SynthesisPloS one2015
Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean.
Synthesis in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
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Who cites it
48 citing papers in PubMed.
- Characterization of the major latex protein gene family and functional analysis ofFrontiers in plant science · 2026Article
- Calm in the midst of the storm: inferring gene expression stability in flowering plants.Frontiers in plant science · 2026Article
- Transcriptome-Based Identification of Reference Genes for Expression Analysis in Cassava UnderPlants (Basel, Switzerland) · 2025Article
- Evolutionary Conservation and Regulatory Diversification ofInternational journal of molecular sciences · 2025Article
- Selection and validation of reference genes for quantitative real-time PCR during the developmental stages of seeds inFrontiers in plant science · 2025Article
- StCoExpNet: a global co-expression network analysis facilitates identifying genes underlying agronomic traits in potatoes.Plant cell reports · 2024Article
- Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (International journal of molecular sciences · 2023Article
- Identification of candidate genes responsible for chasmogamy in wheat.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
- Article
- Systematic identification of reference genes for qRT-PCR ofFrontiers in plant science · 2023Article
- Drought Stress Priming Improved the Drought Tolerance of Soybean.Plants (Basel, Switzerland) · 2022Article
- Identification of Diverse Stress-Responsive Xylem Sap Peptides in Soybean.International journal of molecular sciences · 2022Article
- Characterization of two constitutive promotersaBIOTECH · 2022Article
- Oxylipin signaling in salt-stressed soybean is modulated by ligand-dependent interaction of Class II acyl-CoA-binding proteins with lipoxygenase.The Plant cell · 2022Article
- A Selection of Reliable Reference Genes for Gene Expression Analysis in the Female and Male Flowers ofPlants (Basel, Switzerland) · 2022Article
- The Identification ofGenes · 2022Article
- Identification of Reference Genes for Reverse Transcription-Quantitative PCR Analysis of Ginger Under Abiotic Stress and for Postharvest Biology Studies.Frontiers in plant science · 2022Article
- Identification of stably expressed reference genes for expression studies inFrontiers in plant science · 2022Article
- Regulation of gliotoxin biosynthesis and protection in Aspergillus species.PLoS genetics · 2022Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Differential gene expression profiles often provide important clues for gene functions. While reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an important tool, the validity of the results depends heavily on the choice of proper reference genes. In this study, we employed new and published RNA-sequencing (RNA-Seq) datasets (26 sequencing libraries in total) to evaluate reference genes reported in previous soybean studies. In silico PCR showed that 13 out of 37 previously reported primer sets have multiple targets, and 4 of them have amplicons with different sizes. Using a probabilistic approach, we identified new and improved candidate reference genes. We further performed 2 validation tests (with 26 RNA samples) on 8 commonly used reference genes and 7 newly identified candidates, using RT-qPCR. In general, the new candidate reference genes exhibited more stable expression levels under the tested experimental conditions. The three newly identified candidate reference genes Bic-C2, F-box protein2, and VPS-like gave the best overall performance, together with the commonly used ELF1b. It is expected that the proposed probabilistic model could serve as an important tool to identify stable reference genes when more soybean RNA-Seq data from different growth stages and treatments are used.
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