- Research article
- Open Access
Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean
BMC Plant Biology volume 16, Article number: 58 (2016)
Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, development, differentiation, and stress responses. However, no comprehensive analysis of this gene family has been carried out in legume species.
Based on the principles of sequence similarity and domain conservation, a total of 467 LRR-RLK genes were identified in soybean genome. The GmLRR-RLKs are non-randomly distributed across all 20 chromosomes of soybean and about 73.3 % of them are located in segmental duplicated regions. The analysis of synonymous substitutions for putative paralogous gene pairs indicated that most of these gene pairs resulted from segmental duplications in soybean genome. Furthermore, the exon/intron organization, motif composition and arrangements were considerably conserved among members of the same groups or subgroups in the constructed phylogenetic tree. The close phylogenetic relationship between soybean LRR-RLK genes with identified Arabidopsis genes in the same group also provided insight into their putative functions. Expression profiling analysis of GmLRR-RLKs suggested that they appeared to be differentially expressed among different tissues and some of duplicated genes exhibited divergent expression patterns. In addition, artificial selected GmLRR-RLKs were also identified by comparing the SNPs between wild and cultivated soybeans and 17 genes were detected in regions previously reported to contain domestication-related QTLs.
Comprehensive and evolutionary analysis of soybean LRR-RLK gene family was performed at whole genome level. The data provides valuable tools in future efforts to identify functional divergence of this gene family and gene diversity among different genotypes in legume species.
Receptor-like kinases (RLKs) are a diverse group of transmembrane proteins characterized with a ligand-binding domain to receive signal molecules, a membrane-spanning domain to anchor the protein, and a cytoplasmic protein kinase domain to transduce signals downstream . In both plants and animals, RLKs mediate plenty of signaling messages at the cell surface and act as key regulators during developmental processes [2–4]. The first RLK of higher plant was isolated from maize and subsequently numerous RLKs have been identified from more than 20 plant species . In plant, the superfamily of RLKs is divided into three major groups based on the presence or absence of the receptor and kinase domain [1, 6, 7]. According to the divergence of extracellular domains, RLKs can be further classified into 17 subgroups, including leucine-rich repeat (LRR) RLKs, S-domain RLKs, and so on [8, 9]. Among all these subgroups, LRR-RLK is the largest one in plants by far, the members of which contain several tandem repeats of about 24 amino acids with conserved leucine residues in the extracellular regions [7, 10].
Genetic and biochemical studies have demonstrated that plant LRR-RLKs play important roles in diverse processes during growth and development [11, 12]. In Arabidopsis, LRR-RLKs including SERK1/2, EMS1, BAM1/2, RPK2 and FER have been proved to modulate the processes of anther development and fertilization [13–18]. Enough evidences supported that CLV and RPK2 were essential receptor-like kinases in formation and maintenance of shoot apical meristem [19, 20]. Some other reports also revealed that LRR-RLK genes such as BRI and BAK1 were involved in brassinosteroid signaling transduction while a few other LRR-RLK genes were associated with the stress responses of abscisic acid [21–23]. Moreover, some LRR-RLK genes were also reported to possess dual functions due to the cross talks between plant development and defense processes or the recognition of multiple ligands by one receptor . For example, Arabidopsis ERECTA gene has been characterized not only to regulate ovule development  but also to be involved in resistance to bacterial wilt .
The rapidly increasing sequenced genomes have facilitated identification of whole gene family by bioinformatics tools at genomic level in plant. To date, the structure features and expression profiles of LRR-RLK genes have been described in plants including Arabidopsis , rice , and poplar . In most of these species, LRR-RLKs appeared to be large families with hundreds of members and evolved to perform diverse functions [28–30]. Some reports also revealed that LRR-RLK genes had redundant functions due to extensive gene duplication in genome. For example, although single mutant of serk1 or serk2 displays normal anther morphology, serk1 serk2 double mutant could rescue the phenotype of exs or ems mutants which failed to form pollen due to the absence of tapetal cell layer and production of extra sporogenous cells in Arabidopsis [13, 14]. Translational fusion study of SERK1/SERK2 to variants of green fluorescent protein also suggested that SERK1/SERK2 may function as part of a protein complex .
Soybean (Glycine max) is the most important legume source of protein for animal feed and economic source of vegetable oil for human nutrition . During the evolutionary history, soybean genome underwent two rounds of whole genome duplication (WGD) approximately 59 and 13 million years ago (MYA) . Unlike most of other diploids, nearly 75 % of genes exhibit multiple copies in soybean genome due to the lack of immediate diploidization during the relatively recent WGD . Therefore, the structure features of most gene families in soybean are more complex than in Arabidopsis, rice or poplar. Although only a few members of LRR-RLK genes have been functionally characterized in soybean, enough evidences supported that soybean LRR-RLK genes also played important roles in various plant development and defense processes including leaf senescence, cell elongation, and cold stress tolerance [34–36].
In the present study, a genome-wide search for LRR-RLK genes was performed in soybean and a total of 467 GmLRR-RLKs had been identified. Detailed analysis of genome organization, sequence phylogeny, gene structure, conserved domains, duplication status, and expression profiling were carried out. In addition, the evolutionary patterns of the LRR-RLK gene family were examined in soybean by analysis of genes in tandem and segmental duplication regions. Moreover, the effect of artificial selection in soybean LRR-RLK gene family was also detected during soybean domestication. Our results provide a framework for further evolutionary and functional characterization of the LRR-RLK gene family in soybean.
