Genome-wide identification and validation of optimal reference genes for gene expression normalization in pear peel
Genome-wide identification and validation of optimal reference genes for gene expression normalization in pear peel
复制标题
梨皮基因表达标准化的最佳参考基因的全基因组鉴定和验证
DOI：
10.1007/s10725-020-00634-z
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发表时间：
2020-06-02
影响因子：
4.2
通讯作者：
Chen, Jianqing
中科院分区：
文献类型：
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作者：
Chen, Changmei;Wang, Tengyun;Chen, Jianqing
定量逆转录-聚合酶链反应（qRT-PCR）是基因表达研究的首选方法，但基于合适参考基因（RGs）的标准化是获得可靠基因表达结果的关键。在这项研究中，我们选择了六个“常用”的RG，两个“传统”管家基因（HKG），和四个新的基因作为候选RG的基础上，54个公开的果皮转录组库，包括数据的发展，套袋，和收获后的冷冻保存研究的四个梨品种。来自转录组和qRT-PCR分析的这种多方面评估的结果一致地显示，ACT 6/7/8/9在所有候选RG中具有最好的表达稳定性，并且与其他“常用”RG和“传统”HKG相比，新型RG的表达显示出更高的稳定性。其中，ACT 6/7/8/9和核小体组装蛋白1（Nucleosome Assembly Protein 1，NAP 1）表达稳定性和丰度上级，可作为梨果皮基因表达正常化的最佳RG组合。这些全基因组的研究结果提供了更合理的RG使用规范，以及额外的有用和可靠的RG资源，用于精确研究不同品种梨果皮中的基因表达。
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.