ArticlePloS one2011
Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
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Who cites it
88 citing papers in PubMed.
- A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.Genome research · 2026Article
- Deep learning-based semantic matching of cis-regulatory DNA sequences facilitates the prediction of gene function.Nature plants · 2026Article
- Quick creation and mapping of EMS-induced maize kernel mutants identifies classical gene ZmBT1 and novel gene ZmTOP6A.The plant genome · 2026Article
- Expanding the BonnMu sequence-indexed repository of transposon induced maize (Zea mays L.) mutations in dent and flint germplasm.The Plant journal : for cell and molecular biology · 2024Article
- Article
- Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes.Horticulture research · 2024Article
- Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications.Database : the journal of biological databases and curation · 2023Article
- Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture.Plant physiology · 2023Article
- Genome assembly of an Australian native grass species reveals a recent whole-genome duplication and biased gene retention of genes involved in stress response.GigaScience · 2022Article
- The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome.The Plant cell · 2022Article
- Homoeolog gene expression analysis reveals novel expression biases in upland hybrid cotton under intraspecific hybridization.Functional & integrative genomics · 2022Article
- Transcriptomic and alternative splicing analyses provide insights into the roles of exogenous salicylic acid ameliorating waxy maize seedling growth under heat stress.BMC plant biology · 2022Article
- Genome-wide mediation analysis: an empirical study to connect phenotype with genotype via intermediate transcriptomic data in maize.Genetics · 2022Article
- Using iRNA-seq analysis to predict gene expression regulatory level and activity in Zea mays tissues.G3 (Bethesda, Md.) · 2022Article
- Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize.BMC plant biology · 2021Article
- Developmental genetics of maize vegetative shoot architecture.Molecular breeding : new strategies in plant improvement · 2021Article
- Trajectories of Homoeolog-Specific Expression in AllotetraploidFrontiers in plant science · 2021Article
- Evolutionary Dynamics of Transposable Elements Following a Shared Polyploidization Event in the Tribe Andropogoneae.G3 (Bethesda, Md.) · 2020Article
- Article
- Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays).The plant genome · 2020Article
28 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Not all genes are created equal. Despite being supported by sequence conservation and expression data, knockout homozygotes of many genes show no visible effects, at least under laboratory conditions. We have identified a set of maize (Zea mays L.) genes which have been the subject of a disproportionate share of publications recorded at MaizeGDB. We manually anchored these "classical" maize genes to gene models in the B73 reference genome, and identified syntenic orthologs in other grass genomes. In addition to proofing the most recent version 2 maize gene models, we show that a subset of these genes, those that were identified by morphological phenotype prior to cloning, are retained at syntenic locations throughout the grasses at much higher levels than the average expressed maize gene, and are preferentially found on the maize1 subgenome even with a duplicate copy is still retained on the opposite subgenome. Maize1 is the subgenome that experienced less gene loss following the whole genome duplication in maize lineage 5-12 million years ago and genes located on this subgenome tend to be expressed at higher levels in modern maize. Links to the web based software that supported our syntenic analyses in the grasses should empower further research and support teaching involving the history of maize genetic research. Our findings exemplify the concept of "grasses as a single genetic system," where what is learned in one grass may be applied to another.
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