Results and discussions
Identification and genome distribution of LRR-RLK gene family in soybean
In order to identify all members of LRR-RLKs in soybean genome, a batch BLAST search was performed against soybean protein database using the amino acid sequences of all Arabidopsis LRR-RLKs as queries. All of the retrieved soybean proteins were then submitted to SMART and PFAM databases for annotation of the domain structure. Only candidate containing at least one LRR domain and a kinase domain was regarded as a “true” LRR-RLK. After removing of the unsupported sequences and redundant genes manually, a total of 467 putative LRR-RLK genes were identified from the whole genome of soybean. The identified soybean LRR-RLK genes encode peptides ranging from 423 to 1563 a.a. in length. Detailed information for each gene, including the accession number and the characteristics of the encoded protein, was listed in Additional file 1. Among all these putative GmLRR-RLKs, only three proteins (Glyma.03G026800, Glyma.07G047200 and Glyma.13G228300) were predicted to have two kinase domains. Comparing with LRR-RLK genes identified in Arabidopsis, rice and populus genome (213, 309 and 379 members respectively) [26–28], soybean LRR-RLK gene family identified in this study is the largest one in plant so far. The number of GmLRR-RLKs is about 2.2 fold of that of AtLRR-RLKs, which is consistent with the ratio of putative soybean homologs to each Arabidopsis gene [32, 37].
Physical positions of GmLRR-RLKs obtained from the Phytozome database (Additional file 1) were used to map them onto corresponding chromosomes of soybean. Results showed that 464 out of all soybean LRR-RLK genes could be mapped on all chromosomes from chromosome 1 to 20 (Fig. 1) while three other genes could be only mapped to unassembled genomic sequence scaffolds. Although every chromosome contained a certain number of LRR-RLK genes, the distribution of them appeared to be uneven across different chromosomes. The distribution ratio for each chromosome ranged from 2.4 % (11 members on chromosome 20) to 8.4 % (39 members on chromosomes 8 and 18). This distribution pattern is similar with other gene families in soybean and LRR-LRK gene families in other plant species [26–28, 38, 39].
Phylogenetic analysis of soybean LRR-RLKs
To study the evolutionary relationships of LRR-RLK members in soybean, the amino acid sequences of kinase domains from all GmLRR-RLKs were used to perform a multiple alignment with Cluster X and a phylogenetic tree was constructed using MEGA (Fig. 2). The phylogenetic tree showed that all GmLRR-RLKs could be classified into different groups or subgroups according to the nodes of the tree. When all the GmLRR-RLKs were clustered with all AtLRR-RLKs (Additional file 2), the members of each soybean LRR-RLKs group were determined according to the nomenclature of the Arabidopsis homologues within the same group (Table 1 and Fig. 2). Interestingly, some members of GmLRR-RLKs exhibited soybean specific features due to high level of duplication in genome. For examples, although only two members of Arabidopsis LRR-RLKs (AT1G35710 and AT4G08850) in the subgroup XII-b, as many as 45 GmLRR-RLKs were identified as the orthologous genes of these two AtLRR-RLKs (Additional file 2). The rapid expansion of GmLRR-RLKs in subgroup XII-b may result from two large gene clusters in Chromosomes 16 and 18.
Since most of the AtLRR-RLKs with similar functions have a tendency to cluster together, the soybean LRR-RLK genes in the same group or subgroup may have similar functions with their Arabidopsis homologs. Except for groups IV and VIII having no Arabidopsis ortholog with identified function, all the other groups have at least one AtLRR-RLK functional characterized. For example, GmLRR-RLKs in groups I, II, III, VII, and XII were clustered with AtLRR-RLKs involved in organ/tissue development and defense signaling [13, 14, 40–43]. Group V included the Arabidopsis SCM gene related to root hair specification and the SRF gene in cell wall biology [44, 45]. In addition, the Arabidopsis LRR-RLK genes involved in brassinosteroid and peptide signaling fell into the group X  and genes related to cell fate specification, organ morphogenesis , vascular development [48, 49], abscisic acid signaling, and defense response  were grouped in group XI. Moreover, subgroup XIII-a contained two FEI genes which were involved in signaling pathway of cell wall development , while subgroup XIII-b included ERECTA and ERECTA-LIKE genes regulating the stomata development and organ size .
Gene structure and conserved motif analysis
Since exon/intron diversification of members in a gene family always plays an important role in the evolution of this gene family , the exon/intron organization of individual soybean LRR-RLK gene was also analyzed. The results showed that nearly half members of GmLRR-RLKs (217 out of 467) had only one intron while 26 genes had only one exon. Two, three, four, and five introns were found in 46, 19, 4, and 4 soybean LRR-RLK genes. Meanwhile, a total of 151 genes had more than five introns and 96 out of them had more than ten (Additional files 1 and 3). In terms of intron number and length, most of GmLRR-RLKs in the same groups or subgroups have very conserved exon/intron organizations (Fig. 3). For instance, majority of soybean LRR-RLK genes in groups VII, X, and XI contain zero, one, and two introns except for only three members with four introns. However, the members of groups V, VI and XII displayed a large variability in either number or distribution of introns. Most interestingly, the members of subgroup XIII-b contain as many as 26 introns, which is about twice as many as that in the members of subgroup XIII-a. The exon/intron organization indicated the conservation within subgroup and divergence among different subgroups.
