GhKLCR1, a kinesin light chain-related gene, induces drought-stress sensitivity in Arabidopsis

Pan-genome analysis of GT64 gene family and expression response to Verticillium wilt in cotton

BACKGROUND

The GT64 subfamily, belonging to the glycosyltransferase family, plays a critical function in plant adaptation to stress conditions and the modulation of plant growth, development, and organogenesis processes. However, a comprehensive identification and systematic analysis of GT64 in cotton are still lacking.

RESULTS

This study used bioinformatics techniques to conduct a detailed investigation on the GT64 gene family members of eight cotton species for the first time. A total of 39 GT64 genes were detected, which could be classified into five subfamilies according to the phylogenetic tree. Among them, six genes were found in upland cotton. Furthermore, investigated the precise chromosomal positions of these genes and visually represented their gene structure details. Moreover, forecasted cis-regulatory elements in GhGT64s and ascertained the duplication type of the GT64 in the eight cotton species. Evaluation of the Ka/Ks ratio for similar gene pairs among the eight cotton species provided insights into the selective pressures acting on these homologous genes. Additionally, analyzed the expression profiles of the GT64 gene family. Overexpressing GhGT64_4 in tobacco improved its disease resistance. Subsequently, VIGS experiments conducted in cotton demonstrated reduced disease resistance upon silencing of the GhGT64_4, may indicate its involvement in affecting lignin and jasmonic acid biosynthesis pathways, thus impacting cotton resistance. Weighted Gene Co-expression Network Analysis (WGCNA) revealed an early immune response against Verticillium dahliae in G. barbadense compared to G. hirsutum. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis indicated that some GT64 genes might play a role under various biotic and abiotic stress conditions.

CONCLUSIONS

These discoveries enhance our knowledge of GT64 family members and lay the groundwork for future investigations into the disease resistance mechanisms of this gene in cotton.

Genome-Wide and Expression Pattern Analysis of the DVL Gene Family Reveals GhM_A05G1032 Is Involved in Fuzz Development in G. hirsutum

DVL is one of the small polypeptides which plays an important role in regulating plant growth and development, tissue differentiation, and organ formation in the process of coping with stress conditions. So far, there has been no comprehensive analysis of the expression profile and function of the cotton DVL gene. According to previous studies, a candidate gene related to the development of fuzz was screened, belonging to the DVL family, and was related to the development of trichomes in Arabidopsis thaliana. However, the comprehensive identification and systematic analysis of DVL in cotton have not been conducted. In this study, we employed bioinformatics approaches to conduct a novel analysis of the structural characteristics, phylogenetic tree, gene structure, expression pattern, evolutionary relationship, and selective pressure of the DVL gene family members in four cotton species. A total of 117 DVL genes were identified, including 39 members in G. hirsutum. Based on the phylogenetic analysis, the DVL protein sequences were categorized into five distinct subfamilies. Additionally, we successfully mapped these genes onto chromosomes and visually represented their gene structure information. Furthermore, we predicted the presence of cis-acting elements in DVL genes in G. hirsutum and characterized the repeat types of DVL genes in the four cotton species. Moreover, we computed the Ka/Ks ratio of homologous genes across the four cotton species and elucidated the selective pressure acting on these homologous genes. In addition, we described the expression patterns of the DVL gene family using RNA-seq data, verified the correlation between GhMDVL3 and fuzz development through VIGS technology, and found that some DVL genes may be involved in resistance to biotic and abiotic stress conditions through qRT-PCR technology. Furthermore, a potential interaction network was constructed by WGCNA, and our findings demonstrated the potential of GhM_A05G1032 to interact with numerous genes, thereby playing a crucial role in regulating fuzz development. This research significantly contributed to the comprehension of DVL genes in upland cotton, thereby establishing a solid basis for future investigations into the functional aspects of DVL genes in cotton.

