Genome-wide identification and validation of optimal reference genes for gene expression normalization in pear peel
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ORIGINAL PAPER
Genome‑wide identification and validation of optimal reference genes for gene expression normalization in pear peel Changmei Chen1 · Tengyun Wang1 · Zhenmei Cai1 · Guifeng Xie1 · Zhiyi Chen1 · Yafang Yuan2 · Wei Wang1 · Qian Xie1 · Xiayu Guan1 · Qingxi Chen1 · Jianqing Chen1 Received: 8 February 2020 / Accepted: 29 May 2020 © Springer Nature B.V. 2020
Abstract Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) is the preferred method for gene expression research, but normalization based on suitable reference genes (RGs) is the key to obtaining reliable gene expression results. In this study, we selected six “commonly used” RGs, two “traditional” housekeeping genes (HKGs), and four novel genes as candidate RGs based on 54 publicly available peel transcriptome libraries that include data from development, bagging, and post-harvest cryopreservation studies of four pear cultivars. The results of this multifaceted assessment from transcriptome and qRT-PCR analyses consistently revealed that ACT6/7/8/9 had the best expression stability among all candidate RGs, and expression of the novel RGs showed greater stability compared with the other “commonly used” RGs and “traditional” HKGs. Among the candidate RGs, ACT6/7/8/9 and Nucleosome Assembly Protein 1 (NAP1) showed superior expression stability and abundance, and they were recommended as the optimal RG combination for gene expression normalization in pear peel. These genome-wide findings provide more reasonable RG usage specifications, and additional useful and reliable RGs as resources for accurate study of gene expression in pear peel studies of different cultivars. Keywords Reference gene · Pear · Peel · Genome-wide
Introduction Changmei Chen, Tengyun Wang and Zhenmei Cai are Equal contributors. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10725-020-00634-z) contains supplementary material, which is available to authorized users.
Pear (Pyrus L.) is an important economically significant fruit crop grown worldwide. Within its evolutionary process, pear is divided into two categories: Asian pears (including P. bretschneideri, P. pyrifolia, P. sinkiangensis, P. ussuriensis) and European pears (including P. communis) (Wu
* Qingxi Chen [email protected]
Yafang Yuan [email protected]
* Jianqing Chen [email protected]
Wei Wang [email protected]
Changmei Chen [email protected]
Qian Xie [email protected]
Tengyun Wang [email protected]
Xiayu Guan [email protected]
Zhenmei Cai [email protected]
1
College of Horticulture, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Fuzhou 350002, China
2
Department of Horticulture and Landscape Architecture, Fujian Vocational College of Agriculture, Fuzhou 350119, China
Guifeng Xie [email protected] Zhiyi Chen [email protected]
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et al. 2018). P. bretschneideri (cultivar ‘Dangshansuli’) has emerged as a model system for studying pear because of the availability
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