Soybean Family Research Articles

ADP-glucose pyrophosphorylase gene family in soybean and implications in drought stress tolerance.

ADP-glucose pyrophosphorylase (AGPase) is the key rate-limiting enzyme in starch biosynthesis pathway, and has been identified as a potential target for manipulation strategies aimed at improving crop yield and quality. To identify the AGPase gene family members in soybean, and explore the potential implications of GmAGPS2 in drought stress tolerance. Thegenome-wide identification and sequence analysis of soybean AGPase gene family was carried out by bioinformatics methods. The GmAGP gene expression was analyzed using transcriptome data and quantitative real-time PCR (qRT-PCR). Furthermore, transgenic yeast strains overexpressing GmAGPS2 were generated, and their growth was observed under drought stress. In this study, we searched for AGPase genes (GmAGP) in the soybean genome and identified a total of 14 GmAGP genes. The GmAGP proteins had a unique conserved NTP_transferase domain and were mainly located in the chloroplast and cytosol. Evolutionarily, theGmAGP proteins can be clustered into two distinct subgroups; within the same subgroup, they displayed a similar distribution pattern of conserved motifs. The GmAGP genes exhibited an uneven distribution on 10 chromosomes, and segmental duplication contributed to AGPase gene family expansion in soybean. The GmAGP genes presented different tissue expression pattern, in which GmAGPL6, GmAGPL9, and GmAGPL10 mainly exhibited tissue-specific expression pattern. The promoter of GmAGP genes had multiple cis-acting elements related to phytohormones and stress responses, and 8 GmAGP genes contained drought-responsive cis-acting elements. qRT‒PCR analysis demonstrated a significant upregulation expression of GmAGPL6, GmAGPL10, and GmAGPS2 in response to drought stress. Further functional analysis indicated that GmAGPS2 gene could improve yeast growth under drought stress conditions and enhance the drought tolerance of yeast. These results will contribute to further elucidation of the function of GmAGP genes, and offer important candidate genes for the genetic improvement of starch and yield-related traits and the breeding of high drought stress tolerance varieties in soybean.

Comprehensive characterization and expression profiling of BBX gene family in soybean in response to UV-B stress

The BBX gene family encodes transcription factors that regulate several biological processes, such as plant growth, development, and stress response. They have been identified and thoroughly studied in numerous plant species. The functional role of the BBX gene family against UV-B stress in soybean has not been well documented. Herein, this study focused on a comprehensive investigation of the GmBBX genes in soybean and their expression patterns in response to UV-B exposure. A total of 184 BBX genes were identified and analyzed to determine the conserved domain. Single and double B-box and CCT domains were found across these proteins, indicating potential functional diversity. The protein physicochemical properties showcased diverse characteristics, highlighting molecular size, stability, and hydrophobicity. Phylogenetic analysis revealed five distinct clades, showcasing a non-uniform distribution of GmBBX genes. Chromosomal mapping showed a non-uniform distribution of GmBBX genes across the 20 chromosomes of soybean. The highest number of genes (26) were found on chromosome 13, whereas chromosomes 5 and 15 displayed the lowest number of genes (3 genes each). Gene structure analysis revealed variations in exon-intron patterns, while motif composition analysis unveiled conserved motifs among GmBBX proteins. Gene duplication indicated that the expansion of the GmBBX genes was linked with tandem and dispersed duplications. Gene ontology analysis revealed enrichment of terms associated with light stimulus, response to abiotic stress, and molecular functions such as zinc ion binding. The promoter region reveals cis-acting elements related to hormones, light, and stress responses. The GmBBX genes exhibited differential expression in response to UV-B stress, suggesting their possible role in plant defense against UV-B stress. This study will provide a solid foundation for further analysis of the molecular mechanisms of GmBBX genes in soybean against UV-B stress.