Effect of ABA Pre-Treatment on Rice Plant Transcriptome Response to Multiple Abiotic Stress

Half of the world's population depends on rice plant cultivation, yet environmental stresses continue to substantially impact the production of one of our most valuable staple foods. The aim of this study was to investigate the changes in the transcriptome of the IAC1131 rice genotype when exposed to a suite of multiple abiotic stresses, either with or without pre-treatment with the plant hormone ABA (Abscisic acid). Four groups of IAC1131 rice plants were grown including control plants incubated with ABA, non-ABA-incubated control plants, stressed plants incubated with ABA, and non-ABA-incubated stressed plants, with leaf samples harvested after 0 days (control) and 4 days (stressed). We found that high concentrations of ABA applied exogenously to the control plants under normal conditions did not alter the IAC1131 transcriptome profile significantly. The observed changes in the transcriptome of the IAC1131 plants in response to multiple abiotic stress were made even more pronounced by ABA pre-treatment, which induced the upregulation of a significant number of additional genes. Although ABA application impacted the plant transcriptome, multiple abiotic stress was the dominant factor in modifying gene expression in the IAC1131 plants. Exogenous ABA application may mitigate the effects of stress through ABA-dependent signalling pathways related to biological photosynthesis functions. Pre-treatment with ABA alters the photosynthesis function negatively by reducing stomatal conductance, therefore helping plants to conserve the energy required for survival under unfavourable environmental conditions.

Transcriptome and Small RNA Sequencing Reveals the Basis of Response to Salinity, Alkalinity and Hypertonia in Quinoa (Chenopodium quinoa Willd.)

Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous cereal that is rich in nutrients. This important crop has been shown to have significant tolerance to abiotic stresses such as salinization and drought. Understanding the underlying mechanism of stress response in quinoa would be a significant advantage for breeding crops with stress tolerance. Here, we treated the low-altitude quinoa cultivar CM499 with either NaCl (200 mM), Na₂CO₃/NaHCO₃ (100 mM, pH 9.0) or PEG6000 (10%) to induce salinity, alkalinity and hypertonia, respectively, and analyzed the subsequent expression of genes and small RNAs via high-throughput sequencing. A list of known/novel genes were identified in quinoa, and the ones responding to different stresses were selected. The known/novel quinoa miRNAs were also identified, and the target genes of the stress response ones were predicted. Both the differently expressed genes and the targets of differently expressed miRNAs were found to be enriched for reactive oxygen species homeostasis, hormone signaling, cell wall synthesis, transcription factors and some other factors. Furthermore, we detected changes in reactive oxygen species accumulation, hormone (auxin and ethylene) responses and hemicellulose synthesis in quinoa seedlings treated with stresses, indicating their important roles in the response to saline, alkaline or hyperosmotic stresses in quinoa. Thus, our work provides useful information for understanding the mechanism of abiotic stress responses in quinoa, which would provide clues for improving breeding for quinoa and other crops.

Functional characterization of TBL genes revealed the role of GhTBL7 and GhTBL58 in cotton fiber elongation

TBL (Trichome Birefringence Like) gene family members are involved in trichome initiation and xylan acetylation in several plant species. In our research, we identified 102 TBLs from G. hirsutum. The phylogenetic tree classified TBL genes into five groups. Collinearity analysis of TBL genes indicated 136 paralogous gene pairs in G. hirsutum. Gene duplication indicated that WGD or segmental duplication contributed to the GhTBL gene family expansion. Promoter cis-elements of GhTBLs were related to growth and development, seed-specific regulation, light, and stress responses. GhTBL genes (GhTBL7, GhTBL15, GhTBL21, GhTBL25, GhTBL45, GhTBL54, GhTBL67, GhTBL72, and GhTBL77) exhibited upregulated response under exposure to cold, heat, NaCl, and PEG. GhTBL genes exhibited high expression during fiber development stages. Two GhTBL genes (GhTBL7 and GhTBL58) showed differential expression at 10 DPA fiber, as 10 DPA is a fast fiber elongation stage and fiber elongation is a very important stage of cotton fiber development. Subcellular localization of GhTBL7 and GhTBL58 revealed that these genes reside inside the cell membrane. Promoter GUS activity of GhTBL7 and GhTBL58 exhibited deep staining in roots. To further validate the role of these genes in cotton fiber elongation, we silenced these genes and observed a significant reduction in the fiber length at 10 DPA. In conclusion, the functional study of cell membrane-associated genes (GhTBL7 and GhTBL58) showed deep staining in root tissues and potential function during cotton fiber elongation at 10 DPA fiber.

