Journal Article

FZJ-2025-03463

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

Engelhorn, J. ; Snodgrass, S. J. ; Kok, A. ; Seetharam, A. S. ; Schneider, M.FZJ* ; Kiwit, T. ; Singh, A. ; Banf, M. ; Doan, D. T. H. ; Khaipho-Burch, M. ; Runcie, D. E. ; Sánchez-Camargo, V. A. ; Bader, R. ; Vladimir Torres-Rodriguez, J. ; Sun, G. ; Stam, M. ; Fiorani, F.FZJ* ; Beier, S.FZJ* ; Schnable, J. C. ; Bass, H. W. ; Hufford, M. B. ; Stich, B. ; Frommer, W. B. ; Ross-Ibarra, J. ; Hartwig, T. (Corresponding author)

2025
Macmillan Publishers Limited, part of Springer Nature London

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Please use a persistent id in citations: doi:10.1038/s41588-025-02246-7  doi:10.34734/FZJ-2025-03463

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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Contributing Institute(s):

1. Pflanzenwissenschaften (IBG-2)

Research Program(s):

1. 2171 - Biological and environmental resources for sustainable use (POF4-217) (POF4-217)

Appears in the scientific report 2025

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Database coverage:
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