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Identifying stable reference genes for qRT-PCR normalisation in gene expression studies of narrow-leafed lupin (Lupinus angustifolius L.)

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posted on 2023-01-24, 04:00 authored by Candy M Taylor, Ricarda JostRicarda Jost, W Erskine, MN Nelson
Quantitative Reverse Transcription PCR (qRT-PCR) is currently one of the most popular, high-throughput and sensitive technologies available for quantifying gene expression. Its accurate application depends heavily upon normalisation of gene-of-interest data with reference genes that are uniformly expressed under experimental conditions. The aim of this study was to provide the first validation of reference genes for Lupinus angustifolius (narrow-leafed lupin, a significant grain legume crop) using a selection of seven genes previously trialed as reference genes for the model legume, Medicago truncatula. In a preliminary evaluation, the seven candidate reference genes were assessed on the basis of primer specificity for their respective targeted region, PCR amplification efficiency, and ability to discriminate between cDNA and gDNA. Following this assessment, expression of the three most promising candidates [Ubiquitin C (UBC), Helicase (HEL), and Polypyrimidine tract-binding protein (PTB)] was evaluated using the NormFinder and RefFinder statistical algorithms in two narrow-leafed lupin lines, both with and without vernalisation treatment, and across seven organ types (cotyledons, stem, leaves, shoot apical meristem, flowers, pods and roots) encompassing three developmental stages. UBC was consistently identified as the most stable candidate and has sufficiently uniform expression that it may be used as a sole reference gene under the experimental conditions tested here. However, as organ type and developmental stage were associated with greater variability in relative expression, it is recommended using UBC and HEL as a pair to achieve optimal normalisation. These results highlight the importance of rigorously assessing candidate reference genes for each species across a diverse range of organs and developmental stages. With emerging technologies, such as RNAseq, and the completion of valuable transcriptome data sets, it is possible that other potentially more suitable reference genes will be identified for this species in future.

Funding

The Grains Research and Development Corporation contributed to the funding of this research via award of an Undergraduate Honours Scholarship (award number: UHS10659) to CMT. The URL for the Grains Research and Development Corporation is http://www.grdc.com.au/. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.

History

Publication Date

2016-02-12

Journal

PLoS One

Volume

11

Issue

2

Article Number

e0148300

Pagination

18p.

Publisher

PLOS

ISSN

1932-6203

Rights Statement

© 2016 Taylor et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.