Genome-wide re-identification of the CrRLK1L family in soybean and functional characterization of GmCrRLK1L2 in salt stress response

The Catharanthus roseus receptor-like kinase 1-like (CrRLK1L), a member of the plant receptor-like kinase family, plays crucial roles in plant development and stress response. Despite previous screenings of soybean CrRLK1Ls, their specific function in stress response remains unclear. Utilizing recent soybean whole genome sequencing data, a comprehensive genome-wide analysis was performed to identify CrRLK1Ls in soybean. This study identified 45 CrRLK1L members in soybean, with CrRLK1L2 singled out for further functional investigation. Phylogenetic analysis categorized GmCrRLK1L genes into six classes, some of which exhibited homologs in Arabidopsis. Gene structure and motif analysis revealed a predominance of intron-lacking and relatively conserved GmCrRLK1L genes, with conserved motif patterns across members. Collinearity analysis indicated that both gene tandem and segmental duplication events drove the expansion of the GmCrRLK1L gene family, with segmental duplications being the primary driver. Expression profiling under salt treatment revealed significant up or downregulation of several GmCrRLK1L genes. Overexpression of GmCrRLK1L2 in soybean resulted in reduced plant height and salt tolerance, while knockout did not affect salt tolerance, suggesting potential genetic compensations by other genes. RNA-seq data showed that GmCrRLK1L2 overexpression influenced the expression of metabolic pathways and salt stress-responsive genes, including ACS3, ACO1, PER64, PER53, SAT3, and BCAT2. These findings lay the groundwork for elucidating the biological roles of GmCrRLK1Ls in soybean growth, development, and response to salinity stress.

Genome-wide identification, structural and gene expression analysis of BTB gene family in soybean

BackgroundThe Bric-a-Brac/Tramtrack/Broad Complex (BTB) gene family plays essential roles in various biological processes in plants. These genes encode proteins that contain a conserved BTB domain, which is involved in protein-protein interactions and regulation of gene expression. However, there is no systematic reports on the BTB gene family in G.max.ResultsIn total, 122 soybean BTB genes were identified, which were classified into four groups based on the phylogenetic analysis. Gene structures analysis indicated that the number of exon–intron in GmBTBs ranges from 0 to18. Cis-element analysis revealed that most GmBTB genes contained cis-elements related to an abiotic stress response. In addition, qRT-PCR analyses indicated that most GmBTBs are significantly up-regulated under salinity, drought, and nitrate stresses. They suggested their potential for targeted improvement of soybean response to multiple abiotic stresses and nitrate availability.ConclusionThese results provide valuable information for identifying the members of the GmBTB gene family in soybean and could provide a functional characterization of GmBTB genes in further research.

Genome-wide analysis of soybean hypoxia inducible gene domain containing genes: a functional investigation of GmHIGD3.

The response of Hypoxia Inducible Gene Domain (HIGD) proteins to hypoxia plays a crucial role in plant development. However, the research on this gene family in soybean has been lacking. In this study, we aimed to identify and comprehensively analyze soybean HIGD genes using the Glycine max genome database. As a result, six GmHIGD genes were successfully identified, and their phylogeny, gene structures, and putative conserved motifs were analyzed in comparison to Arabidopsis and rice. Collinearity analysis indicated that the HIGD gene family in soybean has expanded to some extent when compared to Arabidopsis. Additionally, the cis-elements in the promoter regions of GmHIGD and the transcription factors potentially binding to these regions were identified. All GmHIGD genes showed specific responsiveness to submergence and hypoxic stresses. Expression profiling through quantitative real-time PCR revealed that these genes were significantly induced by PEG treatment in root tissue. Co-expressed genes of GmHIGD were primarily associated with oxidoreductase and dioxygenase activities, as well as peroxisome function. Notably, one of GmHIGD genes, GmHIGD3 was found to be predominantly localized in mitochondria, and its overexpression in Arabidopsis led to a significantly reduction in catalase activity compared to wild-type plants. These results bring new insights into the functional role of GmHIGD in terms of subcellular localization and the regulation of oxidoreductase activity.

A comprehensive analysis of the WRKY family in soybean and functional analysis of GmWRKY164-GmGSL7c in resistance to soybean mosaic virus

BackgroundSoybean mosaic disease caused by soybean mosaic virus (SMV) is one of the most devastating and widespread diseases in soybean producing areas worldwide. The WRKY transcription factors (TFs) are widely involved in plant development and stress responses. However, the roles of the GmWRKY TFs in resistance to SMV are largely unclear.ResultsHere, 185 GmWRKYs were characterized in soybean (Glycine max), among which 60 GmWRKY genes were differentially expressed during SMV infection according to the transcriptome data. The transcriptome data and RT-qPCR results showed that the expression of GmWRKY164 decreased after imidazole treatment and had higher expression levels in the incompatible combination between soybean cultivar variety Jidou 7 and SMV strain N3. Remarkably, the silencing of GmWRKY164 reduced callose deposition and enhanced virus spread during SMV infection. In addition, the transcript levels of the GmGSL7c were dramatically lower upon the silencing of GmWRKY164. Furthermore, EMSA and ChIP-qPCR revealed that GmWRKY164 can directly bind to the promoter of GmGSL7c, which contains the W-box element.ConclusionOur findings suggest that GmWRKY164 plays a positive role in resistance to SMV infection by regulating the expression of GmGSL7c, resulting in the deposition of callose and the inhibition of viral movement, which provides guidance for future studies in understanding virus-resistance mechanisms in soybean.

