ArticleThe Plant cell2014
Insights into the maize pan-genome and pan-transcriptome.
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 286 papers, 2 of them syntheses that pooled it.
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Who cites it
286 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Meta-QTLs, ortho-meta-QTLs and candidate genes for grain yield and associated traits in wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Pooled it
- Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions.Scientific reports · 2021Pooled it
- Review
- Pangenomic analyses in the cultivated grapevine confirm high genomic collinearity and extensive dispensable gene content likely involved in adaptation.G3 (Bethesda, Md.) · 2026Article
- Harnessing genomics approaches for heat stress resilience in wheat: from discovery to deployment.Journal of experimental botany · 2026Review
- A pangenome framework uncovers the role of deletions in repeated evolution of cave-derived traits.Genome research · 2026Article
- Article
- Unveiling the interactions between design optimization, modeling strategies, and spatial analysis in genomic selection.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Empowering Plant Biotechnology Research: Super-Pangenomes as a Novel Arsenal for Crop Breeding and Improvement.Molecular biotechnology · 2026Review
- Chromosome-scale assembly of the eliteHorticulture research · 2026Article
- Graph-based pan-genome reveals structural and functional diversity across oil palm domestication gradients.BMC plant biology · 2026Article
- A tissue-resolved, network-based transcriptomic framework for abiotic stress responses in sorghum.The Plant journal : for cell and molecular biology · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Pan-genome of wild and cultivated rice uncovers genetic diversity, lost and selected sequences during rice domestication.Rice (New York, N.Y.) · 2026Article
- Benchmarking Feature Selection Methods and Prediction Models for Flowering Time Prediction in Maize.International journal of molecular sciences · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- Pan-genome analysis reveals structural variation- associated expression and evolutionary diversity of theFrontiers in plant science · 2026Article
- Genetic enhancement of root, tuber and cereal crops via pangenomics, multi-omics integration and AI-driven prediction.Frontiers in plant science · 2026Review
- Beyond efficiency: The multi-scale architecture of robust water transport in plants.Quantitative plant biology · 2026Review
226 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
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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.