Plant height is a key agronomic trait that influences plant architecture and mechanical harvesting suitability in cotton; however, the molecular mechanisms underlying its dynamic development remain unclear. In this study, two recombinant inbred line (RIL) populations sharing CCRI127 as a common paternal parent (RIL-GH07, n = 150; RIL-2358B, n = 276) were developed. Based on stable plant-height performance across multiple environments, tall and short extreme lines were selected from the two RIL populations for transcriptome sequencing. By integrating differential expression analysis with weighted gene co-expression network analysis (WGCNA), we identified hub genes associated with cotton plant height development, characterized the molecular features and core pathways governing dynamic stem elongation at different growth stages, thereby providing insights into the transcriptional regulation of plant height development in cotton. The two RIL populations showed broadly similar plant-height growth patterns, with slow elongation at 15 DOS, rapid elongation during 30-60 DOS, and reduced growth after 70 DOS. Transcriptome differential expression analysis identified 15,052 non-redundant DEGs, which exhibited clear population- and stage-specific expression patterns. In the GH07 population, the largest number of DEGs was detected at 15 DOS (7193), whereas in the 2358B population relatively large numbers of DEGs were maintained at both 30 DOS (3839) and 70 DOS (3118). Analysis of DEGs shared by the two populations across four developmental stages showed that, in addition to genes with consistent expression trends, each stage also contained a substantial number of DEGs with opposite expression directions. WGCNA identified 25 gene expression modules, among which the green and yellow modules were significantly positively correlated with plant height. Functional enrichment analysis indicated that genes in these two modules were mainly enriched in hormone regulation and signal transduction, protein modification and degradation, and intracellular transport. Seven hub genes were identified by integrating intramodular connectivity and kME values. Functional prediction suggested that these genes may play important roles in cotton plant height development. This study provides genetic resources and a theoretical basis for subsequent functional validation of cotton plant height-related genes and the improvement of plant architecture in cotton.

Climate change has increased the sensitivity of cropping systems to environmental variability, making the genetic dissection of G × E and phenotypic plasticity essential for adaptive breeding. In this study, a recombinant inbred line population of upland cotton was evaluated across 16 environments from multi-year and multi-location field trials to assess the plasticity of yield- and fiber-quality traits. By integrating the Finlay–Wilkinson regression model with CERIS sliding-window analyses, 13 key meteorological factors and 4 principal component variables were identified, together with their effective time windows. QTL mapping based on trait plasticity slopes and environmental response slopes detected 172 environment-associated loci. A major locus at 188 Mb on chr10 influenced boll weight and seed index in response to multiple environmental variables, including photoperiod, cumulative radiation, growing degree days, and the product of radiation and photoperiod, suggesting a key regulatory site for environmental signal perception. Haplotype analysis further supported functional divergence of alleles within this region in relation to environmental adaptation. Overall, this study identifies critical environmental factors shaping cotton yield and fiber quality and reveals multiple G × E–related loci underlying environmental responsiveness and phenotypic plasticity, providing a theoretical foundation for environmentally informed precision breeding.

The simultaneous improvement of fiber strength (FS) and lint percentage (LP) is a critical objective for achieving high-quality and high-yield cotton production. Identifying key genes and their regulatory networks that govern the synergistic development of FS and LP is essential for achieving their simultaneous improvement. In our previous study, a stable chromosome segment, Seg-D06-2, was identified for its ability to concurrently enhance both FS and LP with high reliability. In the present study, homozygous individuals harboring the Seg-D06-2 segment within a nearly uniform genetic background were selected to construct a large BC6F2 chromosome segment substitution line (CSSL) population comprising 3324 individuals. Extreme individuals characterized by simultaneous improvement in FS and LP, which shared similar genetic and phenotypic backgrounds, were subjected to comparative transcriptomic and weighted gene co-expression network analysis (WGCNA) at 0, 5, 10, 15, 20, and 25 days post-anthesis (DPA). The results highlighted the 'blue' and 'yellow' modules as being significantly associated with the simultaneous improvement of FS and LP. Four hub genes (GH_D06G0542, GH_D06G1609, GH_D06G0627 and GH_D06G2689) and two DEGs (GH_D06G0564 and GH_D06G0723) were identified in the 'blue' module. Three hub genes (GH_D06G0540, GH_D06G0558 and GH_D06G0636) and one DEG (GH_D06G0527) were identified in the 'yellow' module. These 10 key genes likely play pivotal roles in regulating the synergistic development of FS and LP, warranting further investigation. The reliability of the RNA-seq data was confirmed by qRT-PCR. This study provides a valuable resource for molecular breeding aimed at the simultaneous improvement of FS and LP and offers new insights into the molecular mechanisms governing their synergistic development.