The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development.

Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.

Genome-wide analysis of filamentous temperature-sensitive H protease (ftsH) gene family in soybean.

The filamentous temperature-sensitive H protease (ftsH) gene family belongs to the ATP-dependent zinc metalloproteins, and ftsH genes play critical roles in plant chloroplast development and photosynthesis. In this study, we performed genome-wide identification and a systematic analysis of soybean ftsH genes. A total of 18 GmftsH genes were identified. The subcellular localization was predicted to be mainly in cell membranes and chloroplasts, and the gene structures, conserved motifs, evolutionary relationships, and expression patterns were comprehensively analyzed. Phylogenetic analysis of the ftsH gene family from soybean and various other species revealed six distinct clades, all of which showed a close relationship to Arabidopsis thaliana. The members of the GmftsH gene family were distributed on 13 soybean chromosomes, with intron numbers ranging from 3 to 15, 13 pairs of repetitive segment. The covariance between these genes and related genes in different species of Oryza sativa, Zea mays, and Arabidopsis thaliana was further investigated. The transcript expression data revealed that the genes of this family showed different expression patterns in three parts, the root, stem, and leaf, and most of the genes were highly expressed in the leaves of the soybean plants. Fluorescence-based real-time quantitative PCR (qRT-PCR) showed that the expression level of GmftsH genes varied under different stress treatments. Specifically, the genes within this family exhibited various induction levels in response to stress conditions of 4℃, 20% PEG-6000, and 100 mmol/L NaCl. These findings suggest that the GmftsH gene family may play a crucial role in the abiotic stress response in soybeans. It was also found that the GmftsH7 gene was localized on the cell membrane, and its expression was significantly upregulated under 4 ℃ treatment. In summary, by conducting a genome-wide analysis of the GmftsH gene family, a strong theoretical basis is established for future studies on the functionality of GmftsH genes. This research can potentially serve as a guide for enhancing the stress tolerance characteristics of soybean.

Genome-wide identification and expression analysis of the WNK kinase gene family in soybean.

The online version contains supplementary material available at 10.1007/s11032-024-01440-5.

Characterization of the pyruvate kinase gene family in soybean and identification of a putative salt responsive gene GmPK21.

As a key regulatory enzyme in the glycolysis pathway, pyruvate kinase (PK) plays crucial roles in multiple physiological processes during plant growth and is also involved in the abiotic stress response. However, little information is known about PKs in soybean. In this study, we identified 27 PK family genes against the genome of soybean cultivar Zhonghuang13. They were classified into 2 subfamilies including PKc and PKp. 22 segmental duplicated gene pairs and 1 tandem duplicated gene pair were identified and all of them experienced a strong purifying selective pressure during evolution. Furthermore, the abiotic stresses (especially salt stress) and hormone responsive cis-elements were present in the promoters of GmPK genes, suggesting their potential roles in abiotic stress tolerance. By performing the qRT-PCR, 6 GmPK genes that continuously respond to both NaCl and ABA were identified. Subsequently, GmPK21, which represented the most significant change under NaCl treatment was chosen for further study. Its encoded protein GmPK21 was localized in the cytoplasm and plasma membrane. The transgenic Arabidopsis overexpressing GmPK21 exhibitedweakenedsalinitytolerance. This study provides genomic information of soybean PK genes and a molecular basis for mining salt tolerance function of PKs in the future.

Identification and Expression Analysis of the Nucleotidyl Transferase Protein (NTP) Family in Soybean (Glycine max) under Various Abiotic Stresses.

