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DOE OSTI · 3673214

Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

Engelhorn, Julia (ORCID:0000000266803012)·Snodgrass, Samantha (ORCID:0000000192096051)·Kok, Amelie (ORCID:0009000959305232)·Seetharam, Arun (ORCID:0000000267899298)·Schneider, Michael (ORCID:0000000264918852)·Kiwit, Tatjana·Singh, Ayush (ORCID:0000000301844486)·Banf, Michael·Doan, Duong·Khaipho-Burch, Merritt·Runcie, Daniel (ORCID:0000000230089312)·Sánchez-Camargo, Victor (ORCID:0000000271840301)·Bader, Rechien (ORCID:000900014738190X)·Vladimir Torres-Rodriguez, J.·Sun, Guangchao (ORCID:0000000339426175)·Stam, Maike (ORCID:0000000303634677)·Fiorani, Fabio (ORCID:0000000187751541)·Beier, Sebastian (ORCID:0000000221778781)·Schnable, James (ORCID:0000000167395527)·Bass, Hank (ORCID:0000000305220881)·Hufford, Matthew (ORCID:0000000339451143)·Stich, Benjamin (ORCID:0000000167918068)·Frommer, Wolf (ORCID:0000000164650115)·Ross-Ibarra, Jeffrey (ORCID:0000000316564954)·Hartwig, Thomas (ORCID:0000000227072771)
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Abstract

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 tocis-element occupancy. Three lines of evidence support the functional significance of bQTL: (1) coincidence with causative loci that regulate traits, includingvgt1,ZmTRE1and the MITE transposon nearZmNAC111under 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 functionalcis-variation accessible at scale for genetic studies and targeted engineering of complex traits.

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Engelhorn, Julia (ORCID:0000000266803012), Snodgrass, Samantha (ORCID:0000000192096051), Kok, Amelie (ORCID:0009000959305232), Seetharam, Arun (ORCID:0000000267899298), Schneider, Michael (ORCID:0000000264918852), Kiwit, Tatjana, Singh, Ayush (ORCID:0000000301844486), Banf, Michael, Doan, Duong, Khaipho-Burch, Merritt, Runcie, Daniel (ORCID:0000000230089312), Sánchez-Camargo, Victor (ORCID:0000000271840301), Bader, Rechien (ORCID:000900014738190X), Vladimir Torres-Rodriguez, J., Sun, Guangchao (ORCID:0000000339426175), Stam, Maike (ORCID:0000000303634677), Fiorani, Fabio (ORCID:0000000187751541), Beier, Sebastian (ORCID:0000000221778781), Schnable, James (ORCID:0000000167395527), Bass, Hank (ORCID:0000000305220881), Hufford, Matthew (ORCID:0000000339451143), Stich, Benjamin (ORCID:0000000167918068), Frommer, Wolf (ORCID:0000000164650115), Ross-Ibarra, Jeffrey (ORCID:0000000316564954), Hartwig, Thomas (ORCID:0000000227072771). 2025-08-11. Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. https://doi.org/10.1038/s41588-025-02246-7

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