Nonadditive regulation confers phenotypic variation in hybrid maize

Abstract

• Our knowledge of how the parental genomes interact to shape hybrid performance remains limited.
• This work established four hybrid maize populations and evaluated plant height (PH) in both the parental and hybrid populations, generating an extensive transcriptome and translatome dataset. We conducted a genome-wide association study, expression quantitative trait locus (eQTLs) mapping, transcriptome-wide association mapping (TWAS), and allele-specific expression analysis to elucidate the regulatory mechanisms underlying PH variation in hybrids.
• QTLs, eQTLs, and TWAS-associated genes (TAGs) exhibited both distinct variations and conserved patterns between the maternal and hybrid populations. The functional route (FR)-following QTLs demonstrated significant nonadditive effects on PH and expression traits. The intergenomic interactions of eQTLs in the heterozygous state drive the nonadditive regulation of eQTL-regulated genes (eGenes), resulting in the transformation of eGenes into TAGs and eQTLs into nonadditive QTLs for PH. This regulatory mechanism is further supported by the nonadditive regulation of phytohormone-related genes. Additionally, nonadditive TAGs and QTLs are implicated in regulating nonadditive translation.
• This study elucidates how nonadditive QTLs contribute to phenotypic variation in hybrid maize, offering a fresh perspective on the understanding of plant heterosis.