To further understand the potential functions of the LRR-RLK genes in soybean, all putative motifs of these proteins were predicted by using the program MEME (Multiple Em for Motif Elicitation). The results suggested that the motif compositions among groups or subgroups were consistent with the phylogenetic classification. Differences among groups or subgroups were observed in not only types of motifs but also number of specific motif in one protein (Additional file 4). In addition, searching for the possible signal peptides in all soybean LRR-RLKs using SignalP showed that 359 members have signal peptides. Meanwhile, the transmembrane (TM) domain was also predicted with TMHMM and a total of 442 GmLRR-RLKs had at least one while 25 members had no TM domain, among which 205 proteins had at least two TM domains. These results also indicated that most of the closely related members in the phylogenetic tree exhibited similar motif, which further suggested that a great deal of functional redundancy existed among soybean LRR-RLK proteins in the same subgroup (Fig. 3 and Additional file 5).
Gene duplication and orthologous relationships of soybean LRR-RLK genes
Gene duplication is always considered to be one of primary driving forces during the evolution of genomes . Segmental duplication, tandem duplication and transposition events are regarded as three main causes for the expansion of gene family in plant . In our analysis, the tandem duplication cluster was defined as a region containing two or more soybean LRR-RLK genes within 200 kb. The results showed that about 20.3 % (94 out of 464) genes in this gene family were located in regions with tandem duplications and composed 33 clusters in total (Additional file 6). The largest tandem duplication cluster contained as many as ten genes while the smallest one contained only two. Further analysis also revealed that the tandem duplication clusters were distributed unevenly among 14 phylogenetic groups. Group XII contained the most clusters with eight clusters including 35 genes while Groups III, IV, V, VI, VII, IX, XIV had no cluster.
Segmental duplications generate duplicated genes through polyploidy followed by chromosome rearrangements . Our results showed that a total of 329 putative paralogous gene pairs (340 genes or 73.3 % of total genes) were resulted from segmental duplications (Additional file 7), suggesting that segmental duplication might be the main mechanism of gene expansion in soybean LRR-RLK gene family. In order to estimate the date of the segmental duplication event, Ks value was used for calculating the separation time of each putative paralogous gene pair (Additional file 7). The distribution analysis of Ks values suggested that all the Ks values ranged from 0 to 1.0 with two peaks at 0.12–0.18 and 0.54–0.6 (Fig. 4). According to the clock-like rate of synonymous substitution in soybean, the segmental duplications of the soybean LRR-RLK genes originated from 0 to 81.8 MYA and the two peaks were consistent with whole genome duplication events at around 13 and 59 MYA . In addition, the Ka/Ks ratios of 239 paralogous gene pairs were less than 0.3 while the other 90 gene pairs were all larger than 0.3, which demonstrated a possibility of significant functional divergence of some soybean LRR-RLK genes after the duplication events.
Expression profiles of LRR-RLK genes in soybean
To gain a broader understanding of the putative functions of soybean LRR-RLKs, the expression profiles of these genes were examined by using the RNA-Seq dataset from different soybean tissues. The distinct transcript abundance patterns of all 467 LRR-RLK genes were identified from RNA-Seq atlas data of tissues including roots, root hairs, nodules, leaves, stems, flowers, SAM, pods, and seeds. Although some genes exhibited low transcript abundance like genes encoding transcription factors, most of them demonstrated distinct tissue specific expression pattern (Additional file 8). Detailed analysis showed that 53 (11.3 %), 68 (14.6 %), 65 (13.9 %), 53 (11.3 %), 95 (20.3 %), 87 (18.6 %), 75(16.1 %), 67 (14.3 %), and 51 (10.9 %) GmLRR-RLKs had specific transcript accumulation in roots, root hairs, nodules, leaves, stems, SAM, pods, seeds, and flowers respectively, suggesting that these LRR-RLK genes might function as tissue-specific regulators in different cells or organs.
Detailed analysis of the expression profiles also suggested that some GmLRR-RLKs clustered in the same subgroup had similar expression pattern. For example, all the LRR-RLK genes in subgroup XIII-b were mainly expressed in seeds and SAM, also indicating the existence of redundancy among the soybean LRR-RLK genes in these subgroups. However, it has also been reported that more than 50 % of duplicated LRR-RLKs exhibited expressional divergence in both rice and Arabidopsis [57, 58]. Our results showed that only 7 out of 33 clusters of tandem duplicated genes exhibited similar expression patterns in soybean (Fig. 5). In order to validate the expression patterns of these duplicated genes, the expression levels of randomly selected gene pairs were detected by using qRT-PCR. The result showed that similar or distinct expression patterns of these gene pairs identified by RNA-seq dataset were consistent with the results of qRT-PCR (Additional file 9). Moreover, among 329 pairs of LRR-RLK paralogs, only 50 pairs exhibited similar expression patterns and were likely to functionally substitute for each other.
