ArticlePLoS genetics2023
Elucidating the patterns of pleiotropy and its biological relevance in maize.
Article in PLoS genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 9 citations in OpenAlex.
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize.Genome research · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.Nature genetics · 2025Article
- Cross-species modeling of plant genomes at single-nucleotide resolution using a pretrained DNA language model.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Maize inbreds show allelic variation for diel transcription patterns.bioRxiv : the preprint server for biology · 2024Article
- Epistasis and pleiotropy-induced variation for plant breeding.Plant biotechnology journal · 2024Review
- A genome-wide association study uncovers a ZmRap2.7-ZCN9/ZCN10 module to regulate ABA signalling and seed vigour in maize.Plant biotechnology journal · 2024Article
- Cross-species modeling of plant genomes at single nucleotide resolution using a pre-trained DNA language model.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Pleiotropy-when a single gene controls two or more seemingly unrelated traits-has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.
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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.