels. In this study, we assessed the expression stability of 11 candidate gene in I. domestica under drought stress conditions and different tissues using geNorm, NormFinder, BestKeeper and RefFinder tools. The results showed that EF1β was More >

Huanli Wang, Lingjun Yan, Xi Huang, Zhongwei Wang, Yuanhao Yue, Shijie Tang^*

Phyton-International Journal of Experimental Botany, Vol.91, No.10, pp. 2191-2210, 2022, DOI:10.32604/phyton.2022.020735 - 30 May 2022

Abstract Quantitative real-time polymerase chain reaction (qRT-PCR) is a rapid and effective approach toward detecting the expression patterns of target genes. The selection of a stable reference gene under specific test condition is essential for expressing levels of target genes accurately. Tilia miqueliana, considered endangered, is a prominent native ornamental and honey tree in East China. No study has evaluated the optimal endogenous reference gene for qRT-PCR analysis in T. miqueliana systematically. In this study, fifteen commonly used reference genes were selected as candidate genes, and the stabilities of their expressions were assessed using four algorithms (GeNorm, NormFiner,… More >

Yuting Luan¹, Cong Xu¹, Xiaoxiao Wang¹, Daqiu Zhao¹, Jun Tao^1,2,*

Phyton-International Journal of Experimental Botany, Vol.91, No.5, pp. 1045-1059, 2022, DOI:10.32604/phyton.2022.018767 - 24 January 2022

Abstract The definition of relatively stable expressed internal reference genes is essential in both traditional blotting quantification and as a modern data quantitative strategy. Appropriate internal reference genes can accurately standardize the expression abundance of target genes to avoid serious experimental errors. In this study, the expression profiles of ten candidate genes, ACT1, ACT2, GAPDH, eIF1, eIF2, α-TUB, β-TUB, TBP, RNA Pol II and RP II, were calculated for a suitable reference gene selection in Paeonia ostii T. Hong et J. X. Zhang leaves under various drought stress conditions. Data were processed by the four regularly used evaluation software. A comprehensive analysis revealed More >

Yinjie Wang, Yongxia Zhang, Qingquan Liu, Liangqin Liu, Suzhen Huang, Haiyan Yuan^*

Phyton-International Journal of Experimental Botany, Vol.90, No.1, pp. 277-290, 2021, DOI:10.32604/phyton.2020.011545 - 20 November 2020

Abstract Quantitative real-time PCR (qPCR) is an effective and widely used method to analyze expression patterns of target genes. Selection of stable reference genes is a prerequisite for accurate normalization of target gene expression by qRT-PCR. In Iris germanica L., no studies have yet been published regarding the evaluation of potential reference genes. In this study, nine candidate reference genes were assessed at different flower developmental stages and in different tissues by four different algorithms (GeNorm, NormFinder, BestKeeper, and RefFinder). The results revealed that ACT11 (Actin 11) and EF1α (Elongation factor 1 alpha) were the most stable reference… More >

Lu Zhu, Qiuyue Ma, Shushun Li, Jing Wen, Kunyuan Yan, Qianzhong Li^*

Phyton-International Journal of Experimental Botany, Vol.89, No.2, pp. 385-403, 2020, DOI:10.32604/phyton.2020.09259 - 22 April 2020

Abstract Quantitative real-time reverse transcriptase PCR (qRT-PCR) technology has been extensively used to estimate gene expression levels, and the selection of appropriate reference genes for qRT-PCR analysis is critically important for obtaining authentic normalized data. Acer palmatum is an important colorful leaf ornamental tree species, and reference genes suitable for normalization of the qRT-PCR data obtained from this species have not been investigated. In this study, the expression stability of ten candidate reference genes, namely, Actin3, Actin6, Actin9, EF1α, PP2A, SAMDC, TIP41, TUBα, TUBβ and UBQ10, in two distinct tissues (leaves and roots) of A. palmatum under four different abiotic stress conditions (cold,… More >

Gang Li¹, Yao Zhou², Yaqi Zhao², Yaxue Liu², Yuwei Ke², Xiaoqing Jin¹, Haoli Ma^1,2,*

Phyton-International Journal of Experimental Botany, Vol.89, No.2, pp. 329-344, 2020, DOI:10.32604/phyton.2020.08874 - 22 April 2020

Abstract Quantitative real-time PCR (qRT-PCR) is widely used for investigating gene expression patterns and has many advantages, including its high sensitivity, fidelity, and specificity. Selecting a satisfactory internal reference gene is crucial for obtaining precise gene expression results in qRT-PCR analyses. In this study, the transcriptomic data of 2 potato varieties were screened for housekeeping genes with stable expression patterns. A total of 77 putative genes were selected, which were highly and stably expressed. Then, qRT-PCR analyses were performed to examine the expression levels of these 77 candidate reference genes in various potato tissues, including leaves, More >