Comparative Transcriptome Analysis Reveals Divergent Gene Expression Dynamics During Anther Maturation in Maize and Its Wild Progenitor Teosinte

Maize (Zea mays L.), a vital crop for global food security, and its wild progenitor teosinte (Zea mays ssp. parviglumis) exhibit genetic divergence that offers opportunities for maize improvement. This comparative transcriptome analysis of maturing anthers, essential for reproduction and yield, identified substantial transcriptional differences despite morphological similarities. RNA sequencing of six sample from inbred maize B73 and teosinte yielded over 45.35 million clean reads per sample, with alignment rates of 84–87% to the B73 NAM 5.0 genome. Among 29,134 expressed genes, 16,147 were differentially expressed (DEGs; padj < 0.05, |log2FoldChange| > 1), comprising 7,244 upregulated and 8,903 downregulated in teosinte relative to maize. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed significant enrichment in photosynthesis (GO:0009768), ion channel activity (GO:0022843), lipid metabolism (GO:0006629), and carbohydrate metabolism (ko01200). Phylogenetic analysis of 50 anther development-related DEGs delineated three distinct clades, highlighting evolutionary conservation and divergence. Quantitative real-time PCR (qRT-PCR) validation corroborated RNA-seq patterns for 10 selected DEGs, including those of particular biological interest such as fertility regulators and stress-responsive genes. These findings elucidate the transcriptional framework of anther maturation in maize and teosinte, pinpointing candidate genes for anther development that could inform breeding strategies to enhance maize fertility and stress resilience.