Positive Selection and Transcriptional Regulation of the Sweet Corn Adaptation Gene ZmHPC1

Objective Sweet corn is an important vegetable and cereal crop, studies on the adaptation of sweet corn have significant implications for advancing practical breeding strategies and elucidating the theoretical underpinnings of plant domestication and evolution. This study aimed to elucidate the evolutionary history of the key adaptability gene ZmHPC1 in sweet corn and to investigateits regulatory mechanisms governing related genes, thereby exploring its functional role in maize environmental adaptation.

Method By employing a representative panel of 295 sweet corn and 507 field corn inbred lines, we detected selection signals using XP-CLR and Fst analyses, and reconstructed the evolutionary path of ZmHPC1 by integrating haplotype network and phylogenetic tree analyses. Screening of co-expressed genes from the kernel transcriptome data, coupled with functional enrichment analysis and eGWAS, was conducted to parse the regulatory mode.

Result ZmHPC1 was under strong positive selection in the sweet corn population, as evidenced by significant XP-CLR values (top 5%) and high Fst values (0.23-0.24) in comparisons with field corn subpopulations. The reduced nucleotide diversity at the 5' end compared to the 3' end of the gene suggests selective pressure on local functional sites. Haplotype network analysis revealed that the predominant ZmHPC1 haplotypes in sweet corn were not directly derived from those in field corn, a finding supported by phylogenetic analysis indicating a parallel evolution relationship. Co-expression analysis identified 1 884 genes significantly associated with ZmHPC1, which were markedly enriched in pathways related to stress response, hormone synthesis, and flavonoid metabolism. eGWAS analysis revealed that 1 106 expression quantitative trait loci (eQTLs) for those significantly associated with ZmHPC1 gene were broadly and dispersedly distributed across the genome without apparent regulatory hotspots, implying that ZmHPC1 might indirectly coordinate gene expression by influencing metabolites or signaling molecules.

Conclusion ZmHPC1 underwent significant selection during sweet corn improvement and plays a central role in maize adaptive evolution by systematically regulating the expression of stress-responsive and metabolic genes. Its indirect regulatory mode provides a novel perspective for understanding the molecular mechanisms of crop adaptation.