Global genetic dissection of maize–teosinte divergence reveals EL3-2 as a pleiotropic domestication regulator

Understanding the genetic basis of trait divergence between maize and its wild progenitor teosinte is critical for elucidating crop domestication processes and accelerating maize improvement. This divergence is governed by multiple loci, including genes with pleiotropic effects and complex genetic interactions that collectively contribute to morphological variation. Using a maize–teosinte (Mo17– mexicana ) introgression population, we identified 93 additive quantitative trait loci (QTLs) and nine epistatic interaction pairs affecting 20 agronomic traits, revealing a polygenic architecture underlying the domestication and improvement of these traits. The constructed QTL–trait network, together with identified genome-wide selection signals, revealed extensive genetic interconnections, with correlated traits sharing common loci, indicating a shared genetic basis for morphological divergence. Selection feature analysis further demonstrated that domestication, improvement, and mexicana introgression targeted key genomic regions associated with agronomic traits. Furthermore, we cloned an ear length QTL, EL3-2 , which encodes a ULTRAPETALA (ULT) transcriptional regulator. EL3-2 may function as a central pleiotropic regulator of domestication by modulating maize–teosinte divergence and regulating complex gene-expression networks across multiple developmental stages of maize. This study reveals a complex genetic basis for maize–teosinte morphological divergence and highlights the role of pleiotropic regulators in crop domestication. Our findings provide new insights that bridge evolutionary genomics and breeding for complex traits in maize.