Artificial selection analysis for LRR-RLKs during soybean domestication
In order to analyze the selection effects of GmLRR-RLKs during soybean domestication, resequencing data of wild and cultivated soybeans were used [59, 60]. A total of 7239 SNPs have been identified in the genic regions of 407 soybean LRR-RLK genes based on the sequence diversity analysis between 35 cultivated soybeans (G.max) and 21 wild soybeans (G.soja) (Additional file 10). At these loci, the gene diversity was estimated at ~0.25 on average in cultivated population, which was significantly lower than that in wild population (~0.36). SNP149 in Glyma.01G197800 is a typical example which has no diversity in cultivated soybeans while has diversity as high as 0.66 in wild soybeans. The distribution analysis also revealed that the gene diversities of most loci were less than 0.2 in G.max while 0.4–0.6 in G.soja (Fig. 6a), indicating that the gene diversities of these LRR-LRKs in cultivated soybean were reduced when compared with their wild progenitors.
In order to identify the selective GmLRR-RLKs during soybean domestication, F st value of each locus was calculated between two populations (Fig. 6b and Additional file 10). The results showed that 71.6 % loci (5182 out of 7239 loci) underwent non-selection with F st <0.15 during soybean evolution. However, a total of 302 SNPs in 98 soybean LRR-RLK genes were identified as selected loci with F st value cutoff 0.45 (Additional file 11). Although a number of these SNPs (134 out of 302) were located in the introns of GmLRR-RLKs, nearly one third (89 SNPs) of them resulted in non-synonymous alteration. Further analysis showed that all subgroups of GmLRR-RLKs had selected genes except for group XIV. Group XI has the most selected soybean LRR-RLK genes (21 genes) while group IV has only one gene. Especially, although Glyma.11G214400 and Glyma.18G050700 have the largest number of selected SNPs (36 and 32 SNPs respectively), majority SNPs in the first gene resulted in non-synonymous alteration while most of SNPs appeared in the introns of the second one. Furthermore, a number of selected LRR-RLK genes between the wild and cultivated populations were detected in regions previously reported to contain domestication-related QTLs (Additional file 11). These included six GmLRR-RLKs located at QTLs related to pod traits including pod dehiscence/number/maturity [61, 62], five genes located at QTLs conditioning twinning habit [63–65], four genes at QTL regions of seed weight/hard-seededness and two genes at regions related to lodging [63, 65]. These selected genes reflected the important roles of GmLRR-RLKs on soybean domestication and contribute to the cultivation of soybeans in order to meet the demands of human beings.
Here we performed comprehensive and evolutionary analyses of LRR-RLK gene family in soybean, and provided detailed information on its members. A total of 467 putative LRR-RLK genes were identified in the soybean genome, which represented the largest LRR-RLK gene family identified in plant so far and a relatively large gene family in soybean. The distribution of all these genes was non-random across all soybean chromosomes and majority of them were located in segmental duplicated regions rather than tandem duplicated clusters. The exon/intron compositions and motif arrangements were considerably conserved among members in the same groups or subgroups. The transcriptional profiles of many duplicated genes were also similar in different soybean tissues even though some of them exhibited divergent expression patterns. The close phylogenetic relationship of GmLRR-RLKs and identified AtLRR-RLK genes in the same subgroup provided insight into their putative functions. Moreover, some artificial selected GmLRR-RLKs have also been identified by comparing the gene diversities of these loci during the evolution from wild to cultivated soybeans. Taken together, all these results provided valuable tools in future efforts to identify specific gene functions of this family and gene diversity among different genotypes of soybean.
Arabidopsis LRR-RLKs and soybean genome resources
The amino acid sequences of all Arabidopsis LRR-RLKs were acquired from the TAIR database v10.0 (http://www.arabidopsis.org/). The classification of AtLRR-RLKs and nomenclature of groups were based on PlantsP server v.2011 of Arabidopsis 2010 project (http://plantsp.genomics.purdue.edu/projects/lrr/Clouse2010.htm) . The genomic, coding and amino-acid sequences of all annotated soybean genes were according to genome sequence of Glycine max Wm82.a2.v1 from Phytozome v10 (http://phytozome.jgi.doe.gov/pz/portal.html) .
Identification of LRR-RLK genes in soybean genome
The amino-acid sequences of all Arabidopsis LRR-RLK members were used to run a local blast search against the protein database of all annotated soybean genes by using Bioedit v7  and all proteins with an E-value less than 10−6 were selected as putative soybean LRR-LRKs. These putative GmLRR-RLKs were further filtered by removing redundant sequences and functional annotation, following by analysis with SMART (http://smart.embl-heidelberg.de)  and PFAM (http://pfam.xfam.org/)  to ensure the presence of LRR and kinase domains.
Multiple sequence alignments and phylogenetic tree construction
The amino-acid sequence of kinase domain for each GmLRR-RLK and AtLRR-RLK protein was extracted after prediction of kinase domains from these proteins. Multiple sequence alignments were performed by using ClustalX (version 1.83) with default parameters . Unrooted phylogenetic trees were constructed for soybean LRR-RLKs alone or soybean/Arabidopsis together with MEGA 6.0  using the neighbor-joining (NJ) method. The nodes were tested by bootstrap analysis with 1000 replicates and the tree with the highest likelihood was selected for further analysis.
