ArticleBMC genomics2018
Accuracy of RNAseq based SNP discovery and genotyping in Populusnigra.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 41 citations in OpenAlex.
- Transcriptome SNP analysis of tomato seedlings exposed to low‑dose gamma irradiation and cold plasma suggests antiviral responses.Scientific reports · 2026Article
- The transcriptome-identified gene HaSAPK3.8 of sunflower (Helianthus annuus L.) confers drought resistance in tobacco.BMC plant biology · 2025Article
- A protocol for identifying universal reference genes within a genus based on RNA-Seq data: a case study of poplar stem gene expression.Forestry research · 2024Article
- RNAseq based variant dataset in a black poplar association panel.BMC research notes · 2023Article
- Direct inference and control of genetic population structure from RNA sequencing data.Communications biology · 2023Article
- Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone.BMC biology · 2023Article
- Genomic signatures suggesting adaptation to ocean acidification in a coral holobiont from volcanic COCommunications biology · 2023Article
- BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.Bioinformatics (Oxford, England) · 2023Article
- Article
- A Novel Beta-Glucosidase Gene for Plant Type Was Identified by Genome-Wide Association Study and Gene Co-Expression Analysis in Widespread Bermudagrass.International journal of molecular sciences · 2022Article
- eQTLs are key players in the integration of genomic and transcriptomic data for phenotype prediction.BMC genomics · 2022Article
- Natural variation and improved genome annotation of the emerging biofuel crop field pennycress (Thlaspi arvense).G3 (Bethesda, Md.) · 2022Article
- Transcriptomic Reprogramming and Genetic Variations Contribute to Western Hemlock Defense and Resistance Against Annosus Root and Butt Rot Disease.Frontiers in plant science · 2022Article
- Article
- Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize.International journal of molecular sciences · 2020Article
- Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches.BMC plant biology · 2020Article
- Gene expression predictions and networks in natural populations supports the omnigenic theory.BMC genomics · 2020Article
- The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments.Journal of animal science and biotechnology · 2019Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroudPopulus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Polymorphisms (SNPs) typically needed to carry out a genome scan, the present study aimed at evaluating RNA sequencing as a tool to discover and type SNPs in genes within natural populations of P. nigra.
resultsWe have devised a bioinformatics pipeline to call and type SNPs from RNAseq reads and applied it to P. nigra transcriptomic data. The accuracy of the resulting RNAseq-based SNP calling and typing has been evaluated by (i) comparing their position and alleles to those previously reported in candidate genes, (ii) assessing their genotyping accuracy with respect to a previously available SNP chip and (iii) evaluating their inter-annual repeatability. We found that a combination of several callers yields a good compromise between the number of variants type and the accuracy of genotyping. We further used the resulting genotypic data to carry out basic genetic analyses whose results confirm the quality of the RNAseq-based SNP dataset.
conclusionsWe demonstrated the potential and accuracy of RNAseq as an efficient way to genotype SNPs in P. nigra. These results open prospects towards the use of this technology for quantitative and population genomics studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.