Cotton fiber quality-defined by length, strength, and fineness-directly influences the commercial value of textile products, with fiber length being one of the most critical parameters in industrial procurement. In upland cotton (Gossypium hirsutum), fiber development occurs through four overlapping stages, of which the elongation phase (2-20 d post-anthesis, DPA) is pivotal for determining final fiber length. Recent studies have identified a diverse set of genes regulating fiber elongation via distinct molecular mechanisms, categorized into six functional classes: Phytohormone-associated genes; transcription factor-associated genes; cellulose-, lignin-, and sucrose-associated genes; lipid-associated genes; cytoskeleton-associated genes; and other functionally diverse genes. By synthesizing their roles and hierarchical interactions, this review constructs comprehensive genetic networks governing fiber elongation. This work provides a molecular blueprint for precision breeding strategies to enhance cotton fiber length, offering actionable insights for breeding programs aimed at improving fiber quality.

Cotton fiber, the dominant natural fiber worldwide, is a specialized single cell trichome initiating from the ovule epidermis. The structure and composition of its cell wall critically influence fiber quality and its economic value for the textile industry. This review centers on the structure and biosynthesis of major cell wall components, including cellulose, pectin, lignin, and xylan, during different stages of cotton fiber development. A systematic elucidation is therefore merited, regarding how the biosynthesis and remodeling of these components regulated by stage-specific genes and enzymes influence fiber initiation, elongation, secondary wall thickening, and maturation, ultimately determining critical quality traits such as fiber length and strength. Future research on cotton fiber cell walls presents both challenges and opportunities in frontier areas and applications within the textile industry. In-depth investigations understanding and harnessing cell wall components will provide crucial support for enhancing cotton fiber quality through molecular breeding and biotechnological approaches.

The DUF538 gene family, harboring unknown functional proteins, has been reported to take active roles in plant development and response to adversities, while few studies of genome-wide identification and functional verification have been performed in cotton. Hence, two ancestral diploid species, G. arboretum and G. raimondii, and two cultivated tetraploid ones, G. hirsutum and G. barbadense, were chosen in this study to investigate the cotton DUF538 gene family, resulting in 37, 37, 70, and 70 members identified, respectively. A phylogenetic tree was constructed on these cotton DUF538 genes, together with 22 A. thaliana ones, which were divided into seven groups unevenly distributed across nearly all chromosomes. High-degree conservatism, while rich in diversity, was separately observed in gene structure and conserved motif analyses between the same groups and different groups, and a great number of gene-replication events were detected from intraspecific and interspecific collinearity analyses, implying this was the driving force for DUF538 family expansion. Multiple cis-acting elements relevant to adversity-stress responses were found in the promoter region, which were consistent with the transcriptome expression analyses in response to low-temperature and drought stress and Verticillium wilt infection. Coincidentally, GhDUF538-7 showed the core position in the protein-protein interaction network and was identified in the overlapping region of the interval of four reported VW resistance-related QTLs. The gene function of GhDUF538-7 was verified via gene cloning, relative expression-pattern detection, and virus-induced gene silencing (VIGS) experiment. The TRV:DUF538-7 plants showed more serious VW symptoms, significantly severe disease indices, relatively higher fungal biomass, and increased brown vascular bundles compared with TRV:00 plants. Significantly lower expression levels of marker genes PR4 and MYC2 in jasmonate signaling pathways indicated GhDUF538-7 as a potentially positive regulatory factor in plant defense via hormone signal transduction. This study not only broadened the research perspective of evolution and functional differentiation of the cotton DUF538 gene family, but it also revealed the cooperative relationship between DUF538-7 and the JA pathway for further molecular mechanisms of cotton resistance to VW infection.

