Open AccessWhole-Transcriptome Selection and Evaluation of Internal Reference Genes for Expression Analysis in Protocorm Development of Dendrobium officinale Kimura et Migo
Author(s) -
Hongqiang An,
Qiankun Zhu,
Wei Pei,
Jing Fan,
Yi Liang,
Yihui Cui,
Nan Lv,
Wanjun Wang
Publication year - 2016
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0163478
Subject(s) - reference genes , housekeeping gene , gene , biology , transcriptome , dendrobium , gene expression , genetics , gene expression profiling , computational biology , botany
Dendrobium officinale Kimu et Migo has increased many researchers’ interest for its high medical and horticultural values and the molecular mechanism of its protocorm development remains unclear. In this study, 19 genes from 26 most stably expressed genes in whole transcriptome of protocorms and 5 housekeeping genes were used as candidate reference genes and screened with 4 application softwares (geNorm, NormFinder, BestKeeper and RefFinder). The results showed that a few reference genes could effectively normalize expression level of specific genes in protocorm development and the optimal top 2 reference genes were ASS and APH1L . Meanwhile, validation of GNOM , AP2 and temperature induced gene ( TIL ) for normalization demonstrates the usefulness of the validated candidate reference genes. The expression profiles of these genes varied under protocorms and temperature stress according to the stablest and unstablest reference genes, which proved the importance of the choice of appropriate reference genes. The first systematic evaluation of stably expressed genes will be very useful in the future analysis of specific genes expression in D . officinale .