Search Results (16)

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal upstream regulators of MAPK cascades, integrating signals that coordinate plant development and stress responses. However, the specific functions of MAPKKKs, particularly within the MEKK subfamily, in mediating cotton resistance to Verticillium wilt and Fusarium wilt remain poorly characterized. To address this, we conducted a systematic, cross-species analysis of the MAPKKK family in four key cotton species: Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii. Genome-wide identification and phylogenetic analysis revealed 660 MAPKKK genes, classifying them into the MEKK, Raf, and ZIK subfamilies. Evolutionary analysis indicated that Whole-Genome Duplication (WGD) events were the primary driver of family expansion. Promoter cis-element and Gene Ontology (GO) enrichment analyses implicated these genes in hormone signaling and stress adaptation. Expression profiling demonstrated functional modularity, with distinct members responding specifically to cold stress or cooperatively to drought and salt stresses. Upon pathogen infection, members diverged into regulatory modules associated with immune homeostasis, tissue-specific defense, and core signaling potentially governing systemic acquired resistance (SAR). The temporal expression patterns of core candidate genes were validated by qRT-PCR. This study provides, for the first time, a comprehensive evolutionary and functional framework for the MEKK subfamily within the cotton MAPKKK family. It reveals the conserved and divergent roles of this subfamily in stress adaptation and identifies key candidate genes for breeding disease-resistant cotton varieties. Full article

Cottonseed is an important resource for edible oil and protein. Here, we evaluated cottonseed oil, protein, and gossypol contents using traditional chemical methods and near-infrared reflectance spectroscopy (NIRS) in diverse upland cotton (n = 456) and sea island cotton (n = 205) germplasm. In upland cotton, oil content averaged 21.23 ± 3.98% (12.74–43.56%), protein averaged 23.63 ± 4.63% (15.53–49.79%), and gossypol averaged 1.47 ± 0.21 mg/g (0.06–2.07). Correlation analysis showed a significant negative association between oil and protein (r = −0.125, p < 0.01; confirmed by NIRS: r = −0.171, p < 0.01), a significant negative association between protein and gossypol (r = −0.375, p < 0.01), and a significant positive association between oil and gossypol (r = 0.409, p < 0.01). In sea island cotton, oil, protein, and gossypol contents averaged 24.82 ± 6.15% (14.64–41.43%), 25.75 ± 2.04% (18.84–39.00%), and 1.60 ± 0.15 mg/g (1.22–2.08), respectively. The oil–protein association was strongly negative by NIRS (r = −0.744, p < 0.01), whereas correlations with gossypol were weak and not significant by the traditional method. After screening and evaluation, high oil and protein varieties were identified in upland cotton (n = 15) and sea island cotton (n = 6). Fourteen extreme-oil upland materials were further used to examine flowering-date effects on oil accumulation and physiological indicators, showing rapid oil accumulation and a flowering-date-dependent maximum. Finally, qRT-PCR analysis of lipid-metabolism-related candidate genes showed that seven genes were expressed significantly higher in high-oil than in low-oil materials (p < 0.05), peaking at the late stage of oil accumulation. GhDGAT1 and GhDGAT2 showed positive regulatory effects on oil accumulation, whereas GhFAD3 and GhKCR2 showed negative regulatory effects. Collectively, these findings provide compositional benchmarks, clarify trait relationships, and identify candidate genes useful for breeding cotton cultivars with improved seed oil/protein traits. Full article

