ArticleThe Plant cell2024
Pan-transcriptomic analysis reveals alternative splicing control of cold tolerance in rice.
Article in The Plant cell, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Integrated transcriptomic and metabolomic analysis reveals key pathways and metabolites underlying cold tolerance in passion fruit.Horticulture research · 2026Article
- Temperature regulation in plants: From molecular mechanisms to climate-resilient crop improvement.Journal of integrative plant biology · 2026Review
- Splicing Factor SR45 Enhances Cold Tolerance in Cassava by Recruiting Nu4A Complex and Transcription Factors to Activate WRKY30.Plant, cell & environment · 2026Article
- Low temperature-induced profiling of transcription and alternative splicing during seed germination in rice.BMC genomics · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- A Phase-Dependent Model of Sorghum (Biology · 2026Article
- Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits.Plant molecular biology · 2026Article
- Unraveling branch point-driven SR45a splicing dynamics in heat stress for plant adaptation.Science advances · 2026Article
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Global profiling of alternative splicing landscapes in response to cold stress during the cotyledon stage in cotton.BMC genomics · 2026Article
- Transcriptome and miRNAome analysis reveals expression profiles of platycodin biosynthesis-related genes and their potential miRNA regulators inFrontiers in plant science · 2026Article
- Alternative Splicing: Molecular Mechanisms, Biological Functions, Diseases, and Potential Therapeutic Targets.MedComm · 2025Review
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- Overexpression ofJournal of fungi (Basel, Switzerland) · 2025Article
- Pan-omics insights into abiotic stress responses: bridging functional genomics and precision crop breeding.Functional & integrative genomics · 2025Review
- Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton.BMC genomics · 2025Article
- Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress.Nature plants · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- Comprehensive Omics Analysis Reveals Cold-Induced Metabolic Reprogramming and Alternative Splicing inPlants (Basel, Switzerland) · 2025Article
- The role of pangenomics in orphan crop improvement.Nature communications · 2025Review
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Plants have evolved complex mechanisms to adapt to harsh environmental conditions. Rice (Oryza sativa) is a staple food crop that is sensitive to low temperatures. However, its cold stress responses remain poorly understood, thus limiting possibilities for crop engineering to achieve greater cold tolerance. In this study, we constructed a rice pan-transcriptome and characterized its transcriptional regulatory landscape in response to cold stress. We performed Iso-Seq and RNA-Seq of 11 rice cultivars subjected to a time-course cold treatment. Our analyses revealed that alternative splicing-regulated gene expression plays a significant role in the cold stress response. Moreover, we identified CATALASE C (OsCATC) and Os03g0701200 as candidate genes for engineering enhanced cold tolerance. Importantly, we uncovered central roles for the 2 serine-arginine-rich proteins OsRS33 and OsRS2Z38 in cold tolerance. Our analysis of cold tolerance and resequencing data from a diverse collection of 165 rice cultivars suggested that OsRS2Z38 may be a key selection gene in japonica domestication for cold adaptation, associated with the adaptive evolution of rice. This study systematically investigated the distribution, dynamic changes, and regulatory mechanisms of alternative splicing in rice under cold stress. Overall, our work generates a rich resource with broad implications for understanding the genetic basis of cold response mechanisms in plants.
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