Receptor-like kinases (RLKs) are membrane proteins with an extracellular receptor domain, such as leucine rich repeats (LRRs), lectin (Lec), lysine motif (LysM) or wall associated kinases (WAK) [1]. RLK gene families from various plants have been identified in a large number of articles. We summarized these findings in the following.
(1) Whole RLKs: In 2003 and 2004, Shiu et al. identified more than 600 in Arabidopsis thaliana and more than 1200 in Oryza sativa [2–3]. They play important roles in the plant growth, development, defense response to stresses. More than 440 RLKs from O. sativa might have originated from the domain fusion events after the split of rice and Arabidopsis in evolution. In 2009, Lehti-Shiu et al. found that the expansion of RLK members coincided with the establishment of land plants [4]. In 2018, Lin et al. identified 563 RLK genes in Jilin ginseng (Panax ginseng C.A. Meyer), and analyzed their evolution, functional diversity and co-expression networks [5].
(2) LRR-RLKs (subfamily of RLK): In 2013, Zan et al. identified 379 LRR-type RLK genes in Populus trichocarpa. 312 PtLRR-RLK genes out of 379 are located in segmental duplication blocks. Genome-wide analysis of microarray data showed that some PtLRR-RLKs responsed to shoot organogenesis, low ammonium feeding, wounding, hypoxia and seasonal dormancy [6]. In 2017, Liu et al. studied the origin and diversity of LRR-RLKs in plants, and found that most LRR-RLKs were established in early land plants [7]. In 2018, Sun et al. identified a total of 1641 LRR-RLK genes in four Gossypium species (Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii). Tandem duplication played an important role in the expansion of Gossypium LRR-RLK gene family. Expression pattern analysis showed that Gossypium LRR-RLKs were widely involved in various stress defenses and diverse developmental processes [8]. In 2020, Meng et al. identified 329 LRR-RLK genes in Medicago truncatula. Analysis of classification, duplication events, exon/intron organization, expression profiling were performed in M. truncatula LRR-RLKs [9]. In 2021, 437 LRR-RLK genes were identified in Saccharum spontaneum, and categorized into 14 groups. Analysis of promoter sequences and expression profiles showed that SsLRR-RLKs were strongly regulated by various environmental stimuli, transcription factors and phytohormonal factors, suggesting that they responses to various diverse abiotic and biotic stresses [10]. In 2022, Song et al. identified 444 BnLRR-RLKs in Brassica napus cultivar “Zhongshuang 11” and classified them into 22 subfamilies. Based on CRISPR/Cas9 technology, they obtained six partial knockouts of BnBRI1 homologs to generate semi-dwarf lines without decreased yield compared with controls [11]. In 2022, 15 TaRPK1 (Receptor-like protein kinase 1, a calcium independent Serine-Threonine kinase that belongs to the subfamily LRR-RLK) genes were identified in Triticum aestivum. 18 putative miRNAs targeting and Cis-Regulatory elements (light-related, hormone responsiveness,and stress elements) were identified in TaRPK1 genes. In silico expression analysis and qRT-PCR validated that TaRPK1 genes exhibited higher expressions in roots of drought-tolerant varieties than drought-susceptible variety [12].
(3) LecRLKs (subfamily of RLK): In 2020, 46 putative Lectin receptor-like kinases were identified in the cucumber (Cucumis sativus L.) genome, and were classified into three groups including 23 G-type, 22 L-type, and one C-type CsLecRLK gene. Analysis of promoter regulatory elements and expression patterns revealed that some CsLecRLKs were associated with phytohormones and stress responses [13]. In 2020, Singh et al. identified 73 putative VrLecRLKs in mungbean (Vigna radiata L. Wilczek), and classified them into three families, such as G-type, L-type, and C-type VrLecRLKs [14]. In 2021, 1311 AhRLKs including AhLRR-RLKs and AhLec-RLKs were identified from the peanut (Arachis hypogaea) genome. The result of mining transcriptome data showed that 14 of 90 Al-responsive AhRLKs expressed specifically in root tissue [15].
(4) LysM-RLKs (subfamily of RLK): In 2020, Yang et al. identified 493 RLKs (LysM-RLKs and LRR-RLKs) and 228 RLPs (LysM-RLPs and LRR-RLPs) in the genome of Brassica juncea. The majority of RLKs (90.17%) and RLPs (52.83%) of B. juncea are from duplication events, indicating that duplication events significantly contributed to the expansion of RLK and RLP gene families [16]. In 2021, Abedi et al. identified 33 LysM-RLK genes (subfamily of RLK) in three Brassica species (17 in Brassica napus, 8 in Brassica rapa and 8 in Brassica oleracea). RNA-seq expression analysis revealed that BnLYP6 exhibited high expression in response to various biotic stresses. Structural modeling and docking simulation revealed that several residues in the active sites of BnLYP6 could directly contact with the chitin [17].
(5) CRKs (Cysteine-rich receptor-like kinases, subfamily of RLK): In 2019, Quezada et al. identified 46 CRKs in Phaseolus Vulgaris, and performed the comprehensive analysis, including identification, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis [18]. In 2019, Shumayla et al. identified 43, 37, 36, 38 and 170 CRK genes in the genome of Brachypodium distachyon, Hordeum vulgare, O. sativa, Sorghum bicolor and T. aestivum, respectively. These CRKs were tightly clustered into four phylogenetic groups, and were variably conserved in exon/intron, domains and motifs. Tissue-specific expression analysis suggested that some CRK genes are involved in plant development [19].
