Jianqing Chen1,2, Jinyu Zhou3, Yanhong Hong3, Zekun Li3, Xiangyu Cheng3, Aiying Zheng3, Yilin Zhang3, Juanjuan Song3, Guifeng Xie3, Changmei Chen3, Meng Yuan3, Tengyun Wang3, Qingxi Chen4. 1. College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China. Jianqingchen@fafu.edu.cn. 2. FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. Jianqingchen@fafu.edu.cn. 3. College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China. 4. College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou, 350002, China. cqx0246@fafu.edu.cn.
Abstract
BACKGROUND: Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription-quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three "Commonly used" housekeeping genes (HKGs), fifteen "Traditional" HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars. RESULTS: The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the "Commonly used" and "Traditional" HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development. CONCLUSION: These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.
BACKGROUND: Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription-quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three "Commonly used" housekeeping genes (HKGs), fifteen "Traditional" HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars. RESULTS: The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the "Commonly used" and "Traditional" HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development. CONCLUSION: These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.
Entities:
Keywords:
Receptacle development; Reference gene; Strawberry; Ubiquitin 26S proteasome system
Authors: Jim F Huggett; Carole A Foy; Vladimir Benes; Kerry Emslie; Jeremy A Garson; Ross Haynes; Jan Hellemans; Mikael Kubista; Reinhold D Mueller; Tania Nolan; Michael W Pfaffl; Gregory L Shipley; Jo Vandesompele; Carl T Wittwer; Stephen A Bustin Journal: Clin Chem Date: 2013-04-09 Impact factor: 8.327
Authors: Laura Medina-Puche; Guadalupe Cumplido-Laso; Francisco Amil-Ruiz; Thomas Hoffmann; Ludwig Ring; Antonio Rodríguez-Franco; José Luis Caballero; Wilfried Schwab; Juan Muñoz-Blanco; Rosario Blanco-Portales Journal: J Exp Bot Date: 2013-11-25 Impact factor: 6.992