The chromosome location, gene structure, and motif analysis of the soybean LRR-RLK genes
All members of GmLRR-RLKs were mapped onto soybean chromosomes based on the physical positions of them. The image of chromosomal location was produced with MapInspect software (http://mapinspect.software.informer.com). The number and positions of exons and introns for soybean LRR-RLK genes were determined by comparison of the coding sequences with their corresponding genomic DNA sequences using GSDS v2.0 . The presence of signal peptides and transmembrane domains was predicted with Signalp v4.1 (http://www.cbs.dtu.dk/services/SignalP/) , TMHMM v2.0 (http://www.cbs.dtu.dk/services/TMHMM/)  and Phobius (http://phobius.sbc.su.se/)  respectively. The combination of phylogenetic tree, gene and protein structures was generated using iTOL tool (http://itol.embl.de) .
Duplication analysis and calculating the date of duplication events
Tandem duplications were characterized as multiple members of this gene family occurring within neighboring intergenic regions. In this study, soybean LRR-RLK genes clustered together within 200 kb were regard as tandem duplicated genes based on the criteria of other plants in previous reports [28, 78]. The segmental duplicated GmLRR-RLKs were characterized according to the PGDD database (http://chibba.agtec.uga.edu/duplication/). The Ks and Ka values for duplicated gene pairs were also calculated by using PGDD database. The Ks values were used to calculate the approximately dates of duplication events and the clock-like rate (λ) of synonymous substitution was set 6.1x10−9 substitutions/synonymous site/year for soybean [32, 79, 80].
Transcriptional profile analysis
RNA-seq data of soybean tissues for roots, root hairs, nodules, leaves, stems, flowers, SAM, pods, and seeds was obtained from Phytozome v10 (http://phytozome.jgi.doe.gov/pz/portal.html) and the expression profiles of all GmLRR-RLKs were selected for further analysis. Soybean LRR-RLK genes were clustered based on the expression profiles and hierarchical clustering of transcriptional data was performed with MultiExperiment Viewer (Mev) v.4.9.0 using Pearson correlation and Average Linkage Clustering algorithm .
Quantitative real time RT-PCR analysis
Soybean plants (ecotype Williams 82) were grown on soil in the chamber under long day conditions (16 h light/8 h dark cycle) at 25 ± 1 °C. Roots, stems, simple leaves, trifoliolate leaves, shoot apical meristem (SAM) from 2-week-old seedlings, flowers, pods and 1-week-old seedlings were collected for total RNA isolation. Total RNA was extracted using TRIzol Reagent (Invitrogen, USA) and was treated with RNase-free DNase (TaKaRa, Japan). Five micrograms of total RNA were reverse-transcribed using the ReverTra Ace qPCR RT Kit (TOYOBO, Japan) in a reaction of 20 μL. The cDNA was diluted 50 times as the template for quantitative RT-PCR. The PCR amplification was carried out on an Applied Biosystems 7300 Real-Time PCR System, using SYBR Premix Ex Taq kit (TaKaRa, Japan). The procedure of the reaction was set according to the manufacturer’s protocol and sequences of primers used were shown in Additional file 12. The relative expression level of each gene, corresponding to the expression level of Actin, was calculated using 2−ΔΔt method .
Selective analysis of GmLRR-RLKs among soja genus
SNP data of 25 wild soybeans and 31 cultivated soybeans were downloaded from NCBI web site (http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/SNP/snp_viewTable.cgi?handle=NFCRI_MOA_CAAS). SNP loci of the GmLRR-RLKs were identified based on the physical position of each gene. The v1.1 version of soybean gene annotation was used since the physical positions of all SNPs were based on this version of soybean genome. The gene diversity of each SNP loci in G.max and G.soja, and F st value were calculated by Genepop V4.0 . The SNP locus with F st >0.45 was defined as a putative selective site during domestication.
Availability of data and materials
The data supporting the results of this article is included within the article and its additional files.
Walker JC. Structure and function of the receptor-like protein kinases of higher plants. Plant Mol Biol. 1994;26(5):1599–609.
Afzal AJ, Wood AJ, Lightfoot DA. Plant receptor-like serine threonine kinases: roles in signaling and plant defense. Mol Plant Microbe In. 2008;21(5):507–17.
Gish LA, Clark SE. The RLK/Pelle family of kinases. Plant J. 2011;66(1):117–27.
Johnson KL, Ingram GC. Sending the right signals: regulating receptor kinase activity. Curr Opin Plant Biol. 2005;8(6):648–56.
Walker JC, Zhang R. Relationship of a putative receptor protein kinase from maize to the S-locus glycoproteins of Brassica. Nature. 1990;345(6277):743–6.
Braun DM, Walker JC. Plant transmembrane receptors: new pieces in the signaling puzzle. Trends Biochem Sci. 1996;21(2):70–3.
Torii KU. Transmembrane receptors in plants: receptor kinases and their ligands. Annu Plant Rev. 2008;33:1–29.
Shiu SH, Bleecker AB. Plant receptor-like kinase gene family: diversity, function, and signaling. Sci STKE. 2001;2001(113):re22.
Shiu SH, Bleecker AB. Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci U S A. 2001;98(19):10763–8.
Zhang XR. Leucine-rich repeat receptor-like kinases in plants. Plant Mol Biol Rep. 1998;16(4):301–11.
Dievart A, Clark SE. LRR-containing receptors regulating plant development and defense. Development. 2004;131(2):251–61.
Butenko MA, Aalen RB. Receptor ligands in development. In: Tax F, Kemmerling B, editors. Receptor-like kinases in plants: from development to defense. Berlin: Springer; 2012. p. 195–226.
Albrecht C, Russinova E, Hecht V, Baaijens E, de Vries S. The Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES 1 and 2 control male sporogenesis. Plant Cell. 2005;17(12):3337–49.