(6) PERKs (Proline-rich extensin-like receptor kinases, subfamily of RLK): In 2004, 15 predicted AtPERKs in A. thaliana, and some AtPERK members were identified as tissue-specific genes [20]. In 2022, 37 TaPERKs were identified in wheat (T. aestivum L.), and were classified into eight well-defined groups. Analysis of cis-acting regulatory elements and expression profile revealed that some TaPERKs are in response to phytohormones, various biotic and abiotic stresses [21].
Some articles had reported that RLKs play important roles in response to abiotic and botic stresses, such as drought, heat, salinity and cold. Transgenic Arabidopsis plant (35S:PdERECTA) of over-expression PdERECTA (transformed with Populus deltoides PdERECTA, an LRR-type RLK) improves the water use efficiency and enhances the drought resistance [22]. Rice (O. sativa) OsSIK1 (LRRs RLK) improves the tolerance of drought and salt stress. Transgenic rice plants with overexpression of OsSIK1 enhance the tolerance to salt and drought stresses, while the knock-out and RNA interference plants exhibit sensitive to drought and salt stresses [23]. OsLecRLK overexpression and downregulation (through artificial miRNA) transgenic lines proved that rice OsLecRLK enhances salinity tolerance through ion homeostasis [24]. The interaction network of 255 Arabidopsis LRR-RLKs (567 pairs interaction relationships) was established by using a sensitized high-throughput interaction assay. Plants have evolved LRR-RLK networks to process extracellular signals into cell, functioning in plant growth and immunity [25]. MtDMI2 (a Leu rich repeat-type receptor kinase) and MtPUB2 (a novel plant U-box (PUB)-type E3 ligase) interact to form a negative feedback loop, playing an important role in nodulation homeostasis [26]. The systemin receptor SYR1 (an LRR-RLK) of tomato is not decisive for local and systemic wound responses, but important for defense against insect herbivory [27]. The A. thaliana lectin RLK AtLecRK-IX.2 can modify pathogen effector AvrPtoB to dampen their virulence in Arabidopsis [28]. By using a map-based cloning strategy, Duriez et al. identified a sunflower protein HaOr7 (LRR-RLK) as a gene that confers resistance to Orobanche cumana [29]. Rao et al. constructed nine higher order mutants of A. thaliana receptor-like cytoplasmic kinase (RLCK) subfamily VII, revealing that numerous RLCK VII members are involved in plant development and pattern-triggered immune signaling [30]. A. thaliana AtRIPK (RPM1-INDUCED PROTEIN KINASE), an RLCK VII subfamily member, contributes to ROS (reactive oxygen species) production in plant immune system [31].
In recent years, biological functions of wheat RLKs mediating the response to botic stress have been reported. In 2016, Rajaraman et al. found that a barley LRR-type RLK gene HvLEMK1 was a factor mediating non-host resistance in barley and quantitative host resistance in wheat to the wheat powdery mildew fungus [32]. In 2018, Saintenac et al. discovered that the RLK gene Stb6 (a conserved wall-associated receptor kinase (WAK)-like protein, subfamily of RLK) in wheat is a natural resistance gene to fungal pathogen Zymoseptoria tritici [33]. In 2019, Wang et al. found an LRR-type RLK gene TaXa21 in wheat is highly homologous to the rice bacterial blight resistance gene Xa21. They also found that TaXa21 is a positive regulator of wheat high-temperature seedling plant (HTSP) resistance to Puccinia striiformis f. sp. tritici. This process is mediated by the H2O2 and ethylene (ET) signaling pathway, and associating with the transcription factor TaWRKY76 and TaWRKY62 [34]. In 2020, Gu et al. discovered a novel cysteine-rich RLK gene TaCRK2 which positively regulates the leaf rust resistance in wheat [35]. Using comparative genomics, mutagenesis and complementation, Saintenac et al. identified a wheat cysteine-rich RLK gene Stb16q, which exhibited resistance against Septoria tritici blotch (Stb, pathogen Zymoseptoria tritici), and localized at the plasma membrane in infection cycle [36]. In 2021, Guo et al. identified a novel CRK RLK gene TaCRK3 which could defend against Rhizoctonia cerealis in wheat. TaCRK3 protein contains two DUF26 (DOMAIN OF UNKNOWN FUNCTION 26) domains which could inhibit the growth of R. cerealis mycelia [37]. In 2021, the Wheat Wall-Associated Receptor-Like Kinase (WAK, subfamily of RLK) TaWAK-6D and TaWAK7D were identified to mediate broad resistance to Fungal pathogens (Fusarium pseudograminearum and R. cerealis) [38–39]. In 2022, TaPsIPK1 (a wheat receptor-like cytoplasmic kinase gene) is identified to be a susceptibility gene as the target of stripe rust (caused by P. striiformis f. sp. tritici) effectors [40].
In this study, we performed genome-wide identification, classification, evolutionary analysis of RLK gene family in 15 representative plants, including four wheat and Aegilops tauschii. Several conserved intron–exon structures within conserved kinase domain were found in 15 representative plants, suggesting that these RLKs might play important roles in plant developmental and evolutionary processes. Chromosome locations and collinearity events among T. aestivum, B. distachyon and O. sativa RLKs were determined to study the expansion of wheat RLKs. Some tandem gene clusters of wheat RLKs were found on 21 chromosomes. Global expression analysis of stresses were performed in individual T. aestivum RLKs. QRT-PCR of 9 selected RLKs were performed to validate the prediction of transcriptome under drought condition and Fusarium graminearum infection. Our results will help researchers study evolutionary history and molecular mechanisms of wheat RLKs.