Verticillium wilt, primarily caused by Verticillium dahliae, represents a major constraint on both quality and yield in upland cotton (Gossypium hirsutum). Calcium (Ca2+) functions as a pivotal second messenger in plant signal transduction, regulating the expression of stress-induced genes. The Soybean gene Regulated by Cold-2 (SRC2), which encodes a protein containing C2 domains, is known to play important roles in plant development and environmental adaptation. In this study, a total of 31 SRC2 members were identified in five cotton species and classified into five distinct groups. Analyses of gene structure and conserved protein motifs revealed that SRC2 genes are evolutionarily conserved. GhSRC2 genes were widely expressed in various cotton tissues and showed responsiveness to cold, heat, drought and salt stresses. Notably, GhSRC2-3D expression was significantly induced upon V. dahliae infection. Subcellular localization assays indicated that GhSRC2-3D localizes to the cell membrane. Complementation of Arabidopsis src2 mutant with GhSRC2-3D restored resistance to V. dahliae, while a C2 domain deletion variant (ΔGhSRC2-3D) failed to confer resistance. Furthermore, down-regulation of GhSRC2-3D mediated by virus-induced gene silencing (VIGS) compromised V. dahliae resistance in upland cotton. Collectively, our findings demonstrate the conserved role of GhSRC2-3D in plant defense against V. dahliae infection and underscore the essential contribution of its C2 domain to protein function.

Gibberellins (GAs) play a crucial regulatory role in the growth and development of cotton (Gossypium hirsutum L.). Through bioinformatics analyses, we identified a total of 39 GA2ox genes (encoding gibberellin 2-oxidases) in the cotton genome, designated GhGA2ox1 to GhGA2ox39. Based on phylogenetic analysis, these genes were classified into five groups. We further examined their gene structures, conserved motifs, and chromosomal distributions, revealing that members within the same group shared similar structural and motif organizations. Collinearity and cis-element analyses provided important insights into the evolutionary history and regulatory potential of the GA2ox gene family in cotton. Notably, using nucleotide diversity (π) and population differentiation (FST) analyses across the entire family, we screened and identified nine candidate genes that underwent strong artificial selection during cotton domestication and improvement. Further haplotype-phenotype association analysis identified GH_D09G0919 (GhGA2ox31) as a key regulator of Plant Height (PH). To validate their regulatory roles, we analyzed the genotype distribution in accessions with extreme phenotypes. The results revealed divergent selection histories for these two loci: the favorable allele of GH_D01G0720 (GhGA2ox23) was already fixed in the tested population, whereas GH_D09G0919 maintained significant natural variation. Specifically, the Hap2 allele of GH_D09G0919 was significantly enriched in the shortest accessions compared to the tallest ones. Importantly, quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed that the Hap2 allele drives significantly higher gene expression in leaves, suggesting that enhanced GA catabolism underlies the compact phenotype. Additionally, transcriptomic profiling revealed the tissue-specific expression patterns of candidate genes, implying their functional roles in development. Furthermore, functional validation using the Arabidopsis mutant of the homologous gene (AtGA2ox8) confirmed its conserved role in regulating plant height, as the mutant exhibited a distinct short-stature phenotype. These results uncover valuable genetic resources for molecular breeding to shape compact cotton architecture. Collectively, this study aims to analyze the evolutionary patterns of the cotton GA2ox gene family and to identify key genes that regulate plant height under artificial selection, providing theoretical support for molecular breeding of compact plant types.