Colcombet J, Boisson-Dernier A, Ros-Palau R, Vera CE, Schroeder JI. Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASES 1 and 2 are essential for tapetum development and microspore maturation. Plant Cell. 2005;17(12):3350–61.
Escobar-Restrepo JM, Huck N, Kessler S, Gagliardini V, Gheyselinck J, Yang WC, et al. The FERONIA receptor-like kinase mediates male–female interactions during pollen tube reception. Science. 2007;317(5838):656–60.
Hord CLH, Chen CB, DeYoung BJ, Clark SE, Ma H. The BAM1/BAM2 receptor-like kinases are important regulators of Arabidopsis early anther development. Plant Cell. 2006;18(7):1667–80.
Mizuno S, Osakabe Y, Maruyama K, Ito T, Osakabe K, Sato T, et al. Receptor-like protein kinase 2 (RPK 2) is a novel factor controlling anther development in Arabidopsis thaliana. Plant J. 2007;50(5):751–66.
Zhao DZ, Wang GF, Speal B, Ma H. The EXCESS MICROSPOROCYTES 1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther. Gene Dev. 2002;16(15):2021–31.
Kinoshita A, Betsuyaku S, Osakabe Y, Mizuno S, Nagawa S, Stahl Y, et al. RPK2 is an essential receptor-like kinase that transmits the CLV3 signal in Arabidopsis. Development. 2010;137(22):3911–20.
Muller R, Bleckmann A, Simon R. The receptor kinase CORYNE of Arabidopsis transmits the stem cell-limiting signal CLAVATA3 independently of CLAVATA1. Plant Cell. 2008;20(4):934–46.
He K, Gou XP, Yuan T, Lin HH, Asami T, Yoshida S, et al. BAK1 and BKK1 regulate brassinosteroid-dependent growth and brassinosteroid independent cell-death pathways. Curr Biol. 2007;17(13):1109–15.
Nam KH, Li JM. BRI1/BAK1, a receptor kinase pair mediating brassinosteroid signaling. Cell. 2002;110(2):203–12.
Osakabe Y, Maruyama K, Seki M, Satou M, Shinozaki K, Yamaguchi-Shinozaki K. Leucine-rich repeat receptor-like kinase 1 is a key membrane-bound regulator of abscisic acid early signaling in Arabidopsis. Plant Cell. 2005;17(4):1105–19.
Torii KU, Mitsukawa N, Oosumi T, Matsuura Y, Yokoyama R, Whittier RF, et al. The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. Plant Cell. 1996;8(4):735–46.
Godiard L, Sauviac L, Torii KU, Grenon O, Mangin B, Grimsley NH, et al. ERECTA, an LRR receptor-like kinase protein controlling development pleiotropically affects resistance to bacterial wilt. Plant J. 2003;36(3):353–65.
Dievart A, Gilbert N, Droc G, Attard A, Gourgues M, Guiderdoni E, et al. Leucine-rich repeat receptor kinases are sporadically distributed in eukaryotic genomes. BMC Evol Biol. 2011;11:367.
Sun XL, Wang GL. Genome-wide identification, characterization and phylogenetic analysis of the rice LRR-kinases. PLoS ONE. 2011;6(3):e16079.
Zan YJ, Ji Y, Zhang Y, Yang SH, Song YJ, Wang JH. Genome-wide identification, characterization and expression analysis of populus leucine-rich repeat receptor-like protein kinase genes. BMC Genomics. 2013;14:318.
Shiu SH, Bleecker AB. Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis. Plant Physiol. 2003;132(2):530–43.
Shiu SH, Karlowski WM, Pan RS, Tzeng YH, Mayer KFX, Li WH. Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell. 2004;16(5):1220–34.
Hartman GL, West ED, Herman TK. Crops that feed the world 2. Soybean-worldwide production, use, and constraints caused by pathogens and pests. Food Secur. 2011;3(1):5–17.
Schmutz J, Cannon SB, Schlueter J, Ma JX, Mitros T, Nelson W, et al. Genome sequence of the palaeopolyploid soybean. Nature. 2010;463(7278):178–83.
Kim KD, Shin JH, Van K, Kim DH, Lee SH. Dynamic rearrangements determine genome organization and useful traits in soybean. Plant Physiol. 2009;151(3):1066–76.
Kim S, Kim SJ, Shin YJ, Kang JH, Kim MR, Nam K, et al. An atypical soybean leucine-rich repeat receptor-like kinase, GmLRK1, may be involved in the regulation of cell elongation. Planta. 2009;229(4):811–21.
Li XP, Gan R, Li PL, Ma YY, Zhang LW, Zhang R, et al. Identification and functional characterization of a leucine-rich repeat receptor-like kinase gene that is involved in regulation of soybean leaf senescence. Plant Mol Biol. 2006;61(6):829–44.
Yang L, Wu KC, Gao P, Liu XJ, Li GP, Wu ZJ. GsLRPK, a novel cold-activated leucine-rich repeat receptor-like protein kinase from Glycine soja, is a positive regulator to cold stress tolerance. Plant Sci. 2014;215:19–28.
Kaul S, Koo HL, Jenkins J, Rizzo M, Rooney T, Tallon LJ, et al. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000;408(6814):796–815.
