The Genome Wide Comparative Analysis of PAL Gene Family in Rice (

Phenylalanine ammonia-lyase (PAL) is a pivotal enzyme initiating the phenylpropanoid pathway by catalyzing the deamination of phenylalanine to cinnamic acid. This pathway plays a vital role in the biosynthesis of secondary metabolites responsible for plant defense, lignin formation, UV protection, and adaptation to abiotic stresses. A total of 67 PAL genes were identified—9 in rice, 9 in barley, 13 in maize, and 36 in wheat. Gene structure analysis indicated that exon-intron organization ranged from one to four introns, and genes sharing similar structures clustered within the same phylogenetic clades. Phylogenetic analysis grouped all PAL genes into four major clusters, suggesting a closer evolutionary relationship between wheat and barley, while maize shared higher similarity with rice. Cis-regulatory element analysis using PlantCARE showed that MeJA-responsive motifs were the most abundant (24%), indicating that PAL genes are strongly regulated by environmental and hormonal cues. Gene Ontology (GO) annotation revealed that PAL genes are primarily involved in phenylalanine catabolic and phenylpropanoid metabolic processes, localized in the cytoplasm. Furthermore, predicted miRNA analysis demonstrated that osa-miR6246 and tae-miR1119, target multiple PAL genes, implying post-transcriptional regulatory control in stress and metabolic pathways. In conclusion, this comprehensive comparative analysis highlights the structural conservation, regulatory diversity, and evolutionary relationships of PAL gene families among cereals. The results provide essential molecular insights for functional characterization of PAL genes and their potential application in improving crop resilience and secondary metabolism through genetic engineering and breeding strategies.