Verticillium wilt (VW) is a soil-borne fungal plant disease. Gossypium hirsutum varieties with the widest planting area are highly susceptible to VW pathogens, because their narrow genetic background of germplasm resources causes difficulties in cultivating VW-resistant varieties through intraspecific breeding. Therefore, G. barbadense cultivars, harboring a natural VW resistance, become ideal donor materials to cultivate high-yield and multi-resistance chromosome segment substitution lines (CSSLs) through hybridization and backcrossing with G. hirsutum receptor and recurrent parent. In order to investigate the molecular mechanism of cotton response to VW infection, a BC5F3:5 CSSL MBI9626 and its parents, CCRI36 (G. hirsutum) and Hai1 (G. barbadense), were chosen to perform transcriptome and metabolome sequencing on their root samples at 0, 7, and 15 days after inoculation (DAI) of V. dahliae V991. In total, 36,564 differentially expressed genes (DEGs) and 102 differentially accumulated metabolites (DAMs) were separately identified from 12 pairwise comparison groups among the 27 samples. Of those, 125 common DEGs were found to participate in the biological processes of oxylipin metabolism, jasmonic acid (JA) biosynthesis/metabolism, and response to wounding in Gene Ontology (GO) enrichment analyses, while most of the DAMs were significantly enriched in tyrosine, purine, and phenylalanine metabolism pathways in enrichment analyses of Kyoto Encyclopedia of Genes and Genomes (KEGG). Having performed a conjoint KEGG analysis of all the DEGs and DAMs, we found two commonly enriched pathways, namely plant hormone signal transduction and flavonoid biosynthesis, which were consistent with the enrichment annotations of the significant model in weighted gene co-expression network analysis on the 2091 DEGs identified by an intersection of the genes in 40 previous QTLs and the total DEGs of this RNA-seq data. Among the ABA signaling pathway, the gene GH_D12G0236 (GHABF3) was selected to be used to perform virus-induced gene silencing (VIGS) verification in CCRI36 and MBI9626, and GHABF3-silenced plants showed a more serious wilting phenotype, an increased disease index (DI), and higher accumulation of fungal biomass compared to their empty-vector plants. These results provide a high-efficiency strategy for screening vital genes affecting cotton VW resistance, and lay a solid foundation for further cotton molecular breeding.

Cotton is a crucial cash crop widely valued for its fiber. It is an important source of natural fiber and has diverse applications. Improving fiber quality is of significant economic and agricultural importance. Purple acid phosphatases (PAPs) are multifunctional enzymes critical for plant cell wall biosynthesis, root architecture modulation, low-phosphorus stress adaptation, and salt/ROS stress tolerance. In this study, a comprehensive genome-wide analysis of the PAP gene family was performed for four cotton species (G. hirsutum, G. barbadense, G. raimondii, and G. arboreum) to explore its potential role in improving fiber quality. A total of 193 PAP genes were identified in these species, revealing several conserved domains that contribute to their functional diversity. Phylogenetic analysis showed that the cotton PAP2 genes exhibited high homology with NtPAP12, a cell wall synthesis-related gene. Using cotton varieties with contrasting fiber thickness (EZ60, micronaire 4.5 vs. CCRI127, micronaire 3.5), qRT-PCR analysis demonstrated significantly higher expression levels of GhPAP2.2, GhPAP2.6, GhPAP2.8, and GhPAP2.9 in EZ60 fibers during 20–25 DPA compared to CCRI127. These results highlight the potential influence of PAP genes on cotton fiber development and provide valuable insights for improving fiber quality in cotton breeding.

Coenzyme Q (CoQ) was an electron carrier within the mitochondrial respiratory chain, serves as a cofactor for various mitochondrial dehydrogenases thereby playing a significant role in plant growth and development. In this study, GhCoQ9 was identified through transcriptomic analysis of cotton under salt stress. GhCoQ9 participates in the synthesis of coenzyme Q. Under salt stress condition, cotton plants with GhCoQ9 silenced exhibited more pronounced growth inhibition compared to the control group. Additionally, the catalase (CAT) and superoxide dismutase (SOD) levels were significantly increased, while the level of malondialdehyde (MDA) showed an upward trend. Microscopic analysis of cotton leaves revealed that under salt stress conditions GhCoQ9 -silenced plants exhibited reduced stomatal aperture, cellular destruction, cell shrinkage and deformation, and increased intercellular space compared to the control plants. The ultrastructure of GhCoQ9-silenced plants exhibited increased susceptibility to salt stress, primarily manifested as damage to the chloroplast and mitochondrial structures. We also investigated the function of CoQ9 in Arabidopsis, the results showed that coq9 mutant exhibited reduced germination rate and significant inhibited growth under salt stress. These findings suggest that GhCoQ9 plays a crucial role in the adaptation of cotton to salt stress by preserving the integrity of chloroplast and mitochondrial structures.