Nucleotidyl transferases (NTPs) are common transferases in eukaryotes and play a crucial role in nucleotide modifications at the 3' end of RNA. In plants, NTPs can regulate RNA stability by influencing 3' end modifications, which in turn affect plant growth, development, stress responses, and disease resistance. Although the functions of NTP family members have been extensively studied in Arabidopsis, rice, and maize, there is limited knowledge about NTP genes in soybeans. In this study, we identified 16 members of the NTP family in soybeans, including two subfamilies (G1 and G2) with distinct secondary structures, conserved motifs, and domain distributions at the protein level. Evolutionary analysis of genes in the NTP family across multiple species and gene collinearity analysis revealed a relatively conserved evolutionary pattern. Analysis of the tertiary structure of the proteins showed that NTPs have three conserved aspartic acids that bind together to form a possible active site. Tissue-specific expression analysis indicated that some NTP genes exhibit tissue-specific expression, likely due to their specific functions. Stress expression analysis showed significant differences in the expression levels of NTP genes under high salt, drought, and cold stress. Additionally, RNA-seq analysis of soybean plants subjected to salt and drought stress further confirmed the association of soybean NTP genes with abiotic stress responses. Subcellular localization experiments revealed that GmNTP2 and GmNTP14, which likely have similar functions to HESO1 and URT1, are located in the nucleus. These research findings provide a foundation for further investigations into the functions of NTP family genes in soybeans.

Genome-wide identification and tissue expression pattern analysis of TPS gene family in soybean (Glycine max).

The terpene synthase (TPS) plays a pivotal roles in plant growth, development, and enhancing resilience against environmental stresses. Despite this, the bioinformatics analysis of the TPS family gene in soybean (Glycine max) is lacking. In this study, we investigated 36 GmTPS members in soybean, exhibiting a diverse range of protein lengths, spanning from 144 to 835 amino acids. A phylogenetic tree was constructed from these GmTPS genes revealed a classification into five distinct subgroups: Group1, Group2, Group3, Group4 and Group5. Notably, within each subgroup, we identified the motifs of GmTPS proteins were similar, although variations existed among different subfamilies. Gene duplication events analysis demonstrated that TPS genes expand differently in G. max, A. thaliana and O. sativa. Among, both tandem duplication and Whole genome duplication contributive to the expansion of TPS genes in G. max, and Whole genome duplication played a major role. Moreover, the cis-element analysis suggested that TPS is related to hormone signals, plant growth and development and environmental stress. Yeast two-hybrid (Y2H) assay results indicated TPS protein may form heterodimer to function, or may form complex with P450 proteins to function. RNA-seq results revealed a higher expression of most GmTPS genes in flowers, suggesting their potential contribution to flower development. Collectively, these findings offer a provide a holistic knowledge of the TPS gene family in soybean and will facilitate further characterization of TPSs effectively.

Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation.

F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.

Genome-wide analysis of the soybean eEF gene family and its involvement in virus resistance.

Eukaryotic elongation factors (eEFs) are protein factors that mediate the extension of peptide chain, among which eukaryotic elongation factor 1 alpha (eEF1A) is one of the most abundant protein synthesis factors. Previously we showed that the P3 protein of Soybean mosaic virus (SMV), one of the most destructive and successful viral pathogens of soybean, targets a component of the soybean translation elongation complex to facilitate its pathogenesis. Here, we conducted a systematic analyses of the soybean eEF (GmeEF) gene family in soybean and examinedits role in virus resistance. In this study, GmeEF family members were identified and characterized based on sequence analysis. The 42 members, which were unevenly distributed across the 15 chromosomes, were renamed according to their chromosomal locations. The GmeEF members were further divided into 12 subgroups based on conserved motif, gene structure, and phylogenetic analyses. Analysis of the promoter regions showed conspicuous presence of myelocytomatosis (MYC) and ethylene-responsive (ERE) cis-acting elements, which are typically involved in drought and phytohormone response, respectively, and thereby in plant stress response signaling. Transcriptome data showed that the expression of 15 GmeEF gene family members changed significantly in response to SMV infection. To further examine EF1A function in pathogen response, three different Arabidopsis mutants carrying T-DNA insertions in orthologous genes were analyzed for their response to Turnip crinkle virus (TCV) and Cucumber mosaic virus (CMV). Results showed that there was no difference in viral response between the mutants and the wild type plants. This study provides a systematic analysis of the GmeEF gene family through analysis of expression patterns and predicted protein features. Our results lay a foundation for understanding the role of eEF gene in soybean anti-viral response.