Genomic identification of cotton SAC genes branded ovule and stress-related key genes in Gossypium hirsutum

SAC genes have been identified to play a variety of biological functions and responses to various stresses. Previously, SAC genes have been recognized in animals and Arabidopsis. For the very first time, we identified 157 SAC genes in eight cotton species including three diploids and five tetraploids with 23 SAC members in G. hirsutum. Evolutionary analysis classified all cotton SAC gene family members into five distinct groups. Cotton SAC genes showed conserved sequence logos and WGD or segmental duplication. Multiple synteny and collinearity analyses revealed gene family expansion and purifying selection pressure during evolution. G. hirsutum SAC genes showed uneven chromosomal distribution, multiple exons/introns, conserved protein motifs, and various growth and stress-related cis-elements. Expression pattern analysis revealed three GhSAC genes (GhSAC3, GhSAC14, and GhSAC20) preferentially expressed in flower, five genes (GhSAC1, GhSAC6, GhSAC9, GhSAC13, and GhSAC18) preferentially expressed in ovule and one gene (GhSAC5) preferentially expressed in fiber. Similarly, abiotic stress treatment verified that GhSAC5 was downregulated under all stresses, GhSAC6 and GhSAC9 were upregulated under NaCl treatment, and GhSAC9 and GhSAC18 were upregulated under PEG and heat treatment respectively. Overall, this study identified key genes related to flower, ovule, and fiber development and important genetic material for breeding cotton under abiotic stress conditions.

Genome-Wide Identification and Expression Analysis of Kinesin Family in Barley (Hordeum vulgare)

Kinesin, as a member of the molecular motor protein superfamily, plays an essential function in various plants' developmental processes. Especially at the early stages of plant growth, including influences on plants' growth rate, yield, and quality. In this study, we did a genome-wide identification and expression profile analysis of the kinesin family in barley. Forty-two HvKINs were identified and screened from the barley genome, and a generated phylogenetic tree was used to compare the evolutionary relationships between Rice and Arabidopsis. The protein structure prediction, physicochemical properties, and bioinformatics of the HvKINs were also dissected. Our results reveal the important regulatory roles of HvKIN genes in barley growth. We found many cis- elements related to GA3 and ABA in homeopathic elements of the HvKIN gene and verified them by QRT-PCR, indicating their potential role in the barley kinesin family. The current study revealed the biological functions of barley kinesin genes in barley and will aid in further investigating the kinesin in other plant species.

Genome-wide identification of cystathionine beta synthase genes in wheat and its relationship with anther male sterility under heat stress

Cystathionine beta synthase (CBS) domains containing proteins (CDCPs) plays an important role in plant development through regulation of the thioredoxin system, as well as its ability to respond to biotic and abiotic stress conditions. Despite this, no systematic study has examined the wheat CBS gene family and its relation to high temperature-induced male sterility. In this study, 66 CBS family members were identified in the wheat genome, and their gene or protein sequences were used for subsequent analysis. The TaCBS gene family was found to be unevenly distributed on 21 chromosomes, and they were classified into four subgroups according to their gene structure and phylogeny. The results of collinearity analysis showed that there were 25 shared orthologous genes between wheat, rice and Brachypodium distachyon, and one shared orthologous gene between wheat, millet and barley. The cis-regulatory elements of the TaCBS were related to JA, IAA, MYB, etc. GO and KEGG pathway analysis identified these TaCBS genes to be associated with pollination, reproduction, and signaling and cellular processes, respectively. A heatmap of wheat plants based on transcriptome data showed that TaCBS genes were expressed to a higher extent in spikelets relative to other tissues. In addition, 29 putative tae-miRNAs were identified, targeting 41 TaCBS genes. Moreover, qRT-PCR validation of six TaCBS genes indicated their critical role in anther development, as five of them were expressed at lower levels in heat-stressed male sterile anthers than in Normal anthers. Together with anther phenotypes, paraffin sections, starch potassium iodide staining, and qRT-PCR data, we hypothesized that the TaCBS gene has a very important connection with the heat-stressed sterility process in wheat, and these data provide a basis for further insight into their relationship.