Understanding the influence of environmental factors on cotton performance is crucial for enhancing yield and fiber quality in the context of climate change. This study investigates genotype-by-environment (G×E) interactions in cotton, using data from 250 recombinant inbred lines (CCRI70 RILs) cultivated across 14 diverse environments in China’s major cotton cultivation areas. Our findings reveal that environmental effects predominantly influenced yield-related traits (boll weight, lint percentage, and the seed index), contributing to 34.7% to 55.7% of their variance. In contrast fiber quality traits showed lower environmental sensitivity (12.3–27.0%), with notable phenotypic plasticity observed in the boll weight, lint percentage, and fiber micronaire. Employing six machine learning models, Random Forest demonstrated superior predictive ability (R2 = 0.40–0.72; predictive Pearson correlation = 0.63–0.86). Through SHAP-based interpretation and sliding-window regression, we identified key environmental drivers primarily active during mid-to-late growth stages. This approach effectively reduced the number of influential input variables to just 0.1–2.4% of the original dataset, spanning 2–9 critical time windows per trait. Incorporating these identified drivers significantly improved cross-environment predictions, enhancing Random Forest accuracy by 0.02–0.15. These results underscore the strong potential of machine learning to uncover critical temporal environmental factors underlying G×E interactions and to substantially improve predictive modeling in cotton breeding programs, ultimately contributing to more resilient and productive cotton cultivation.

Cottonseed is a globally significant oilseed crop due to its high contribution to vegetable oil supply. The process of lipid accumulation is essential for seed maturation and oil buildup. In this study, we analyzed lipid metabolites and gene expression patterns related to fatty acid synthesis in two cotton genotypes with varying oil content. Our lipid analysis identified 588 kinds of lipids in developing embryos of upland cotton, with glycerophospholipids (64.29 %), glycerolipids (17.69 %), and saccharolipids (13.61 %) being the main components. Transcriptome analysis of key genes involved in fatty acid biosynthesis and lipid droplet formation revealed potential regulatory regions influencing lipid content in developing embryos of upland cotton. This research provides valuable insights into the lipidome profiles during embryo development and lays the groundwork for future investigations on lipid accumulation in economically important crops.

Arabinogalactan proteins (AGPs) constitute a diverse class of hydroxyproline-rich glycoproteins implicated in various aspects of plant growth and development. However, their functional characterization in cotton (Gossypium spp.) remains limited. As a globally significant economic crop, cotton serves as the primary source of natural fiber, making it essential to understand the genetic mechanisms underlying its growth and development. This study aims to perform a comprehensive genome-wide identification and characterization of the AGP gene family in Gossypium spp., with a particular focus on elucidating their structural features, evolutionary relationships, and functional roles. A genome-wide analysis was conducted to identify AGP genes in Gossypium spp., followed by classification into distinct subfamilies based on sequence characteristics. Protein motif composition, gene structure, and phylogenetic relationships were examined to infer potential functional diversification. Subcellular localization of a key candidate gene, GhAGP50, was determined using fluorescent protein tagging, while gene expression patterns were assessed through β-glucuronidase (GUS) reporter assays. Additionally, hormonal regulation of GhAGP50 was investigated via treatments with methyl jasmonate (MeJA), abscisic acid (ABA), indole-3-acetic acid (IAA), and gibberellin (GA). A total of 220 AGP genes were identified in Gossypium spp., comprising 19 classical AGPs, 28 lysine-rich AGPs, 55 AG peptides, and 118 fasciclin-like AGPs (FLAs). Structural and functional analyses revealed significant variation in gene organization and conserved motifs across subfamilies. Functional characterization of GhAGP50, an ortholog of AGP18 in Arabidopsis thaliana, demonstrated its role in promoting epidermal hair formation in leaves and stalks. Subcellular localization studies indicated that GhAGP50 is targeted to the nucleus and plasma membrane. GUS staining assays revealed broad expression across multiple tissues, including leaves, inflorescences, roots, and stems. Furthermore, hormonal treatment experiments showed that GhAGP50 expression is modulated by MeJA, ABA, IAA, and GA, suggesting its involvement in hormone-mediated developmental processes. This study presents a comprehensive genome-wide analysis of the AGP gene family in cotton, providing new insights into their structural diversity and functional significance. The identification and characterization of GhAGP50 highlight its potential role in epidermal hair formation and hormonal regulation, contributing to a deeper understanding of AGP functions in cotton development. These findings offer a valuable genetic resource for future research aimed at improving cotton growth and fiber quality through targeted genetic manipulation.

