Nonadditive regulation confers phenotypic variation in hybrid maize

Area of Science:

• Plant genetics and genomics
• Maize breeding and genetics

Background:

• Limited understanding of parental genome interactions in shaping hybrid performance.
• Plant height (PH) is a key trait in hybrid maize, influenced by complex genetic factors.

Purpose of the Study:

• To elucidate the regulatory mechanisms underlying PH variation in hybrid maize.
• To investigate the role of intergenomic interactions in nonadditive gene regulation and phenotypic outcomes.

Main Methods:

• Genome-wide association study (GWAS) and expression quantitative trait loci (eQTLs) mapping.
• Transcriptome-wide association mapping (TWAS) and allele-specific expression analysis.
• Analysis of transcriptome and translatome data in parental and hybrid maize populations.

Main Results:

• QTLs, eQTLs, and TWAS-associated genes (TAGs) showed distinct and conserved patterns between maternal and hybrid populations.
• Functional route (FR)-following QTLs exhibited significant nonadditive effects on PH and gene expression.
• Intergenomic interactions involving eQTLs in heterozygotes drive nonadditive regulation of eGenes, transforming them into TAGs and eQTLs into nonadditive QTLs for PH.

Conclusions:

• Nonadditive QTLs play a crucial role in phenotypic variation in hybrid maize, particularly for plant height.
• Intergenomic interactions and nonadditive gene regulation are key mechanisms underlying plant heterosis.
• This study provides a novel perspective on the genetic basis of hybrid vigor in maize.