Characterization of Histone H3 Gene Family Reveals That GmHH3-3 is Associated With Higher Seed Weight in Glycine max

The main function of histone protein is to provide support to the structure of chromosomes. It helps in binding a long thread of DNA into a more condensed shape to fit into the nucleus. From histone variants, histone H3 (HH3) plays a crucial role in plant growth and development. Characterization of histones has not been reported in Glycine max till now. The objective of this study was to characterize the HH3 gene family for molecular breeding of G. max. In this study, 17 HH3 members in G. max were identified by performing local BLASTp using HH3 members from Arabidopsis as a query. Phylogenetic analysis classified HH3 genes in seven clades. Sequence logo analysis among Arabidopsis thaliana, Oryza sativa, and Glycine max showed a higher level of similarity in amino acids. Furthermore, conserveness of G. max HH3 genes was also confirmed by Gene Structure Display. Ten paralogous gene pairs were identified in GmHH3 genes in the Glycine max genome by conducting collinearity analysis. G. max HH3 genes have experienced strong purifying selection pressure, with limited functional divergence originating from the segmental and whole-genome duplication, as evidenced by the Ka/Ks ratio. The KASP marker was developed for GmHH3-3 gene. Genotyping was performed on 46 G. max genotypes. This differentiation was based upon the presence of either GmHH3-3-C or GmHH3-3-T allele in the CDS region. The results showed that G. max accessions containing the GmHH3-3-T allele at respective locus showed higher thousand seed weight than that of those accessions that contain the GmHH3-3-C allele. This research provides the basic information to further decipher the function of HH3 in soybean.

Tissue-Specific Expression of the Terpene Synthase Family Genes in Rosa chinensis and Effect of Abiotic Stress Conditions

Rose (Rosa chinensis) is one of the most famous ornamental plants worldwide, with a variety of colors and fragrances. Terpene synthases (TPSs) play critical roles in the biosynthesis of terpenes. In this work, we report a comprehensive study on the genome-wide identification and characterization of the TPS family in R. chinensis. We identified 49 TPS genes in the R. chinensis genome, and they were grouped into five subfamilies (TPS-a, TPS-b, TPS-c, TPS-g and TPS-e/f). Phylogenetics, gene structure and conserved motif analyses indicated that the RcTPS genes possessed relatively conserved gene structures and the RcTPS proteins contained relatively conserved motifs. Multiple putative cis-acting elements involved in the stress response were identified in the promoter region of RcTPS genes, suggesting that some could be regulated by stress. The expression profile of RcTPS genes showed that they were predominantly expressed in the petals of open flowers, pistils, leaves and roots. Under osmotic and heat stresses, the expression of most RcTPS genes was upregulated. These data provide a useful foundation for deciphering the functional roles of RcTPS genes during plant growth as well as addressing the link between terpene biosynthesis and abiotic stress responses in roses.

Genome-wide characterization and expression analysis of cystathionine β-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.)

Cystathionine β-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.

Genome-wide analysis of ZAT gene family revealed GhZAT6 regulates salt stress tolerance in G. hirsutum