Mainali HR, Chapman P, Dhaubhadel S. Genome-wide analysis of Cyclophilin gene family in soybean (Glycine max). BMC Plant Biol. 2014;14:282.
Wang XB, Zhang HW, Gao YL, Sun GL, Zhang WM, Qiu LJ. A comprehensive analysis of the Cupin gene family in soybean (Glycine max). PLoS ONE. 2014;9(10):e110092.
Agusti J, Lichtenberger R, Schwarz M, Nehlin L, Greb T. Characterization of transcriptome remodeling during cambium formation identifies MOL1 and RUL1 as opposing regulators of secondary growth. PLoS Genet. 2011;7(2):e1001312.
Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, et al. MAP kinase signalling cascade in Arabidopsis innate immunity. Nature. 2002;415(6875):977–83.
Fontes EPB, Santos AA, Luz DF, Waclawovsky AJ, Chory J. The geminivirus nuclear shuttle protein is a virulence factor that suppresses transmembrane receptor kinase activity. Gene Dev. 2004;18(20):2545–56.
Chinchilla D, Zipfel C, Robatzek S, Kemmerling B, Nurnberger T, Jones JDG, et al. A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence. Nature. 2007;448(7152):497–500.
Dolan L. Positional information and mobile transcriptional regulators determine cell pattern in the Arabidopsis root epidermis. J Exp Bot. 2006;57(1):51–4.
Eyuboglu B, Pfister K, Haberer G, Chevalier D, Fuchs A, Mayer KFX, et al. Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana. BMC Plant Biol. 2007;7:16.
Kinoshita T, Cano-Delgado AC, Seto H, Hiranuma S, Fujioka S, Yoshida S, et al. Binding of brassinosteroids to the extracellular domain of plant receptor kinase BRI1. Nature. 2005;433(7022):167–71.
DeYoung BJ, Bickle KL, Schrage KJ, Muskett P, Patel K, Clark SE. The CLAVATA1-related BAM1, BAM2 and BAM3 receptor kinase-like proteins are required for meristem function in Arabidopsis. Plant J. 2006;45(1):1–16.
Etchells JP, Turner SR. The PXY-CLE41 receptor ligand pair defines a multifunctional pathway that controls the rate and orientation of vascular cell division. Development. 2010;137(5):767–74.
Fisher K, Turner S. PXY, a receptor-like kinase essential for maintaining polarity during plant vascular-tissue development. Curr Biol. 2007;17(12):1061–6.
Yamaguchi Y, Huffaker A, Bryan AC, Tax FE, Ryan CA. PEPR2 is a second receptor for the Pep1 and Pep2 peptides and contributes to defense responses in Arabidopsis. Plant Cell. 2010;22(2):508–22.
Xu SL, Rahman A, Baskin TI, Kieber JJ. Two leucine-rich repeat receptor kinases mediate signaling, linking cell wall biosynthesis and ACC synthase in Arabidopsis. Plant Cell. 2008;20(11):3065–79.
Uchida N, Shimada M, Tasaka M. ERECTA-family receptor kinases regulate stem cell homeostasis via buffering its cytokinin responsiveness in the shoot apical meristem. Plant Cell Physiol. 2013;54(3):343–51.
Xu GX, Guo CC, Shan HY, Kong HZ. Divergence of duplicate genes in exon-intron structure. Proc Natl Acad Sci U S A. 2012;109(4):1187–92.
Moore RC, Purugganan MD. The early stages of duplicate gene evolution. Proc Natl Acad Sci U S A. 2003;100(26):15682–7.
Leister D. Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance genes. Trends Genet. 2004;20(3):116–22.
Yu J, Wang J, Lin W, Li SG, Li H, Zhou J, et al. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 2005;3(2):266–81.
Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell. 2004;16(7):1679–91.
Yim WC, Lee BM, Jang CS. Expression diversity and evolutionary dynamics of rice duplicate genes. Mol Genet Genomics. 2009;281(5):483–93.
Lam HM, Xu X, Liu X, Chen WB, Yang GH, Wong FL, et al. Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet. 2010;42(12):1053–9.
Li YH, Zhao SC, Ma JX, Li D, Yan L, Li J, et al. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics. 2013;14:579.
Funatsuki H, Ishimoto M, Tsuji H, Kawaguchi K, Hajika M, Fujino K. Simple sequence repeat markers linked to a major QTL controlling pod shattering in soybean. Plant Breed. 2006;125(2):195–7.
Zhang D, Cheng H, Wang H, Zhang HY, Liu CY, Yu DY. Identification of genomic regions determining flower and pod numbers development in soybean (Glycine max L.). J Genet Genomics. 2010;37(8):545–56.
Liu B, Fujita T, Yan ZH, Sakamoto S, Xu D, Abe J. QTL mapping of domestication-related traits in soybean (Glycine max). Ann Bot. 2007;100(5):1027–38.
Yang K, Jeong N, Moon JK, Lee YH, Lee SH, Kim HM, et al. Genetic analysis of genes controlling natural variation of seed coat and flower colors in soybean. J Hered. 2010;101(6):757–68.
Li YH, Guan RX, Liu ZX, Ma YS, Wang LX, Li LH, et al. Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet. 2008;117(6):857–71.
Gou XP, He K, Yang H, Yuan T, Lin HH, Clouse SD, et al. Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana. BMC Genomics. 2010;11:19.
