ArticleThe Plant cell2014
Genome-wide analysis of alternative splicing in Zea mays: landscape and genetic regulation.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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Who cites it
134 citing papers in PubMed.
- Infection-responsive alternative splicing of GhZDS is associated with Verticillium wilt resistance in cotton.BMC plant biology · 2026Article
- Global profiling of alternative splicing landscapes in response to cold stress during the cotyledon stage in cotton.BMC genomics · 2026Article
- Pre-mRNA splicing and its regulation in microalgae and cyanobacteria.Advanced biotechnology · 2025Review
- Phosphorus starvation-induced alternative splicing landscape of rice confirms the regulatory function of Pup1 QTL.BMC plant biology · 2025Article
- Effect of mAnimals : an open access journal from MDPI · 2025Article
- Pre-mRNA Splicing Functions in Plant Sexual Reproduction Development.Plants (Basel, Switzerland) · 2025Review
- Alternative splicing analysis of stress tolerance to Al and flg22 in Vitis quinquangularis.Planta · 2025Article
- Unravelling alternative splicing patterns in susceptible and resistant Brassica napus lines in response to Xanthomonas campestris infection.BMC plant biology · 2024Article
- Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense.Molecular genetics and genomics : MGG · 2024Article
- Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice.The Plant cell · 2024Article
- Local and systemic transcriptome and spliceome reprogramming induced by the root-knot nematodeHorticulture research · 2024Article
- Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions.Horticulture research · 2024Review
- Transcription factor TaNF-YB2 interacts with partners TaNF-YA7/YC7 and transcriptionally activates distinct stress-defensive genes to modulate drought tolerance in T. Aestivum.BMC plant biology · 2024Article
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut.Plant biotechnology journal · 2024Article
- Alternative Splicing Underpins the ALMT9 Transporter Function for Vacuolar Malic Acid Accumulation in Apple.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Gene expression and alternative splicing contribute to adaptive divergence of ecotypes.Heredity · 2024Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
- Unraveling the Guardians of Growth: A Comprehensive Analysis of thePlants (Basel, Switzerland) · 2023Article
- Alternative Splicing during Fiber Development inInternational journal of molecular sciences · 2023Article
- Mapping intron retention events contributing to complex traits using splice quantitative trait locus.Plant methods · 2023Article
74 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative splicing enhances transcriptome diversity in all eukaryotes and plays a role in plant tissue identity and stress adaptation. To catalog new maize (Zea mays) transcripts and identify genomic loci that regulate alternative splicing, we analyzed over 90 RNA-seq libraries from maize inbred lines B73 and Mo17, as well as Syn10 doubled haploid lines (progenies from B73 × Mo17). Transcript discovery was augmented with publicly available data from 14 maize tissues, expanding the maize transcriptome by more than 30,000 and increasing the percentage of intron-containing genes that undergo alternative splicing to 40%. These newly identified transcripts greatly increase the diversity of the maize proteome, sometimes coding for entirely different proteins compared with their most similar annotated isoform. In addition to increasing proteome diversity, many genes encoding novel transcripts gained an additional layer of regulation by microRNAs, often in a tissue-specific manner. We also demonstrate that the majority of genotype-specific alternative splicing can be genetically mapped, with cis-acting quantitative trait loci (QTLs) predominating. A large number of trans-acting QTLs were also apparent, with nearly half located in regions not shown to contain genes associated with splicing. Taken together, these results highlight the currently underappreciated role that alternative splicing plays in tissue identity and genotypic variation in maize.
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