ArticleGenome biology2023
A role for heritable transcriptomic variation in maize adaptation to temperate environments.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 39 citations in OpenAlex.
- Gene Ontology-Based Comparative Transcriptomics Provides Evidence of Genetic Adaptations in theAnimals : an open access journal from MDPI · 2026Article
- Independent component analysis deciphers the genetic basis of cotton fiber elongation through eQTLs and sQTLs.Journal of advanced research · 2026Article
- Regional transcriptomic divergence reveals thermal adaptation mechanisms in the giant kelp Macrocystis pyrifera.Scientific reports · 2026Article
- Predicting complex phenotypes using multi-omics data in maize.The Plant cell · 2026Article
- CQD: A Rapid and Accurate Tool for Identifying High-Confidence QTLs and Candidate Genes from GWAS Summary Statistics.International journal of molecular sciences · 2026Article
- Chromatin remodeling at the C-REPEAT BINDING FACTOR cluster controls growth retardation at low ambient temperature.The Plant cell · 2026Article
- Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement.Nature communications · 2025Article
- Optimizing thiamine pyrophosphate metabolism enhances crop yield and quality.Nature communications · 2025Article
- Hybrids reveal accessible chromatinbioRxiv : the preprint server for biology · 2025Article
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- Trans-regulatory loci shape natural variation of gene expression plasticity in Arabidopsis.Genetics · 2025Article
- In silico prediction of variant effects: promises and limitations for precision plant breeding.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Genes and pathways determining flowering time variation in temperate-adapted sorghum.The Plant journal : for cell and molecular biology · 2025Article
- A panoramic view of cotton resistance toiMeta · 2025Article
- GWAS-based population genetic analysis identifies bZIP29 as a heterotic gene in maize.Plant communications · 2025Article
- Phenotyping, genome-wide dissection, and prediction of maize root architecture for temperate adaptability.iMeta · 2025Article
- TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean.Plant communications · 2024Article
- Integrating evolutionary genomics of forest trees to inform future tree breeding amid rapid climate change.Plant communications · 2024Review
- Population-level exploration of alternative splicing and its unique role in controlling agronomic traits of rice.The Plant cell · 2024Article
- Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.International journal of molecular sciences · 2023Review
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments.
resultWe generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments.
conclusionOur results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.
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