%0 Journal Article
%A Engelhorn, Julia
%A Snodgrass, Samantha J.
%A Kok, Amelie
%A Seetharam, Arun S.
%A Schneider, Michael
%A Kiwit, Tatjana
%A Singh, Ayush
%A Banf, Michael
%A Doan, Duong Thi Hai
%A Khaipho-Burch, Merritt
%A Runcie, Daniel E.
%A Sánchez-Camargo, Victor A.
%A Bader, Rechien
%A Vladimir Torres-Rodriguez, J.
%A Sun, Guangchao
%A Stam, Maike
%A Fiorani, Fabio
%A Beier, Sebastian
%A Schnable, James C.
%A Bass, Hank W.
%A Hufford, Matthew B.
%A Stich, Benjamin
%A Frommer, Wolf B.
%A Ross-Ibarra, Jeffrey
%A Hartwig, Thomas
%T Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
%J Nature genetics
%V 57
%@ 1061-4036
%C London
%I Macmillan Publishers Limited, part of Springer Nature
%M FZJ-2025-03463
%P 2313–2322
%D 2025
%X 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.
%F PUB:(DE-HGF)16
%9 Journal Article
%$ 40789919
%U <Go to ISI:>//WOS:001548254400001
%R 10.1038/s41588-025-02246-7
%U https://juser.fz-juelich.de/record/1044973