ArticlePloS one2017
Using RNA-seq data to select reference genes for normalizing gene expression in apple roots.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed.
- Identification of Reference Genes and Their Application in Analysis of Ginsenoside Biosynthesis Genes in American Ginseng Under Abiotic Stresses and Hormone Treatments.Plants (Basel, Switzerland) · 2026Article
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- The Identification of Transcriptomic and Phytohormonal Biomarkers for Monitoring Drought and Evaluating the Potential of Acibenzolar-S-Methyl Root Application to Prime Two Apple Rootstock Genotypes for Drought Resistance.International journal of molecular sciences · 2025Article
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- The Synergistic Effects of Environmental and Genetic Factors on the Regulation of Anthocyanin Accumulation in Plant Tissues.International journal of molecular sciences · 2023Article
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- Identification and validation of the reference genes in the echiuran worm Urechis unicinctus based on transcriptome data.BMC genomics · 2023Article
- Selection of Novel Reference Genes by RNA-Seq and Their Evaluation for Normalising Real-Time qPCR Expression Data of Anthocyanin-Related Genes in Lettuce and Wild Relatives.International journal of molecular sciences · 2023Article
- From endodormancy to ecodormancy: the transcriptional landscape of apple floral buds.Frontiers in plant science · 2023Article
- Systematic identification of reference genes for qRT-PCR ofFrontiers in plant science · 2023Article
- Light Induces Carotenoid Biosynthesis-Related Gene Expression, Accumulation of Pigment Content, and Expression of the Small Heat Shock Protein in Apple Fruit.International journal of molecular sciences · 2022Article
- RNA-Seq is not required to determine stable reference genes for qPCR normalization.PLoS computational biology · 2022Article
- Identification of stably expressed reference genes for expression studies inFrontiers in plant science · 2022Article
- Identification and validation of reference genes for qRT-PCR based studies in horse gram (Physiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- CD146 Delineates an Interfascicular Cell Sub-Population in Tendon That Is Recruited during Injury through Its Ligand Laminin-α4.International journal of molecular sciences · 2021Article
- Apple Autotetraploids with Enhanced Resistance to Apple Scab (International journal of molecular sciences · 2021Article
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- High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat,Frontiers in plant science · 2021Article
- Selection and validation of reference genes for quantitative gene expression normalization in Taxus spp.Scientific reports · 2020Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Gene expression in apple roots in response to various stress conditions is a less-explored research subject. Reliable reference genes for normalizing quantitative gene expression data have not been carefully investigated. In this study, the suitability of a set of 15 apple genes were evaluated for their potential use as reliable reference genes. These genes were selected based on their low variance of gene expression in apple root tissues from a recent RNA-seq data set, and a few previously reported apple reference genes for other tissue types. Four methods, Delta Ct, geNorm, NormFinder and BestKeeper, were used to evaluate their stability in apple root tissues of various genotypes and under different experimental conditions. A small panel of stably expressed genes, MDP0000095375, MDP0000147424, MDP0000233640, MDP0000326399 and MDP0000173025 were recommended for normalizing quantitative gene expression data in apple roots under various abiotic or biotic stresses. When the most stable and least stable reference genes were used for data normalization, significant differences were observed on the expression patterns of two target genes, MdLecRLK5 (MDP0000228426, a gene encoding a lectin receptor like kinase) and MdMAPK3 (MDP0000187103, a gene encoding a mitogen-activated protein kinase). Our data also indicated that for those carefully validated reference genes, a single reference gene is sufficient for reliable normalization of the quantitative gene expression. Depending on the experimental conditions, the most suitable reference genes can be specific to the sample of interest for more reliable RT-qPCR data normalization.
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