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001044973 1001_ $$00000-0002-6680-3012$$aEngelhorn, Julia$$b0
001044973 245__ $$aGenetic variation at transcription factor binding sites largely explains phenotypic heritability in maize
001044973 260__ $$aLondon$$bMacmillan Publishers Limited, part of Springer Nature$$c2025
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001044973 520__ $$aComprehensive 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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001044973 7001_ $$00000-0001-9209-6051$$aSnodgrass, Samantha J.$$b1
001044973 7001_ $$00009-0009-5930-5232$$aKok, Amelie$$b2
001044973 7001_ $$00000-0002-6789-9298$$aSeetharam, Arun S.$$b3
001044973 7001_ $$0P:(DE-Juel1)130948$$aSchneider, Michael$$b4$$ufzj
001044973 7001_ $$0P:(DE-HGF)0$$aKiwit, Tatjana$$b5
001044973 7001_ $$00000-0003-0184-4486$$aSingh, Ayush$$b6
001044973 7001_ $$0P:(DE-HGF)0$$aBanf, Michael$$b7
001044973 7001_ $$0P:(DE-HGF)0$$aDoan, Duong Thi Hai$$b8
001044973 7001_ $$0P:(DE-HGF)0$$aKhaipho-Burch, Merritt$$b9
001044973 7001_ $$00000-0002-3008-9312$$aRuncie, Daniel E.$$b10
001044973 7001_ $$00000-0002-7184-0301$$aSánchez-Camargo, Victor A.$$b11
001044973 7001_ $$00009-0001-4738-190X$$aBader, Rechien$$b12
001044973 7001_ $$0P:(DE-HGF)0$$aVladimir Torres-Rodriguez, J.$$b13
001044973 7001_ $$00000-0003-3942-6175$$aSun, Guangchao$$b14
001044973 7001_ $$00000-0003-0363-4677$$aStam, Maike$$b15
001044973 7001_ $$0P:(DE-Juel1)143649$$aFiorani, Fabio$$b16
001044973 7001_ $$0P:(DE-Juel1)191149$$aBeier, Sebastian$$b17
001044973 7001_ $$00000-0001-6739-5527$$aSchnable, James C.$$b18
001044973 7001_ $$00000-0003-0522-0881$$aBass, Hank W.$$b19
001044973 7001_ $$00000-0003-3945-1143$$aHufford, Matthew B.$$b20
001044973 7001_ $$00000-0001-6791-8068$$aStich, Benjamin$$b21
001044973 7001_ $$00000-0001-6465-0115$$aFrommer, Wolf B.$$b22
001044973 7001_ $$00000-0003-1656-4954$$aRoss-Ibarra, Jeffrey$$b23
001044973 7001_ $$00000-0002-2707-2771$$aHartwig, Thomas$$b24$$eCorresponding author
001044973 773__ $$0PERI:(DE-600)1494946-5$$a10.1038/s41588-025-02246-7$$p2313–2322$$tNature genetics$$v57$$x1061-4036$$y2025
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