Goodstein DM, Shu SQ, Howson R, Neupane R, Hayes RD, Fazo J, et al. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2012;40(D1):D1178–86.
Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 1999;41:95–8.
Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2015;43(D1):D257–60.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(D1):D222–30.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25(24):4876–82.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.
Hu B, Jin JP, Guo AY, Zhang H, Luo JC, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–7.
Petersen TN, Brunak S, von Heijne G, Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011;8(10):785–6.
Krogh A, Larsson B, von Heijne G, Sonnhammer ELL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001;305(3):567–80.
Kall L, Krogh A, Sonnhammer ELL. Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res. 2007;35:W429–32.
Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 2011;39:W475–8.
Lehti-Shiu MD, Zou C, Hanada K, Shiu SH. Evolutionary history and stress regulation of plant receptor-like kinase/Pelle genes. Plant Physiol. 2009;150(1):12–26.
Lavin M, Herendeen PS, Wojciechowski MF. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst Biol. 2005;54(4):575–94.
Lynch M, Conery JS. The evolutionary fate and consequences of duplicate genes. Science. 2000;290(5494):1151–5.
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95(25):14863–8.
Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods. 2001;25(4):402–8.
Rousset F. GENEPOP ' 007: a complete re-implementation of the GENEPOP software for Windows and Linux. Mol Ecol Resour. 2008;8(1):103–6.
This work was supported by the National Natural Science Foundation of China (31271753), the State High-tech Research and Development Program (Grant No. 2013AA102602), the Fundamental Research Funds for Excellent Young Scientists of ICS-CAAS (Grant to Y. G.), and the Agricultural Science and Technology Innovation Program (ASTIP) of Chinese Academy of Agricultural Sciences.
The authors declare that they have no competing interests.
FZ performed experiments, analyzed data and wrote draft manuscript. YG designed experiments, analyzed data, wrote and revised the manuscript. LJQ conceived and supervised the project and critically revised the manuscript. All authors read and approved the final manuscript.
List of identified LRR-RLK genes in soybean. The ID, gene code, gene length, physical position on chromosome, number of exon/intron/UTR, length of amino-acid/signal peptide, number and position of TM, position of kinase domain for each soybean LRR-RLK gene annotated in this study were included. (XLSX 66 kb)
Unrooted phylogenetic tree of GmLRR-RLKs and AtLRR-RLKs. The sequences of kinase domains from 467 GmLRR-RLKs and 213 AtLRR-RLKs were aligned by Clustal X 1.8.3 and the phylogenetic tree was constructed using the MEGA 6.0 by the neighbor-joining with 1000 bootstrap replicates. (PDF 1599 kb)
The exon/intron organization of all soybean LRR-RLK genes. Exons are represented by yellow boxes and introns by black lines. UTR regions of some genes are also indicated using blue boxes. The relative sizes of exons, introns and UTR can be estimated by the length of boxes or lines. (PDF 86 kb)
Putative motifs of all GmLRR-RLKs in each subgroup predicted by MEME. Motifs were identified by MEME software using the deduced amino-acid sequences of GmLRR-RLKs in each group and the relative position of each identified motif was shown. (XLSX 3460 kb)
The pattern of signal peptides, LRRs, TMs, and kinases for all GmLRR-RLKs. The signal peptide, transmembrane domain, and kinase domain are represented by black, red and blue boxes respectively. LRR motifs are indicated using green oval shapes. The relative size of each motif can be estimated by the length. (PDF 205 kb)
Soybean LRR-RLK genes located in tandem duplication clusters. A region containing two or more soybean LRR-RLK genes within 200 kb was defined as a tandem duplication cluster. The gene ID, subgroups, and chromosome of each GmLRR-RLK located in tandem duplication clusters were presented. (XLSX 11 kb)
Estimates of the dates for the segmental duplication events of LRR-RLK gene family in soybean. (XLSX 21 kb)
Expression profiles for all soybean LRR-RLK genes across different tissues. The genome-wide RNA-seq data of soybean were obtained from Phytozome v10. The expression data of GmLRR-RLKs in pod, root hair, leaves, root, nodules, seed, stem, SAM, flower was gene-wise normalized and hierarchically clustered. The color scale below represents expression values, green indicating low levels while red indicating high levels of transcript abundance. (PDF 7242 kb)
Comparison of expression pattern for selected tandem duplicated gene pairs by qRT-PCR and RNA-seq dataset. The expression levels of two tandem duplicated gene pairs in different organs analyzed by quantitative RT-PCR (A and C) were consistent with the pattern identified from RNA-seq dataset (B and D). The expression level in the root for each gene was set to 1.0, and error bars represented standard errors of three biological replicates. (PDF 140 kb)
SNP loci located in soybean LRR-RLK genes identified by analysis of the resequencing data of 25 wild soybeans and 31 cultivated soybeans. (XLSX 2377 kb)
Putative artificial selected GmLRR-RLKs during soybean domestication. (XLSX 15 kb)
The primers used for quantitative real time RT-PCR. (PDF 6 kb)
About this article
Cite this article
Zhou, F., Guo, Y. & Qiu, LJ. Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean. BMC Plant Biol 16, 58 (2016). https://0-doi-org.brum.beds.ac.uk/10.1186/s12870-016-0744-1
- Leucine-rich repeat receptor-like kinase (LRR-RLK)
- Phylogenetic analysis
- Expression profiling
- Evolutionary analysis