Selection of optimal reference genes for qRT-PCR analysis of shoot development and graviresponse in prostrate and erect chrysanthemums

Abstract

The prostrate cultivars of ground-cover chrysanthemum have been used in landscape gardening due to their small stature, large crown width and strong branching ability. qRT-PCR is a rapid and powerful tool for gene expression analysis, while its accuracy highly depends on the stability of reference genes. The paucity of authentic reference genes presents a major hurdle in understanding the genetic regulators of prostrate architecture. Therefore, in order to reveal the regulatory mechanism of prostrate growth of chrysanthemum stems, here, stable reference genes were selected for expression analysis of key genes involved in shoot development and graviresponse. Based on transcriptome data, eleven reference genes with relatively stable expression were identified as the candidate reference genes. After the comprehensive analysis of the stability of these reference genes with four programs (geNorm, NormFinder, BestKeeper and RefFinder), we found that TIP41 was the most stable reference gene in all of the samples. SAND was determined as a superior reference gene in different genotypes and during the process of shoot development. The optimal reference gene for gravitropic response was PP2A-1. In addition, the expression patterns of LA1 and PIN1 further verified the reliability of the screened reference genes. These results can provide more accurate and reliable qRT-PCR normalization for future studies on the expression patterns of genes regulating plant architecture of chrysanthemums.

Toxic Effects of Two Representative Rare Earth Elements (La and Gd) on Danio rerio Based on Transcriptome Analysis

“…The following are available online at https://www.mdpi.com/article/ 10.3390/toxics10090519/s1, Table S1: Molarity of each ion in the standard water; Table S2: Ammonia concentration (mg/L) measurements during 72-h acute toxicity; Table S3: Primer sequences used in the experiment; Table S4: Analysis of the water quality of the solution during the toxicity test; Table S5: Gene ontology and gene symbol in zebra fish livers induced by La and Gd. References [49][50][51][52] are cited in the supplementary materials.…”

Identification And Evaluation of Reference Genes For Cynanchum Auriculatum Under Various Stress Conditions

“…Nevertheless, the reliability of qRT-PCR data is affected DNA concentration, primer sequence, and reference gene stability 22 . In plants, common reference genes include Actin (ACT), 18S ribosomal RNA (18S rRNA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), alpha-tubulin/beta-tubulin (TUB-α/TUB-β), elongation factor 1/ elongation factor 2 (EF1/EF2), cyclophilin (CYP), and others 23,24 . Meanwhile, reference gene expression stability differs in different species 25 , tissues 26 , biological processes 27,28 , and environmental conditions 29 .…”