Microplastics are considered to be one of the major threats that have significant effects on marine ecosystems and marine organisms. These tiny plastic particles can also absorb and carry toxic substances to marine life, potentially affecting human health through food chains. This study investigates microplastics in surface seawater and in two species of sea cucumber, Holothuria atra at Similan Island and Holothuria edulis at Surin Island. Color, shape, and components of microplastics were identified to evaluate sources of the microplastics found in the area. The results found that the average abundance of microplastics in seawater at Similan and Surin Islands is 1.93 ± 1.42 and 1.11 ± 0.75 pieces/m³, respectively. Black fiber is a dominant microplastic found in seawater and both species of sea cucumber. Fourier-Transform Infrared spectroscopy (FTIR) indicated that polyethylene terephthalate (PET) and polyester are the major components of microplastics in surface seawater, while cotton blends and other mixed components are the major components in sea cucumbers. These findings imply that microplastics found in surface seawater could potentially degrade from fishing and aquaculture equipment, maritime transport, and materials from plastic containers. Microplastics in sea cucumbers, on the other hand, are probably originating from domestic sewage discharge, especially textile washing and fishing equipment. Full article

Cotton fiber quality improvement remains a fundamental challenge in breeding programs due to the complex genetic architecture underlying fiber development. The narrow genetic base of upland cotton (Gossypium hirsutum L.) and the quantitative nature of fiber quality traits necessitate innovative approaches for identifying and incorporating superior alleles from related species. We developed a BC₆F₂ population by introgressing chromosome segments from the sea island cotton variety Xinhai 36 (G. barbadense) into the upland cotton variety Xinluzhong 60 (G. hirsutum). Based on fiber strength phenotyping, we constructed two DNA bulks representing extreme phenotypes (20 superior and 12 inferior individuals) for bulked segregant analysis sequencing (BSA-Seq). High-throughput sequencing generated 225.13 Gb of raw data with average depths of 20× for parents and 30× for bulks. SNP calling and annotation were performed using GATK and ANNOVAR against the upland cotton reference genome (TM-1). BSA-Seq analysis identified 13 QTLs primarily clustered within a 1.6 Mb region (20.6–22.2 Mb) on chromosome A10. Within this region, we detected nonsynonymous mutation genes involving a total of six genes. GO and KEGG enrichment analyses revealed significant enrichment for carbohydrate metabolic processes, protein modification, and secondary metabolite biosynthesis pathways. Integration with transcriptome data prioritized GH_A10G1043, encoding a β-amylase family protein, as the key candidate gene. Functional validation through overexpression and RNAi knockdown in Arabidopsis thaliana demonstrated that GH_A10G1043 significantly regulates starch content and β-amylase activity, though without visible morphological alterations. This study successfully identified potential genomic regions and candidate genes associated with cotton fiber strength using chromosome segment substitution lines combined with BSA-Seq. The key candidate gene GH_A10G1043 provides a valuable target for marker-assisted selection in cotton breeding programs. Our findings establish a foundation for understanding the molecular mechanisms of fiber quality formation and offer genetic resources for developing superior cotton varieties with enhanced fiber strength. Full article

In this study, GH19 chitinase (Chi) gene family was systematically identified and characterized using genomic assemblies from four cotton species: Gossypium barbadense, G. hirsutum, G. arboreum, and G. raimondii. A suite of analyses was performed, including genome-wide gene identification, physicochemical property characterization of the encoded proteins, subcellular localization prediction, phylogenetic reconstruction, chromosomal mapping, promoter cis-element analysis, and comprehensive expression profiling using transcriptomic data and qRT-PCR (including tissue-specific expression, hormone treatments, and Fusarium oxysporum infection assays). A total of 107 GH19 genes were identified across the four species (35 in G. barbadense, 37 in G. hirsutum, 19 in G. arboreum, and 16 in G. raimondii). The molecular weights of GH19 proteins ranged from 9.9 to 97.3 kDa, and they were predominantly predicted to localize to the extracellular space. Phylogenetic analysis revealed three well-conserved clades within this family. In tetraploid cotton, GH19 genes were unevenly distributed across 12 chromosomes, often clustering in certain regions, whereas in diploid species, they were confined to five chromosomes. Promoter analysis indicated that GH19 gene promoters contain numerous stress- and hormone-responsive motifs, including those for abscisic acid (ABA), ethylene (ET), and gibberellin (GA), as well as abundant light-responsive elements. The expression patterns of GH19 genes were largely tissue-specific; for instance, GbChi23 was predominantly expressed in the calyx, whereas GbChi19/21/22 were primarily expressed in the roots and stems. Overall, this study provides the first comprehensive genomic and functional characterization of the GH19 family in G. barbadense, laying a foundation for understanding its role in disease resistance mechanisms and aiding in the identification of candidate genes to enhance plant defense against biotic stress. Full article