Genetically modified crops have transformed agriculture, but their long-term ecological impacts remain incompletely understood. Here we investigate how herbicide-tolerant transgenic cotton affects rhizosphere microbial communities and nutrient cycling over a 28-day growth period using 16S rRNA amplicon sequencing and multivariate analyses. We sampled rhizosphere soil from greenhouse-grown transgenic and wild-type cotton plants at five time points, analyzing microbial diversity, community structure, and nutrient dynamics. Despite initial concerns about transgenic modifications disrupting soil ecosystems, we found no significant differences in microbial α-diversity or β-diversity between genotypes. Only minor, transient changes occurred at the genus level, including <5% shifts in Flavobacterium and Ramlibacter abundance on day 14, alongside brief nutrient flux variations that normalized by day 28. Notably, transgenic plants showed enhanced above-ground biomass accumulation without compromising rhizosphere stability or soil moisture content. These results demonstrate that herbicide-tolerant cotton maintains rhizosphere homeostasis while improving agronomic performance, supporting the environmental safety of this biotechnology for sustainable agricultural intensification.

Cottonseed oil is rich in unsaturated fatty acids (UFAs), making it suitable for use as edible oil. Fatty acid desaturases (FADs) play a major role in the conversion of monounsaturated fatty acids (MUFAs) to polyunsaturated fatty acids (PUFAs). In total, 39 GhFAD genes were detected in upland cotton and divided into five groups in the present study. Gene structure and domain analysis showed that GhFAD members within each group were highly conserved. Cis-elements associated with environmental stress and hormone responses were identified in GhFAD promoters. The predicted transcription factors and miRNAs targeting these genes suggest extensive roles for GhFADs in diverse stress conditions. Analysis of expression profiles indicated that GhFAD genes participate extensively in developmental processes and stress adaptation in cotton. Among these, the concurrent high expression of GhFAD2-1 and low expression of GhFAD3 are consistent with the typical fatty acid profile of cottonseed oil. GhFAD3-2 and GhFAD3-1 exhibit a complementary expression profiles, suggesting they may operate in a relay manner during fiber development. Additionally, experimental evidence established that GhFAD2-3 is involved in the cold stress response. This research delivers a thorough characterization of the GhFAD genes in upland cotton, thereby establishing a solid groundwork for future functional genomics studies.

We identified two splicing variants of GhLSM1B (GhLSM1BS and GhLSM1BL) with distinct expression patterns and predicted 3D structures, despite sharing the same nuclear localization. Overexpression of GhLSM1BS, but not GhLSM1BL, accelerated cotton callus proliferation and altered cell morphology during somatic embryogenesis, accompanied by altered expression of CYP450 family genes and elevated brassinosteroid levels.

