Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites

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 nearly two-hundred thousand genetic variants (termed binding-QTLs) linked to cis -element occupancy. The functional significance of binding-QTLs is supported by three lines of evidence: i) they coincide with known causative loci that regulate traits, including novel alleles of Upright Plant Architecture2 , Trehalase1 , and the MITE transposon near ZmNAC111 under drought; ii) their footprint bias is mirrored between inbred parents and by ChIP-seq; iii) partitioning genetic variation across genomic regions demonstrates that binding-QTLs capture the majority of heritable trait variation across ∼70% of 143 phenotypes. Our study provides a promising approach to make previously hidden cis -variation more accessible for genetic studies and multi-target engineering of complex traits.