Abstract
Arabis alpina is a perennial arctic-alpine plant and an upcoming model organism for genetics and molecular biology for the Brassicaceae family. One essential method for most molecular approaches is the analysis of gene expression by reverse-transcription quantitative Real-Time PCR (RT-qPCR). For the normalisation of expression data in RT-qPCR experiments, it is essential to use reliable reference genes that are not affected under a wide range of conditions. In this study we establish a set of 15 A. alpina reference genes that were tested under different conditions including cold, drought, heat, salt and gibberellic acid treatments. Data analyses with geNORM, BestKeeper and NormFinder revealed the most stable reference genes for the tested conditions: RAN3, HCF and PSB33 are most suitable for cold treatments; UBQ10 and TUA5 for drought; RAN3, PSB33 and EIF4a for heat; CAC, TUA5, ACTIN 2 and PSB33 for salt and PSB33 and TUA5 for gibberellic acid treatments. CAC and ACTIN 2 showed the least variation over all tested samples. In addition, we show that two reference genes are sufficient to normalize RT-qPCR data under our treatment conditions. In future studies, these reference genes can be used for an adequate normalisation and thus help to generate high quality RT-qPCR data in A. alpina.
Highlights
A. alpina has been established as a new model system in the Brassicaceae family [1,2]
We created a set of 15 reference genes (Table 1), including nine orthologs to A. thaliana reference genes, five novel reference genes and RAN GTPASE 3 (RAN3), a known reference gene for reverse-transcription quantitative Real-Time PCR (RT-Quantitative real-time PCR (qPCR)) in A. alpina [1]
EUKARYOTIC TRANSLATION INITIATION FACTOR 4A1 (EIF4a), ACTIN 2, CLATHRIN ADAPTOR COMPLEX MEDIUM SUBUNIT (CAC), TUBULIN ALPHA 5 (TUA5), HISTONE H3, HSP81.2/90 and SAND were chosen because they were already established as reference genes in other species [13,14,15,16,17,19,20]
Summary
A. alpina has been established as a new model system in the Brassicaceae family [1,2]. It is native to mountains and arctic-alpine habitats [3,4] and combines several features enabling genetic and molecular studies: it is diploid, self-fertile, has a small and sequenced genome and can be transformed with Agrobacterium tumefaciens [1]. A. alpina has an evolutionary distance to A. thaliana of about 26 to 40 million years [4,5]. This facilitates functional comparisons of biological processes, as orthologous genes can be identified by sequence similarity and synteny [6]. Most molecular studies require quantitative analyses of the expression of genes of interest by reverse-transcription quantitative Real-Time PCR (RT-qPCR). In 2009, the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