Genome-wide characterization and expression of the APETALA2 (AP2) gene family in Glycine max L. reveal its importance in cold stress responses modulated by melatonin application.

The soybean (Glycine max L.) is the world's most significant oilseed crop in terms of total production and international trade. Determining the genetic composition of soybeans is essential for identifying their characteristics, enhancing crop productivity and quality, and creating sustainable farming methods. AP2/ERF transcription factors regulate the responses against biotic and abiotic factors in the plants. However, little investigation of the AP2 family has been conducted in soybean. This study aims to introduce the expression of AP2 genes. A total of 50 nonredundant AP2 genes were analyzed by using a systematic genome-wide analysis. These genes were distributed on 19 chromosomes except chromosome number 20 that have no AP2 gene. Analysis of gene structure confirmed the presence of 2-10 introns in the AP2 family. In addition to the signature AP2 domain being completely conserved, 19 other domains were discovered to be conserved in a group-specific way. Synteny analysis expressed an intensive resemblance of orthologous regions between soybean and Arabidopsis thaliana. In-silico expression study based on transcriptome data demonstrated that soybean has differential expression of AP2 genes under cold stress. Additionally, during cold stress, most of these genes had the same patterns of expression but one gene (GLYMA_13G329700) is always upregulated irrespective of stress applied to soybean. This study revealed the characteristics of the AP2 gene family in soybean and provides valuable resources for further evolutionary and functional investigations of AP2 genes in this crop plant.

Genome-Wide Identification, Characterization, and Expression Analysis of the Amino Acid Permease Gene Family in Soybean

Amino acid permeases (AAPs) play important roles in transporting amino acids in plant species, leading to increased low-nitrogen tolerance, grain yield, or protein content. However, very few AAPs have been characterized in soybean (Glycine max). In this study, we scanned the soybean reference genome and identified a total of 36 AAP genes (named GmAAP). The GmAAPs were phylogenetically divided into three evolutionary clades, with the genes in the same clades sharing similar gene structures and domain organization. We also showed that seventeen GmAAP genes on ten chromosomes were in collinearity, likely due to whole-genome duplication. Further analysis revealed a variety of cis-acting regulatory elements (such as hormone response elements (ABRE, ERE, GARE, P-box, and TGA-element), stress response elements (LTR, MBS, MYB-related components, TC-rich repeats, TCA-element, and WUN-motif), the tissue expression element (GCN4-motif), and the circadian regulatory element (circadian) present in the 2 kb region of the GmAAP promoter region, demonstrating functional diversity and expression specificity. RNA-Seq data and quantitative real-time PCR identified five GmAAPs showing differential expression under nitrogen limitation, including GmAAP3, GmAAP5, and GmAAP8 showing downregulation while GmAAP14, GmAAP29 showed upregulation, suggesting their involvement in low-nitrogen stress response. These results provide comprehensive information on soybean AAP genes in nitrogen stress, and provide putative candidates with possible roles in enhancing amino acid delivery to seeds for yield improvement.

Genome- and transcriptome-wide identification of trehalose-6-phosphate phosphatases (TPP) gene family and their expression patterns under abiotic stress and exogenous trehalose in soybean

BackgroundTrehalose-6-phosphate phosphatase (TPP) is an essential enzyme catalyzing trehalose synthesis, an important regulatory factor for plant development and stress response in higher plants. However, the TPP gene family in soybean has not been reported.ResultsA comprehensive analysis of the TPP gene family identified 18 GmTPPs classified into eight groups based on the phylogenetic relationships and the conservation of protein in six monocot and eudicot plants. The closely linked subfamilies had similar motifs and intron/exon numbers. Segmental duplication was the main driving force of soybean GmTPPs expansion. In addition, analysis of the cis-regulatory elements and promoter regions of GmTPPs revealed that GmTPPs regulated the response to several abiotic stresses. Moreover, RNA-seq and qRT-PCR analysis of the tissue-specific GmTPPs under different abiotic stresses revealed that most GmTPPs were associated with response to different stresses, including cold, drought, saline-alkali, and exogenous trehalose. Notably, exogenous trehalose treatment up-regulated the expression of most TPP genes under saline-alkali conditions while increasing the carbohydrate and trehalose levels and reducing reactive oxygen species (ROS) accumulation in soybean sprouts, especially in the saline-alkali tolerant genotype. Furthermore, the interaction network and miRNA target prediction revealed that GmTPPs interacted with abiotic stress response-related transcription factors.ConclusionsThe findings in this study lay a foundation for further functional studies on TPP-based breeding to improve soybean development and stress tolerance.

