Comparative transcriptomic analysis of heterotic maize development during kernel filling

Heterosis, characterized by enhanced performance of a hybrid relative to its parental lines, has been a fundament of plant breeding strategies. Despite the application of heterosis, its molecular mechanisms remain elusive. Here, we focused on the maize heterotic hybrid Yudan132, which showed enhanced agronomic traits compared to its parental lines, including ear and kernel size, kernel weight, and overall yield. Notably, Yudan132 showed increased accumulation of storage substances, characterized by starch, protein contents and grain-filling rates, all of which collectively contribute to the augmented kernel weight. Through gene expression profiling, we identified differentially expressed genes (DEGs) in Yudan132 and its parental lines across four distinct kernel developmental stages (12, 20, 28, and 40 days after pollination). These DEGs displayed both additive and non-additive expression patterns, each contributing to heterosis in maize kernels. The Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis highlighted their involvement in metabolic pathways, biosynthesis of secondary metabolites, carbon metabolism, starch and sucrose metabolism processes. Within these pathways, the enriched DEGs predominantly associated with the gene categories of peroxidase, cytochrome P450, ketoacyl-CoA synthase, and phospholipase D. Furthermore, we identified the transcription factor bZIP88 among the DEGs, which was involved in the regulation of seed size and weight in transgenic Arabidopsis. These results suggested a potential role for bZIP88 in modulating kernel development, thereby further implicating the involvement of the identified DEGs in the molecular mechanisms of heterosis. These findings provide the genetic role of heterosis in kernel and the molecular mechanism regulating kernel development.