TY  - JOUR
AU  - Engelhorn, Julia
AU  - Snodgrass, Samantha J.
AU  - Kok, Amelie
AU  - Seetharam, Arun S.
AU  - Schneider, Michael
AU  - Kiwit, Tatjana
AU  - Singh, Ayush
AU  - Banf, Michael
AU  - Doan, Duong Thi Hai
AU  - Khaipho-Burch, Merritt
AU  - Runcie, Daniel E.
AU  - Sánchez-Camargo, Victor A.
AU  - Bader, Rechien
AU  - Vladimir Torres-Rodriguez, J.
AU  - Sun, Guangchao
AU  - Stam, Maike
AU  - Fiorani, Fabio
AU  - Beier, Sebastian
AU  - Schnable, James C.
AU  - Bass, Hank W.
AU  - Hufford, Matthew B.
AU  - Stich, Benjamin
AU  - Frommer, Wolf B.
AU  - Ross-Ibarra, Jeffrey
AU  - Hartwig, Thomas
TI  - Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
JO  - Nature genetics
VL  - 57
SN  - 1061-4036
CY  - London
PB  - Macmillan Publishers Limited, part of Springer Nature
M1  - FZJ-2025-03463
SP  - 2313–2322
PY  - 2025
AB  - 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.
LB  - PUB:(DE-HGF)16
C6  - 40789919
UR  - <Go to ISI:>//WOS:001548254400001
DO  - DOI:10.1038/s41588-025-02246-7
UR  - https://juser.fz-juelich.de/record/1044973
ER  -