ArticleThe New phytologist2021
Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice.
Article in The New phytologist, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 61 citations in OpenAlex.
- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- Alternative Splicing in Plant Development and Abiotic Stress Responses: A Multifunctional Regulatory Mechanism.International journal of molecular sciences · 2026Review
- Genome-Wide Meta-QTL Analysis and InDel Markers for Salt Tolerance in Rice: Bridging the Gap from Genomics to Breeding.Rice (New York, N.Y.) · 2026Article
- Adaptive Plasticity of Phytochelatin Synthase Under Chromium Stress and Sulfur Availability inPlants (Basel, Switzerland) · 2026Article
- TaPP2C-a5 fine-tunes wheat seed dormancy and germination with a Triticeae-specific, alternatively spliced transcript.Journal of advanced research · 2026Article
- Comparative transcriptomic and transcript-based network analyses revealed genotype-specific alternative splicing induced by Sclerotinia sclerotiorum in Brassica napus.BMC plant biology · 2026Article
- Transcriptome and weighted gene co-enrichment analysis revealed modules and candidate genes associated with barley response to low potassium stress.Frontiers in plant science · 2026Article
- Alternative splicing in plant stress responses: potential application for crop improvement.Planta · 2025Review
- The Role of Alternative Splicing in Polyploids in Response to Abiotic Stress.International journal of molecular sciences · 2025Review
- Transcriptome Analysis Between Parents and Offspring Revealed the Early Salt Tolerance Mechanism of Rice NGY1.Rice (New York, N.Y.) · 2025Article
- The Regulatory Roles of RNA-Binding Proteins in Plant Salt Stress Response.Plants (Basel, Switzerland) · 2025Review
- Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice.The Plant cell · 2024Article
- Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review.Plants (Basel, Switzerland) · 2024Review
- OsMGD1-Mediated Membrane Lipid Remodeling Improves Salt Tolerance in Rice.Plants (Basel, Switzerland) · 2024Article
- Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study inHorticulture research · 2024Article
- Importance of pre-mRNA splicing and its study tools in plants.Advanced biotechnology · 2024Review
- RNA-seq analysis reveals transcriptome reprogramming and alternative splicing during early response to salt stress in tomato root.Frontiers in plant science · 2024Article
- Using single-sample networks and genetic algorithms to identify radiation-responsive genes in rice affected by heavy ions of the galactic cosmic radiation with different LET values.Frontiers in plant science · 2024Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Mapping intron retention events contributing to complex traits using splice quantitative trait locus.Plant methods · 2023Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VaSP). VaSP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions. In total, 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na
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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.