Verticillium wilt (VW) severely limits the cotton yield and fiber quality. Marker-assisted selection is an efficient strategy for breeding resistant varieties. In this study, a high-density genetic map was constructed by using an F8:9 recombinant inbred line (RIL) population derived from CCRI70. Phenotypic data on disease incidence (DINC) and disease index (DI) were collected across six environments. A total of 59 QTLs for DINC and 60 QTLs for DI were identified, with three and six stable across multiple environments, respectively. These QTLs formed 18 clusters across 13 chromosomes, showing consistent additive effects. Transcriptome analysis revealed eight differentially expressed candidate genes within stable QTL regions. Among them, GH_D05G1495, GH_A09G1013, and GH_D05G1683 were further validated by virus-induced gene silencing as key genes conferring V. dahliae resistance in cotton. This study provides valuable genetic resources for improving Verticillium wilt resistance in cotton breeding.

BACKGROUND:Cotton is an important economic crop and a host of Liriomyza sativae. Pectin methylesterase (PME)-mediated pectin metabolism plays an indispensable role in multiple biological processes in planta. However, the pleiotropic functions of PME often lead to unpredictable effects on crop resistance to pests. Additionally, whether and how PME affects susceptibility to Liriomyza sativae remain unclear. RESULTS:Here, we isolated GhPME36, which is located in the cell wall, from upland cotton (Gossypium hirsutum L.). Interestingly, the overexpression of GhPME36 in cotton caused severe susceptibility to Liriomyza sativae but increased leaf biomass in Arabidopsis. Cytological observations revealed that the cell wall was thinner with more demethylesterified pectins in GhPME36-OE cotton leaves than in WT leaves, whereas the soluble sugar content of GhPME36-OE cotton leaf cell walls was accordingly higher; both factors attracted Liriomyza sativae to feed on GhPME36-OE cotton leaves. Metabolomic analysis demonstrated that glucose was significantly differentially accumulated. Transcriptomic analysis further revealed DEGs enriched in glucose metabolic pathways when GhPME36 was overexpressed, suggesting that GhPME36 aggravates susceptibility to Liriomyza sativae by affecting both the structure and components of cell wall biosynthesis. Moreover, GhPME36 interacts with another pectin-modifying enzyme, GhC/VIF1, to maintain the dynamic stability of pectin methyl esterification. CONCLUSIONS:Taken together, our results reveal the cytological and molecular mechanisms by which GhPME36 aggravates susceptibility to Liriomyza sativae. This study broadens the knowledge of PME function and provides new insights into plant resistance to pests and the safety of genetically modified plants.

Sulfate transporter (SULTR) proteins are in charge of the transport and absorption on sulfate substances, and have been reported to play vital roles in the biological processes of plant growth and stress response. However, there were few reports of genome-wide identification and expression-pattern analysis of SULTRs in Hibiscus mutabilis. Gossypium genus is a ideal model for studying the allopolyploidy, therefore two diploid species (G. raimondii and G. arboreum) and two tetraploid species (G. hirsutum and G. barbadense) were chosen in this study to perform bioinformatic analyses, identifying 18, 18, 35, and 35 SULTR members, respectively. All the 106 cotton SULTR genes were utilized to construct the phylogenetic tree together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 8 Zea mays ones, which was divided into Group1-Group4. The clustering analyses of gene structures and 10 conserved motifs among the cotton SULTR genes showed the consistent evolutionary relationship with the phylogenetic tree, and the results of gene-duplication identification among the four representative Gossypium species indicated that genome-wide or segment duplication might make main contributions to the expansion of SULTR gene family in cotton. Having conducted the cis-regulatory element analysis in promoter region, we noticed that the existing salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) elements could have influences with expression levels of cotton SULTR genes. The expression patterns of GhSULTR genes were also investigated on the 7 different tissues or organs and the developing ovules and fibers, most of which were highly expressed in root, stem, sepal, receptacel, ovule at 10 DPA, and fiber at 20 and 25 DPA. In addition, more active regulatory were observed in GhSULTR genes responding to multiple abiotic stresses, and 12 highly expressed genes showed the similar expression patterns in the quantitative Real-time PCR experiments under cold, heat, salt, and drought treatments. These findings broaden our insight into the evolutionary relationships and expression patterns of the SULTR gene family in cotton, and provide the valuable information for further screening the vital candidate genes on trait improvement.