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

Abstract

Background: 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. Results: Our 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. Conclusion: Combined 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.

Phosphorylation‐mediated signalling in flowering: prospects and retrospects of phosphoproteomics in crops

“…Further functional identification of homolog genes and ortholog proteins may accelerate our knowledge on the regulatory mechanisms of fertilization in crops. Other signalling networks that may have a role in the regulation of Ca 2+ circuits, pollen tube growth, and pollen tube reception include Ca 2+ /calmodulin (CaM), FERONIA (FER) RLK, CrRLK1L, pollen‐specific receptor kinases 2 (LePRK2), sterility‐regulating kinase members (SKMs), MAPK3/6, MYB98‐cysteine‐rich peptides (CRPs), RLCKs lost in pollen tube guidance 1 and 2 (LIP1/2), somatic embryogenesis receptor kinases (SERKs), proline‐rich extension‐like receptor protein kinases (PERKs), and Hercules receptor kinase 1 (HERK1) (Johnson, Harper & Palanivelu, 2019; Duan et al ., 2020; Galindo‐Trigo et al ., 2020; Lee, 2020; Ch en et al ., 2020 a ). The mechanisms and phospho‐regulatory pathways by which they act in crop species remain largely elusive.…”

Genome-Wide Identification Analysis of The Auxin Response Factor Gene Family (ARF) in Zizania Latifolia and its Role in Swelling Stem Formation After Ustilago Esculenta Infection

“…latifolia and Z. latifolia-Oryza sativa, which showed Ka/Ks ratios less than 0.45 and indicating the occurrence of strong purifying selection (Fig. 5, Table S3), re ecting the strong control exerted over these genes in evolution [53]. Moreover, the average divergence times of Z. latifolia-Z.…”

PERKing up our understanding of the proline‐rich extensin‐like receptor kinases, a forgotten plant receptor kinase family

“…3). Expression of most of the PERKs was first found to be specific to floral organs such as pollen grain, pollen tube or floral buds (Nakhamchik et al ., 2004; Chen et al ., 2020). However, AtPERK8 and AtPERK13/RHS10 (Root Hair Specific 10) are mainly expressed in roots and root hairs, respectively (Nakhamchik et al ., 2004; Won et al ., 2009; Humphrey et al ., 2015).…”