*Article* **Phenylalanine Ammonia-Lyase (PAL) Genes Family in Wheat (***Triticum aestivum* **L.): Genome-Wide Characterization and Expression Profiling**

**Fatima Rasool 1,2, Muhammad Uzair 2, Muhammad Kashif Naeem 2, Nazia Rehman 2, Amber Afroz 3, Hussain Shah <sup>4</sup> and Muhammad Ramzan Khan 1,2,\***


**Abstract:** Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway and plays a vital role in adoption, growth, and development in plants but in wheat its characterization is still not very clear. Here, we report a genome-wide identification of *TaPAL* genes and analysis of their transcriptional expression, duplication, and phylogeny in wheat. A total of 37 *TaPAL* genes that cluster into three subfamilies have been identified based on phylogenetic analysis. These *TaPAL* genes are distributed on 1A, 1B, 1D, 2A, 2B, 2D, 4A, 5B, 6A, 6B, and 6D chromosomes. Gene structure, conserved domain analysis, and investigation of *cis*-regulatory elements were systematically carried out. Chromosomal rearrangements and gene loss were observed by evolutionary analysis of the orthologs among *Triticum urartu*, *Aegilops tauschii*, and *Triticum aestivum* during the origin of bread wheat. Gene ontology analysis revealed that *PAL* genes play a role in plant growth. We also identified 27 putative miRNAs targeting 37 *TaPAL* genes. The high expression level of *PAL* genes was detected in roots of drought-tolerant genotypes compared to drought-sensitive genotypes. However, very low expressions of *TaPAL10, TaPAL30, TaPAL32, TaPAL3,* and *TaPAL28* were recorded in all wheat genotypes. Arogenate dehydratase interacts with TaPAL29 and has higher expression in roots. The analysis of all identified genes in RNA-seq data showed that they are expressed in roots and shoots under normal and abiotic stress. Our study offers valuable data on the functioning of *PAL* genes in wheat.

**Keywords:** phenylalanine ammonia-lyase (PAL); phylogenetic analysis; expression profiling; gene structure; drought stress