Genome-wide identification and expression analysis of the KCS gene family in soybean (Glycine max) reveal their potential roles in response to abiotic stress.

Very long chain fatty acids (VLCFAs) are fatty acids with chain lengths of 20 or more carbon atoms, which are the building blocks of various lipids that regulate developmental processes and plant stress responses. 3-ketoacyl-CoA synthase encoded by the KCS gene is the key rate-limiting enzyme in VLCFA biosynthesis, but the KCS gene family in soybean (Glycine max) has not been adequately studied thus far. In this study, 31 KCS genes (namely GmKCS1 - GmKCS31) were identified in the soybean genome, which are unevenly distributed on 14 chromosomes. These GmKCS genes could be phylogenetically classified into seven groups. A total of 27 paralogous GmKCS gene pairs were identified with their Ka/Ks ratios indicating that they had undergone purifying selection during soybean genome expansion. Cis-acting element analysis revealed that GmKCS promoters contained multiple hormone- and stress-responsive elements, indicating that GmKCS gene expression levels may be regulated by various developmental and environmental stimuli. Expression profiles derived from RNA-seq data and qRT-PCR experiments indicated that GmKCS genes were diversely expressed in different organs/tissues, and many GmKCS genes were found to be differentially expressed in the leaves under cold, heat, salt, and drought stresses, suggesting their critical role in soybean resistance to abiotic stress. These results provide fundamental information about the soybean KCS genes and will aid in their further functional elucidation and exploitation.

Genome-Wide Identification and Comprehensive Analysis of the FtsH Gene Family in Soybean (Glycine max)

The filamentation temperature-sensitive H (FtsH) gene family is critical in regulating plant chloroplast development and photosynthesis. It plays a vital role in plant growth, development, and stress response. Although FtsH genes have been identified in a wide range of plants, there is no detailed study of the FtsH gene family in soybean (Glycine max). Here, we identified 34 GmFtsH genes, which could be categorized into eight groups, and GmFtsH genes in the same group had similar structures and conserved protein motifs. We also performed intraspecific and interspecific collinearity analysis and found that the GmFtsH family has large-scale gene duplication and is more closely related to Arabidopsis thaliana. Cis-acting elements analysis in the promoter region of the GmFtsH genes revealed that most genes contain developmental and stress response elements. Expression patterns based on transcriptome data and real-time reverse transcription quantitative PCR (qRT-PCR) showed that most of the GmFtsH genes were expressed at the highest levels in leaves. Then, GO enrichment analysis indicated that GmFtsH genes might function as a protein hydrolase. In addition, the GmFtsH13 protein was confirmed to be localized in chloroplasts by a transient expression experiment in tobacco. Taken together, the results of this study lay the foundation for the functional determination of GmFtsH genes and help researchers further understand the regulatory network in soybean leaf development.

Genome-Wide Analysis of Cation/Proton Antiporter Family in Soybean (Glycine max) and Functional Analysis of GmCHX20a on Salt Response

Monovalent cation proton antiporters (CPAs) play crucial roles in ion and pH homeostasis, which is essential for plant development and environmental adaptation, including salt tolerance. Here, 68 CPA genes were identified in soybean, phylogenetically dividing into 11 Na+/H+ exchangers (NHXs), 12 K+ efflux antiporters (KEAs), and 45 cation/H+ exchangers (CHXs). The GmCPA genes are unevenly distributed across the 20 chromosomes and might expand largely due to segmental duplication in soybean. The GmCPA family underwent purifying selection rather than neutral or positive selections. The cis-element analysis and the publicly available transcriptome data indicated that GmCPAs are involved in development and various environmental adaptations, especially for salt tolerance. Based on the RNA-seq data, twelve of the chosen GmCPA genes were confirmed for their differentially expression under salt or osmotic stresses using qRT-PCR. Among them, GmCHX20a was selected due to its high induction under salt stress for the exploration of its biological function on salt responses by ectopic expressing in Arabidopsis. The results suggest that the overexpression of GmCHX20a increases the sensitivity to salt stress by altering the redox system. Overall, this study provides comprehensive insights into the CPA family in soybean and has the potential to supply new candidate genes to develop salt-tolerant soybean varieties.