High salt environments can induce stress in different plants. The genes containing the ZAT domain constitute a family that belongs to a branch of the C₂H₂ family, which plays a vital role in responding to abiotic stresses. In this study, we identified 169 ZAT genes from seven plant species, including 44 ZAT genes from G. hirsutum. Phylogenetic tree analysis divided ZAT genes in six groups with conserved gene structure, protein motifs. Two C₂H₂ domains and an EAR domain and even chromosomal distribution on At and Dt sub-genome chromosomes of G. hirsutum was observed. GhZAT6 was primarily expressed in the root tissue and responded to NaCl and ABA treatments. Subcellular localization found that GhZAT6 was located in the nucleus and demonstrated transactivation activity during a transactivation activity assay. Arabidopsis transgenic lines overexpressing the GhZAT6 gene showed salt tolerance and grew more vigorously than WT on MS medium supplemented with 100 mmol NaCl. Additionally, the silencing of the GhZAT6 gene in cotton plants showed more obvious leaf wilting than the control plants, which were subjected to 400 mmol NaCl treatment. Next, the expressions of GhAPX1, GhFSD1, GhFSD2, and GhSOS3 were significantly lower in the GhZAT6-silenced plants treated with NaCl than the control. Based on these findings, GhZAT6 may be involved in the ABA pathway and mediate salt stress tolerance by regulating ROS-related gene expression.

Systematic Characterization of TCP Gene Family in Four Cotton Species Revealed That GhTCP62 Regulates Branching in Arabidopsis

TEOSINTE-BRANCHED1/CYCLOIDEA/PCF (TCP) transcription factors play an essential role in regulating various physiological and biochemical functions during plant growth. However, the function of TCP transcription factors in G. hirsutum has not yet been studied. In this study, we performed genome-wide identification and correlation analysis of the TCP transcription factor family in G. hirsutum. We identified 72 non-redundant GhTCP genes and divided them into seven subfamilies, based on phylogenetic analysis. Most GhTCP genes in the same subfamily displayed similar exon and intron structures and featured highly conserved motif structures in their subfamily. Additionally, the pattern of chromosomal distribution demonstrated that GhTCP genes were unevenly distributed on 24 out of 26 chromosomes, and that fragment replication was the main replication event of GhTCP genes. In TB1 sub-family genes, GhTCP62 was highly expressed in the axillary buds, suggesting that GhTCP62 significantly affected cotton branching. Additionally, subcellular localization results indicated that GhTCP62 is located in the nucleus and possesses typical transcription factor characteristics. The overexpression of GhTCP62 in Arabidopsis resulted in fewer rosette-leaf branches and cauline-leaf branches. Furthermore, the increased expression of HB21 and HB40 genes in Arabidopsis plants overexpressing GhTCP62 suggests that GhTCP62 may regulate branching by positively regulating HB21 and HB40.

Minc00344 and Mj-NULG1a effectors interact with GmHub10 protein to promote the soybean parasitism by Meloidogyne incognita and M. javanica

Several economically important crops are susceptible to root-knot nematode (RKNs). Meloidogyne incognita and M. javanica are the two most reported species from the RKN complex, causing damage to several crops worldwide. The successful outcome of the Meloidogyne-plant interaction is associated with molecular factors secreted by the nematode to suppress the plant's immune response and promote nematode parasitism. In contrast, several plant factors are associated with defense against nematode infection. In this study, we identified and characterized the specific interaction of Minc00344 and Mj-NULG1a effectors with soybean GmHub10 (Glyma.19G008200) protein in vitro and in vivo. An Arabidopsis thaliana T-DNA mutant of AtHub10 (AT3G27960, an orthologous gene of GmHub10) showed higher susceptibility to M. incognita. Thus, since soybean and A. thaliana Hub10 proteins are involved in pollen tube growth and indirect activation of the defense response, our data suggest that effector-Hub10 interactions could be associated with an increase in plant susceptibility. These findings indicate the potential of these effector proteins to develop new biotechnological tools based on RNA interference and the overexpression of engineered Hub10 proteins for the efficient management of RKN in crops.

