A Dominant-Negative Pleiotropic QTL from Elite Maize Inbred Line Zheng58 Underpins Ideal Plant Architecture for High-Density Maize Breeding

Abstract

The elite maize inbred line Zheng58, female parent of the widely cultivated hybrid Zhengdan958, is renowned for conferring short stature and high-density tolerance. Despite its critical role in modern breeding, the genetic basis of its dominant dwarfing effect has remained elusive. In this study, we dissected the genetic architecture of six plant architecture traits in a recombinant inbred line (RIL) population derived from elite inbred lines Zheng58 and PH6WC. Phenotypic evaluations across four environments revealed high heritability with additive effects accounting for 45.5–64.6% of the total genetic variance. A total of 125 QTLs were identified for the traits in single-environment QTL mapping, and multi-environment analysis further detected 77 QTLs for the six traits. Notably, a major dominant-negative pleiotropic QTL was identified on chromosome 2 that consistently explains plant height (PH), plant height above ear (PHAE), and average internode length above ear (AILAE) across multiple environments. The Zheng58 allele at this locus acts dominantly to reduce plant height by approximately 8.7 cm, providing a genetic explanation for Zheng58’s characteristic dwarfing effect. Regional association mapping refined this QTL to a 351.9 kb interval harboring 13 candidate genes. Transcriptome analysis uncovered 205 differentially expressed genes (DEGs) within the QTL region, with only one DEG (Zm00001d005848) located in the pleiotropic hotspot QTL on chromosome 2. This candidate gene encodes a rhomboid protease homolog, and population-wide expression data showed significantly negative correlation with PH. Our study unveils the genetic mystery of Zheng58′s dominant dwarfing phenotype by pinpointing a pleiotropic QTL hotspot, offering a strategic target for molecular breeding of compact, high-density-tolerant hybrids in maize.