Genome-wide analysis of proline-rich extension-like receptor protein kinase (PERK) in Brassica rapa and its association with the pollen development

Guohu Chen,Lei Zhang,Jinfeng Hou,Jie Li,Chenggang Wang,Hao Wang,Jianghua Song,Jian Wang,Lingyun Yuan,Xiaoyan Tang

doi:10.1186/s12864-020-06802-9

Abstract

BackgroundProline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development.ResultsOur study identified 25 putative PERK genes from the whole Brassica rapa genome (AA). Phylogenetic analysis of PERK protein sequences from 16 Brassicaceae species divided them into four subfamilies. The biophysical properties of the BrPERKs were investigated. Gene duplication and synteny analyses and the calculation of Ka/Ks values suggested that all 80 orthologous/paralogous gene pairs between B. rapa and A. thaliana, B. nigra and B. oleracea have experienced strong purifying selection. RNA-Seq data and qRT-PCR analyses showed that several BrPERK genes were expressed in different tissues, while some BrPERKs exhibited high expression levels only in buds. Furthermore, comparative transcriptome analyses from six male-sterile lines of B. rapa indicated that 7 BrPERK genes were downregulated in all six male-sterile lines. Meanwhile, the interaction networks of the BrPERK genes were constructed and 13 PERK coexpressed genes were identified, most of which were downregulated in the male sterile buds.ConclusionCombined with interaction networks, coexpression and qRT-PCR analyses, these results demonstrated that two BrPERK genes, Bra001723.1 and Bra037558.1 (the orthologs of AtPERK6 (AT3G18810)), were downregulated beginning in the meiosis II period of male sterile lines and involved in anther development. Overall, this comprehensive analysis of some BrPERK genes elucidated their roles in male sterility.

Highlights

Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development
A maximum likelihood (ML) tree was generated for these Prolinerich extension-like receptor protein kinase (PERK) proteins, showing that all PERKs were grouped into four subfamilies (Groups I-IV; Fig. 1, Table S2)
Among Brassica species, 25, 27 and 22 PERK family members were identified in B. rapa (AA), B. nigra (BB) and B. oleracea (CC), respectively (Table S1; Fig. S1)

Summary

Introduction

Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development. Unique membrane receptor-like kinases (RKs) have evolved to regulate biological processes in plants [1, 2]. These plasma membrane RKs perceive various stimuli. Recent work addressing the PERK family of Gossypium hirsutum has revealed the expression patterns of these genes in response to various abiotic stresses and hormonal homeostasis [15]. In addition to these functions, PERKs are thought to act as sensors/receptors to monitor changes in the cell wall during its expansion [1, 12]

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Discussion

Conclusion