Genome-Wide Analysis and Characterization of the Proline-Rich Extensin-like Receptor Kinases (PERKs) Gene Family Reveals Their Role in Different Developmental Stages and Stress Conditions in Wheat (Triticum aestivum L.)

Abstract

Proline-rich extensin-like receptor kinases (PERKs) are a class of receptor kinases implicated in multiple cellular processes in plants. However, there is a lack of information on the PERK gene family in wheat. Therefore, we identified 37 PERK genes in wheat to understand their role in various developmental processes and stress conditions. Phylogenetic analysis of PERK genes from Arabidopsis thaliana, Oryza sativa, Glycine max, and T. aestivum grouped them into eight well-defined classes. Furthermore, synteny analysis revealed 275 orthologous gene pairs in B. distachyon, Ae. tauschii, T. dicoccoides, O. sativa and A. thaliana. Ka/Ks values showed that most TaPERK genes, except TaPERK1, TaPERK2, TaPERK17, and TaPERK26, underwent strong purifying selection during evolutionary processes. Several cis-acting regulatory elements, essential for plant growth and development and the response to light, phytohormones, and diverse biotic and abiotic stresses, were predicted in the promoter regions of TaPERK genes. In addition, the expression profile of the TaPERK gene family revealed differential expression of TaPERK genes in various tissues and developmental stages. Furthermore, TaPERK gene expression was induced by various biotic and abiotic stresses. The RT-qPCR analysis also revealed similar results with slight variation. Therefore, this study’s outcome provides valuable information for elucidating the precise functions of TaPERK in developmental processes and diverse stress conditions in wheat.

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

“…Since the ratio of Ka/Ks is a good indicator of the selection pressure occurring at the protein level, we evaluated the values of Ks (synonymous) and Ka (nonsynonymous) as well as the ratio of Ka/Ks ( Table S4 ). Ka/Ks < 1, Ka/Ks = 1, and Ka/Ks > 1 generally indicate negative, neutral, and positive selection, respectively [ 30 ]. A total of 240 segmental duplicated gene pairs had Ka/Ks < 1, ranging from 0 to 0.94, with mean values of Ka, Ks, and Ka/Ks of 0.06, 0.22, and 0.28, respectively.…”

Genome-Wide Identification and Analysis of FKBP Gene Family in Wheat (Triticum asetivum)

“…Genome-wide analysis of a gene family is a way of rapidly and efficiently analyzing pathways to characterize gene functions and evolution [ 36 , 37 , 38 , 39 ]. In wheat, various genes are involved in drought, salt and metal stress responses by characterizing genes families [ 40 , 41 , 42 ].…”

Identification of YABBY Transcription Factors and Their Function in ABA and Salinity Response in Nelumbo nucifera

“…Many articles on abiotic stress have been published, and many transcription factors involved in the responses to abiotic stress in plants have been revealed. Proline-rich extensin-like receptor kinases (PERKs) are involved in the responses to biological and abiotic stresses in wheat [ 31 ]. When plants are under abiotic stress, long non-coding RNAs can interact with miRNAs to regulate transcription factors related to the stress response [ 32 ].…”