Identification of BR biosynthesis genes in cotton reveals that GhCPD-3 restores BR biosynthesis and mediates plant growth and development

Brassinosteroid (BR) synthesis genes in different cotton species was comprehensively identified, and the participation of GhCPD-3 in the BR synthesis signaling pathway for regulating plant development was verified. Brassinosteroid is a natural steroidal phytohormone that plays fundamental roles in plant growth and development. In cotton, detailed characterization and functional validation of BR biosynthesis genes remain rare. Here, 16, 8 and 9 BR biosynthesis genes were identified in Gossypium hirsutum, Gossypium raimondii and Gossypium arboreum, respectively, and their phylogenetic relationships, gene structures, conserved motifs of the encoded proteins, chromosomal locations were determined and a synteny analysis was performed. Gossypium hirsutum and Arabidopsis BR biosynthesis genes closely clustered in the phylogenetic tree and fragment duplication was likely the primary cause promoting gene family expansion in G. hirsutum. Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed their relevance as BR biosynthesis genes. GhCPD-3 was highly expressed in roots and stems and the loci of single nucleotide polymorphisms (SNPs) were significantly associated with these traits.Ectopic overexpression of GhCPD-3 in the cpd91 Arabidopsis mutant rescued the mutant phenotype by increasing plant height and leaf size in comparison to those of cpd91 and WT plants. Moreover, overexpressed GhCPD-3 in cpd91 mutants showed greater hypocotyl and root lengths than those of cpd91 and WT plants under light and dark conditions, respectively, indicating that BR actively promotes hypocotyl and root growth. Similar to CPD (CONSTITUTIVE PHOTOMORPHOGENIC DWARF), GhCPD-3 restores BR biosynthesis thereby mediating plant growth and development.

Identification and Analysis of GhEXO Gene Family Indicated That GhEXO7_At Promotes Plant Growth and Development Through Brassinosteroid Signaling in Cotton (Gossypium hirsutum L.)

Brassinosteroids (BRs), an efficient plant endogenous hormone, significantly promotes plant nutrient growth adapting to biological and abiotic adversities. BRs mainly promote plant cell elongation by regulating gene expression patterns. EXORDIUM (EXO) genes have been characterized as the indicators of BR response genes. Cotton, an ancient crop, is of great economic value and its fibers can be made into all kinds of fabrics. However, EXO gene family genes have not been full identified in cotton. 175 EXO genes were identified in nine plant species, of which 39 GhEXO genes in Gossypium hirsutum in our study. A phylogenetic analysis grouped all of the proteins encoded by the EXO genes into five major clades. Sequence identification of conserved amino acid residues among monocotyledonous and dicotyledonous species showed a high level of conservation across the N and C terminal regions. Only 25% the GhEXO genes contain introns besides conserved gene structure and protein motifs distribution. The 39 GhEXO genes were unevenly distributed on the 18 At and Dt sub-genome chromosomes. Most of the GhEXO genes were derived from gene duplication events, while only three genes showed evidence of tandem duplication. Homologous locus relationships showed that 15 GhEXO genes are located on collinear blocks and that all orthologous/paralogous gene pairs had Ka > Ks values, indicating purifying selection pressure. The GhEXO genes showed ubiquitous expression in all eight tested cotton tissues and following exposure to three phytohormones, IAA, GA, and BL. Furthermore, GhEXO7_At was mainly expressed in response to BL treatment, and was predominantly expressed in the fibers. GhEXO7_At was found to be a plasma membrane protein, and its ectopic expression in Arabidopsis mediated BR-regulated plant growth and development with altered expression of DWF4, CPD, KCS1, and EXP5. Additionally, the functions of GhEXO7_At were confirmed by virus-induced gene silencing (VIGS) in cotton. This study will provide important genetic resources for future cotton breeding programs.

Identification of GhLOG gene family revealed that GhLOG3 is involved in regulating salinity tolerance in cotton (Gossypium hirsutum L.)

Cytokinin (CK) is an important plant hormone that promotes plant cell division and differentiation, and participates in salt response under osmotic stress. LOGs (LONELY GUY) are CK-activating enzymes involved in CK synthesis. The LOG gene family has not been comprehensively characterized in cotton. In this study we identified 151 LOG genes from nine plant species, including 28 LOG genes in Gossypium hirsutum. Phylogenetic analysis divided LOG genes into three groups. Exon/intron structures and protein motifs of GhLOG genes were highly conserved. Synteny analysis revealed that several gene loci were highly conserved between the A and D sub-genomes of G. hirsutum with purifying selection pressure during evolution. Expression profiles showed that most LOG genes were constitutively expressed in eight different tissues. Furthermore, LOG genes can be regulated by abiotic stresses and phytohormone treatments. Moreover, subcellular localization revealed that GhLOG3_At resides inside the cell membrane. Overexpression of GhLOG3 enhanced salt tolerance in Arabidopsis. Virus-induced gene silencing (VIGS) of GhLOG3_At in cotton enhanced sensitivity of plants to salt stress with increased H₂O₂ contents and decreased chlorophyll and proline (PRO) activity. Our results suggested that GhLOG3_At induces salt stress tolerance in cotton, and provides a basis for the use of CK synthesis genes to regulate cotton growth and stress resistance.

