Analysis of the Dirigent Pan-Gene Family in 26 Diverse Inbred Lines Reveals Genomic Diversity in Maize

Dirigent genes play crucial roles in regulating plant architecture development and responses to environmental stress. However, the pan-genomic attributes of these genes remain poorly characterized.

The dirigent pan-gene family was reconstructed using the public genome assemblies from the 26 maize Nested Association Mapping project founder lines. Orthogroup classification based on multiple sequence alignment revealed both core and variable family members. Evolutionary pressures were assessed through Ka/Ks ratio analysis, and promoter regions were examined for cis-acting regulatory elements. Haplotype, transcriptomic and genome-wide association study (GWAS) analyses were integrated to explore genetic diversity and functional relevance.

Most dirigent members were under purifying selection, whereas a subset may have undergone positive selection. Promoter analysis demonstrated enrichment of stress- and phytohormone-responsive cis-acting regulatory elements, suggesting that regulatory divergence was associated with environmental adaptation. Haplotype analysis revealed allelic diversity among heterotic clusters, potentially contributing to heterosis. Integration with public genome-wide association study datasets identified candidate genes significantly associated with plant architecture and kernel-quality-related traits. Transcriptome profiles indicated that several dirigent genes were preferentially expressed in the roots, suggesting their involvement in root development and nutrient uptake. In addition, public gene expression data showed that certain dirigent genes are induced in response to salt stress, supporting their putative roles in abiotic stress tolerance.

These findings provide insights into the molecular mechanisms underlying dirigent gene functions and reveal candidate genes with potential utility for improving maize performance and stress resilience through molecular breeding.