Microarray-based uncovering reference genes for quantitative real time PCR in grapevine under abiotic stress.

BMC Research Notes
João L CoitoSara Amâncio

Abstract

Quantitative real time polymerase chain reaction is becoming the primary tool for detecting mRNA and transcription data analysis as it shows to have advantages over other more commonly used techniques. Nevertheless, it also presents a few shortcomings, with the most import being the need for data normalisation, usually with a reference gene. Therefore the choice of the reference gene(s) is of great importance for correct data analysis. Microarray data, when available, can be of great assistance when choosing reference genes. Grapevine was submitted to water stress and heat stress as well as a combination of both to test the stability of the possible reference genes. Using the analysis of microarray data available for grapevine, six possible reference genes were selected for RT-qPCR validation: PADCP, ubiq, TIF, TIF-GTP, VH1-IK, aladin-related. Two additional genes that are commonly used as reference genes were included: act and L2. The stability of those genes was tested in leaves of grapevine in both field plants and in greenhouse plants under water or heat stress or a combination of both. Gene stability was analyzed with the softwares GeNorm, NormFinder and the ΔCq method resulting in several combinations of reference genes s...Continue Reading

References

Jul 15, 1998·Plant Physiology· Kumar Tewari A, Charan Tripathy B
Jan 5, 2000·Journal of Biotechnology·O ThellinE Heinen
Feb 16, 2002·The Plant Journal : for Cell and Molecular Biology·Teruaki TajiKazuo Shinozaki
Dec 18, 2003·Biotechnology Letters·Bo-Ra KimYung-Jin Chang
Jun 23, 2004·Journal of Experimental Botany·Claire GachonBénédicte Charrier
Aug 20, 2004·BMC Plant Biology·Amy M BrunnerSteven H Strauss
Apr 9, 2005·Genes and Immunity·J HuggettA Zumla
Jun 16, 2005·Journal of Molecular Endocrinology·S A BustinM W Pfaffl
Sep 29, 2005·Journal of Experimental Botany·Nathalie NicotDanièle Evers
Nov 19, 2005·BMC Molecular Biology·Pål A OlsvikIvar Hordvik
May 13, 2006·Biochemical and Biophysical Research Communications·Mukesh JainJitendra P Khurana
Feb 24, 2009·BMC Molecular Biology·Anna R PaolacciMario Ciaffi
Dec 9, 2009·Methods : a Companion to Methods in Enzymology·Stefaan DerveauxJan Hellemans
Apr 12, 2011·Journal of Agricultural and Food Chemistry·Angeles ObreroClara I González-Verdejo
Jun 3, 2011·Molecular Biology Reports·Jiawen YanZiniu Deng
Oct 12, 2011·BMC Research Notes·Jose CondoriFabricio Medina-Bolivar
Nov 17, 2011·Biochemical and Biophysical Research Communications·Hongjian WanYuejian Yang

❮ Previous
Next ❯

Citations

Aug 7, 2012·Naunyn-Schmiedeberg's Archives of Pharmacology·Franziska BollmannAndrea Pautz
Sep 12, 2014·Plant, Cell & Environment·Luísa C CarvalhoSara Amâncio
Mar 15, 2018·Scientific Reports·Meng LuoShiping Wang
Jun 11, 2020·American Journal of Physiology. Lung Cellular and Molecular Physiology·Thomas H HamptonBruce A Stanton
Jan 5, 2021·Frontiers in Plant Science·Luísa CarvalhoAntero Martins

❮ Previous
Next ❯

Methods Mentioned

BETA
transcription profiling
GTPase
electrophoresis
PCRs
PCR

Software Mentioned

stepwise
ΔCq
NormFinder
GeNorm
Gen5
Primer Premier
MS Excel
SAS
GalSynt
Excel

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.