Identification and Characterization of the ERF Subfamily B3 Group Revealed GhERF13.12 Improves Salt Tolerance in Upland Cotton

The APETALA2 (AP2)/ethylene response factor plays vital functions in response to environmental stimulus. The ethylene response factor (ERF) subfamily B3 group belongs to the AP2/ERF superfamily and contains a single AP2/ERF domain. Phylogenetic analysis of the ERF subfamily B3 group genes from Arabdiposis thaliana, Gossypium arboreum, Gossypium hirsutum, and Gossypium raimondii made it possible to divide them into three groups and showed that the ERF subfamily B3 group genes are conserved in cotton. Collinearity analysis identified172 orthologous/paralogous gene pairs between G. arboreum and G. hirsutum; 178 between G. hirsutum and G. raimondii; and 1,392 in G. hirsutum. The GhERF subfamily B3 group gene family experienced massive gene family expansion through either segmental or whole genome duplication events, with most genes showing signature compatible with the action of purifying selection during evolution. Most G. hirsutum ERF subfamily B3 group genes are responsive to salt stress. GhERF13.12 transgenic Arabidopsis showed enhanced salt stress tolerance and exhibited regulation of related biochemical parameters and enhanced expression of genes participating in ABA signaling, proline biosynthesis, and ROS scavenging. In addition, the silencing of the GhERF13.12 gene leads to increased sensitivity to salt stress in cotton. These results indicate that the ERF subfamily B3 group had remained conserved during evolution and that GhERF13.12 induces salt stress tolerance in Arabidopsis and cotton.

AtMAD: Arabidopsis thaliana multi-omics association database

Integration analysis of multi-omics data provides a comprehensive landscape for understanding biological systems and mechanisms. The abundance of high-quality multi-omics data (genomics, transcriptomics, methylomics and phenomics) for the model organism Arabidopsis thaliana enables scientists to study the genetic mechanism of many biological processes. However, no resource is available to provide comprehensive and systematic multi-omics associations for Arabidopsis. Here, we developed an Arabidopsis thaliana Multi-omics Association Database (AtMAD, http://www.megabionet.org/atmad), a public repository for large-scale measurements of associations between genome, transcriptome, methylome, pathway and phenotype in Arabidopsis, designed for facilitating identification of eQTL, emQTL, Pathway-mQTL, Phenotype-pathway, GWAS, TWAS and EWAS. Candidate variants/methylations/genes were identified in AtMAD for specific phenotypes or biological processes, many of them are supported by experimental evidence. Based on the multi-omics association strategy, we have identified 11 796 cis-eQTLs and 10 119 trans-eQTLs. Among them, 68 837 environment-eQTL associations and 149 622 GWAS-eQTL associations were identified and stored in AtMAD. For expression–methylation quantitative trait loci (emQTL), we identified 265 776 emQTLs and 122 344 pathway-mQTLs. For TWAS and EWAS, we obtained 62 754 significant phenotype-gene associations and 3 993 379 significant phenotype-methylation associations, respectively. Overall, the multi-omics associated network in AtMAD will provide new insights into exploring biological mechanisms of plants at multi-omics levels.

