Genome-wide analysis of bZIP-encoding genes in maize

Area of Science:

• Plant molecular biology
• Genomics
• Bioinformatics

Background:

• Basic leucine zipper (bZIP) proteins are crucial regulators of diverse plant biological processes, including development and stress responses.
• Understanding the maize bZIP gene family is essential for deciphering plant gene regulation.

Purpose of the Study:

• To conduct a comprehensive genome-wide identification and analysis of bZIP genes in the maize genome.
• To classify maize bZIP proteins based on phylogenetic relationships, intron patterns, conserved motifs, and structural features.
• To investigate the chromosomal distribution, evolutionary expansion, and expression patterns of maize bZIP genes in development and stress conditions.

Main Methods:

• Genome-wide identification and analysis of bZIP genes in maize.
• Phylogenetic analysis with Arabidopsis and rice bZIP proteins to define 11 groups.
• Analysis of intron patterns, conserved motifs, and 3D structures of bZIP domains.
• Prediction of DNA-binding and dimerization properties.
• Chromosomal distribution and genetic analysis, including segmental duplication.
• Gene expression profiling across 60 developmental stages and 11 organs.
• Analysis of gene expression in response to drought stress and fungal infections using Pearson's correlation coefficient.

Main Results:

• Identified 125 bZIP genes encoding 170 proteins in the maize genome, classified into 11 groups.
• Defined six intron patterns and identified group-specific conserved motifs.
• Predicted DNA-binding and dimerization properties, supporting the classification into 26 subfamilies.
• Found that 58 ZmbZIP genes are in segmental duplicate regions, indicating their role in family expansion.
• Revealed three distinct expression patterns across maize development.
• Identified 22 ZmbZIP genes potentially involved in drought stress.
• Observed significant negative (13 pairs) and positive (143 pairs) correlations in gene expression during fungal infections.

Conclusions:

• The maize bZIP gene family is extensive and diversified, with significant roles in plant development and stress responses.
• Segmental chromosomal duplications have driven the expansion of the ZmbZIP family.
• Expression patterns highlight the involvement of ZmbZIP genes in developmental processes, drought tolerance, and defense against fungal pathogens.