Cotton is an economically critical crop worldwide, and drought stress strongly affects its growth and development. Ubiquitination modifies protein activity and is crucial in numerous biological processes. Ubiquitin-conjugating enzymes serve as intermediaries in the protein ubiquitination process and play important roles in plant responses to abiotic stress. However, the impact of ubiquitination on the response of cotton to abiotic stress is not fully understood. Bioinformatic methods were employed in this study to analyze the physiochemical characteristics, gene structure, collinearity, expression patterns, and evolutionary relationships of GbUBC gene family members in sea-island cotton. In sea-island cotton, a minimum of 125 GbUBC genes are irregularly distributed across the 26 chromosomes, with multiple instances of gene duplication observed among the members. Phylogenetic analysis categorized the GbUBC gene family into 15 ubiquitin-conjugating enzyme (E2) subgroups, one ubiquitin E2 enzyme variant (UEV) subgroup, and one COP10 subgroup. GbUBC gene expression pattern analyses revealed that most GbUBC genes responded differently to cold, heat, NaCl, and polyethylene glycol (PEG) treatments, with certain GbUBC genes exhibiting high expression levels in specific fiber development period and organs. Furthermore, molecular biology methods were employed to elucidate the biological functions of GbUBC23. The GbUBC23 gene was highly expressed in the cotyledons of sea-island cotton and was activated by PEG treatment. GbUBC23 is localized to the nucleus and cytomembrane. The silencing of the GbUBC23 gene under drought conditions led to decreased drought tolerance and survival rates in sea-island cotton. Compared with those in the control plants, the activity of proline and superoxide dismutase and the expression levels of the drought-induced genes GbNCED3, GbRD22, GbRD26 were significantly lower, but the levels of malondialdehyde and hydrogen peroxide were significantly higher. Our findings revealed 125 members of the GbUBC gene family in sea-island cotton, with the GbUBC23 gene critically contributing to the abiotic stress response. These findings indicate that the GbUBC gene family may play a crucial role in the drought stress response in sea-island cotton. Full article

Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding. Full article

Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root secretions from the highly resistant cultivar Xinhai 41 and sensitive cultivar Xinhai 14 to investigate their interaction with F. ox by a weighted correlation network analysis (WGCNA). As a result, two modules that related to the fungal pathogenicity emerged. Additionally, a total of twenty-five chitinase genes were identified. Finally, host-induced gene silencing (HIGS) of FoChi20 was conducted, and the cotton plants showed noticeably milder disease with a significantly lower disease index than the control. This study illuminated that chitinase genes play crucial roles in the pathogenicity of cotton wilt fungi, and the FoChi20 gene could participate in the pathogenesis of F. ox and host–pathogen interactions, which establishes a theoretical framework for disease control in Sea Island cotton. Full article

Protein palmitoylation, the most common and the only reversible post-translational lipid modification following protein translation, plays a pivotal role in the biochemical and physiological processes of both animals and plants. DHHC proteins, enriched with DHHC (Asp-His-His-Cys) domains, serve as catalyst for protein palmitoylation. However, research on DHHC in cotton remains scarce. This study conducted a systematic characterization and bioinformatics analysis on G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, detecting 38, 37, 74, and 74 DHHC genes, respectively. Phylogenetic analysis categorized the DHHC gene family into six subgroups, consistent with previous evolutionary studies in Arabidopsis and rice. A further examination of protein structure revealed a correlation between genetic relatedness, structural similarity, and functional identity. Cis-element analysis identified elements predominantly associated with light response, stress, growth and development, and plant hormones. The integration of cotton seed development transcriptome, tissue expression pattern analysis, and population transcriptome data collectively suggests that Ghir_A05G027650 and Ghir_D05G027670 are promising candidate genes influencing seed development in upland cotton. Conversely, Gbar_A04G010750 and Gbar_A12G020520 emerge as potential candidates affecting both seed and fiber development in sea island cotton. These findings lay down a theoretical foundation for delving into the functional diversity of DHHC genes in cotton, thereby paving the way for the development of new breeding strategies and the optimization of cotton seed and fiber production, ultimately contributing to improved crop yield and quality. Full article

