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

作者：Julia Engelhorn, Samantha J. Snodgrass, Amelie Kok, Arun S. Seetharam, Michael Schneider, Tatjana Kiwit, Ayush Singh, Michael Banf, Merritt Khaipho-Burch, Daniel E. Runcie, Víctor A. Sánchez-Camargo, J. Vladimir Torres‐Rodríguez, Guangchao Sun, Maike Stam, Fabio Fiorani, Sebastian Beier, James C. Schnable, Hank W. Bass, Matthew B. Hufford, Benjamin Stich, Wolf B. Frommer, Jeffrey Ross‐Ibarra, Thomas Hartwig · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2023 · DOI：10.1101/2023.08.08.551183 · 被引用次数：21 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Genetics and Plant Breeding、Genetic and phenotypic traits in livestock

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 two-hundred thousand genetic variants (termed binding-QTL) linked to cis -element occupancy. Three lines of evidence support the functional significance of binding-QTL: i) they coincide with numerous known causative loci that regulate traits, including VGT1 , 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-QTL 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.