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

Autor: Engelhorn, Julia; Snodgrass, Samantha J.; Kok, Amelie; Seetharam, Arun S.; Schneider, Michael; Kiwit, Tatjana; Singh, Ayush; Banf, Michael; Doan, Duong Thi Hai; Khaipho-Burch, Merritt; Runcie, Daniel E.; Sánchez-Camargo, Victor A.; Bader, Rechien; Torres-
In:

Nature Genetics

DOI: 10.1038/s41588-025-02246-7
Seite: 1 - 21
Jahr: 2025

Einordung:
Institut: Professur Züchterische Nutzung pflanzengenetischer Ressourcen

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 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.

Ansprechpartner

Weitere Information im WWW

Zur Publikation: Mitarbeiter, Projekte
Weitere Publikationen im Forschungsteilschwerpunkt