ArticleNature genetics2025
Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- PlantCAD2: A DNA foundation model for interpreting genomes across flowering plants.Cell genomics · 2026Article
- Upstream, downstream: nemo learns where plant regulatory sequences act.Plant physiology · 2026Article
- Article
- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- The cistrome response to hypoxia in human umbilical vein endothelial cells.bioRxiv : the preprint server for biology · 2026Article
- Genome-wide modelling of plant transcription factor binding captures regulatory variants associated with phenotypic traits.Nature communications · 2026Article
- Power-law penalties correct distance bias in single-cell co-accessibility and deep-learning chromatin interaction predictions.NAR genomics and bioinformatics · 2026Article
- Functional genomic map of local adaptation in sorghum to guide allele mining.bioRxiv : the preprint server for biology · 2026Article
- Integrating AI in seed science: Toward an intelligent design paradigm.Plant communications · 2026Review
- Chromatin accessibility landscape and its association with heterosis in maize hybrids.Nature communications · 2026Article
- Cis-regulatory architecture downstream of FLOWERING LOCUS T underlies quantitative control of flowering in Arabidopsis thaliana.Genome biology · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Many roads lead to a plant cistrome: mapping and interpreting transcription factor binding in plants.Genome biology · 2026Review
- Allelic Variation in Maize Malate Dehydrogenase 7 Shapes Promoter Methylation and Banded Leaf and Sheath Blight Resistance.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution.iScience · 2026Review
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Widespread turnover of a conserved cis-regulatory code across 589 grass species.Molecular biology and evolution · 2026Article
- PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms.bioRxiv : the preprint server for biology · 2025Article
- Domestication shaped the chromatin landscape of grain amaranth.Nature communications · 2025Article
- Vegetative to generative1 (Vgt1) is an enhancer affecting flowering time and jasmonate signaling in maize by promoting the expression of Zea mays Related to APETALA 2.7.Plant physiology · 2025Article
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25 authors.
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Abstract
Comprehensive maps of functional variation at transcription factor (TF) binding sites (cis-elements) are crucial for elucidating how genotype shapes phenotype. Here, we report the construction of a pan-cistrome of the maize leaf under well-watered and drought conditions. We quantified haplotype-specific TF footprints across a pan-genome of 25 maize hybrids and mapped over 200,000 variants, genetic, epigenetic, or both (termed binding quantitative trait loci (bQTL)), linked to cis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, including vgt1, ZmTRE1 and the MITE transposon near ZmNAC111 under drought; (2) bQTL allelic bias is shared between inbred parents and matches chromatin immunoprecipitation sequencing results; and (3) partitioning genetic variation across genomic regions demonstrates that bQTL capture the majority of heritable trait variation across ~72% of 143 phenotypes. Our study provides an auspicious approach to make functional cis-variation accessible at scale for genetic studies and targeted engineering of complex traits.
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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.