Genome-wide characterization and expression analysis of geranylgeranyl diphosphate synthase genes in cotton (Gossypium spp.) in plant development and abiotic stresses

Background

GGPP (geranylgeranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has not been performed in any plant species except Arabidopsis thaliana. Here, we performed a complete computational and bioinformatics analysis of GGPPS and detected their transcription expression pattern in Gossypium hirsutum for the first time so that to explore their evolutionary relationship and potential functions. Finally, we unravelled evolutionary relationship, conserved sequence logos, gene duplication and potential involvement in plant development and abiotic stresses tolerance of GGPPS genes in G. hirsutum and other plant species.

Results

A total of 159 GGPPS genes from 18 plant species were identified and evolutionary analysis divided these GGPPS genes into five groups to indicate their divergence from a common ancestor. Further, GGPPS family genes were conserved during evolution and underwent segmental duplication. The identified 25 GhGGPPS genes showed diverse expression pattern particularly in ovule and fiber development indicating their vital and divers roles in the fiber development. Additionally, GhGGPPS genes exhibited wide range of responses when subjected to abiotic (heat, cold, NaCl and PEG) stresses and hormonal (BL, GA, IAA, SA and MeJA) treatments, indicating their potential roles in various biotic and abiotic stresses tolerance.

Conclusions

The GGPPS genes are evolutionary conserved and might be involve in different developmental stages and stress response. Some potential key genes (e.g. GhGGPP4, GhGGPP9, and GhGGPP15) were suggested for further study and provided valuable source for cotton breeding to improve fiber quality and resistant to various stresses.

Genome-wide identification of GhAAI genes reveals that GhAAI66 triggers a phase transition to induce early flowering

Plants undergo a phase transition from vegetative to reproductive development that triggers floral induction. Genes containing an AAI (α-amylase inhibitor) domain form a large gene family, but there have been no comprehensive analyses of this gene family in any plant species. Here, we identified 336 AAI genes from nine plant species including122 AAI genes in cotton (Gossypium hirsutum). The AAI gene family has evolutionarily conserved amino acid residues throughout the plant kingdom. Phylogenetic analysis classified AAI genes into five major clades with significant polyploidization and showing effects of genome duplication. Our study identified 42 paralogous and 216 orthologous gene pairs resulting from segmental and whole-genome duplication, respectively, demonstrating significant contributions of gene duplication to expansion of the cotton AAI gene family. Further, GhAAI66 was preferentially expressed in flower tissue and as responses to phytohormone treatments. Ectopic expression of GhAAI66 in Arabidopsis and silencing in cotton revealed that GhAAI66 triggers a phase transition to induce early flowering. Further, GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis of RNA sequencing data and qRT-PCR (quantitative reverse transcription-PCR) analysis indicated that GhAAI66 integrates multiple flower signaling pathways including gibberellin, jasmonic acid, and floral integrators to trigger an early flowering cascade in Arabidopsis. Therefore, characterization of the AAI family provides invaluable insights for improving cotton breeding.

Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.

Genome-Wide Identification and Characterization of the PERK Gene Family in Gossypium hirsutum Reveals Gene Duplication and Functional Divergence

Proline-rich extensin-like receptor kinases (PERKs) are an important class of receptor kinases in plants. Receptor kinases comprise large gene families in many plant species, including the 15 PERK genes in Arabidopsis. At present, there is no comprehensive published study of PERK genes in G. hirsutum. Our study identified 33 PERK genes in G. hirsutum. Phylogenetic analysis of conserved PERK protein sequences from 15 plant species grouped them into four well defined clades. The GhPERK gene family is an evolutionarily advanced gene family that lost its introns over time. Several cis-elements were identified in the promoter regions of the GhPERK genes that are important in regulating growth, development, light responses and the response to several stresses. In addition, we found evidence for gene loss or addition through segmental or whole genome duplication in cotton. Gene duplication and synteny analysis identified 149 orthologous/paralogous gene pairs. Ka/Ks values show that most GhPERK genes experienced strong purifying selection during the rapid evolution of the gene family. GhPERK genes showed high expression levels in leaves and during ovule development. Furthermore, the expression of GhPERK genes can be regulated by abiotic stresses and phytohormone treatments. Additionally, PERK genes could be involved in several molecular, biological and physiological processes that might be the result of functional divergence.