Sea Island cotton is renowned for its superior fiber quality. Although mechanical harvesting has the potential to significantly increase efficiency and reduce the production cost of Sea Island cotton, there is still little research in this area. In this study, we analyzed 240 Sea Island cotton germplasm resources and evaluated 19 traits related to mechanical harvesting. The coefficient of variation ranged from 5.42% to 66.96%, and the genetic diversity index spanned from 1.57 to 2.07. In most traits studied, there was a strong correlation between the height of the first fruiting branch and the defoliation rate. The 19 traits were categorized into 6 factorial groups by principal component analysis, in which the defoliation factor contributed the most (30.89%). The cluster analysis divided the 240 cotton accessions into four main groups, with the second group exhibiting favorable mechanical harvesting characteristics such as higher defoliation rate and first fruit branch height. Using stepwise regression, a model was constructed with the joint evaluation score F-value as the response variable and eight traits (X₁: PH, X₂: SNB, X₃: SBN, X₄: MBL, X₅: AFBM, X₇: MLIA, X₈: NB, and X₁₃: 15 d DR) as predictors: Y = −7.2 + 0.01X₁ + 0.23X₂ + 0.192X₃ + 0.038X₄ + 0.007X₅ + 0.014X₇ + 0.025X₈ + 2.952X₁₃. Selected materials suitable for machine harvesting, such as MoShi729, were identified. This study provides valuable theoretical insights into the mechanical harvesting of Sea Island cotton germplasm resources and identifies promising materials for targeted breeding and improvement programs. Full article

Cotton is a major source of natural fibre for the global textile industry and is also an important oilseed crop. Cotton fibre is the main source of textiles, the seeds are used for oil and the remaining bagasse is used as high-protein animal feed. In addition, cotton’s so-called short fibre is used in more than 50 industries. Cotton breeding is generally based on crossing the best yielding and fibre quality genotypes. However, cotton breeding programmes are negatively affected by the narrow genetic diversity of varieties. It is for this reason that the identification of genetic resources and the disclosure of genetic diversity are so important. Here, the genetic diversity of G. hirsutum and G. barbadense genotypes was determined using high-resolution capillary gel electrophoresis. Using 19 EST-SSR markers, a total of 47 genotypes were screened. The PIC values of the markers used ranged from 0.268 to 0.889. The mean PIC value was calculated to be 0.603. In terms of clustering, PCoA and population structure analyses gave similar results, and the genotypes could be divided into three main groups. Genetic admixture with G. hirsutum was found in some genotypes of the G. barbadense species. We can conclude that (i) the EST-SSR markers used in this study are effective in the determination of genetic diversity, (ii) the genetic diversity should be increased through the collection of genetic resources and (iii) the genetic EST-SSR markers in this study should be considered in breeding programmes by using them in QTL studies. Full article

The Sea Island cotton Gossypium barbadense has been present in Brazil for at least 750 years. Cultivated worldwide, the fibres present superior quality; therefore, farmers’ seeds are an important genetic resource and in situ maintenance is essential to complement ex situ conservation. To understand how the species has been conserved in situ and investigate the socio-economic aspects which may ensure the continuity of its conservation, we conducted expeditions to three different municipalities situated in Brazilian Cerrado, Goiás state, Brazil—one of which is a traditional community, the quilombo Kalunga community—interviewed plant maintainers and compared our results with data from the Brazilian Institute of Geography and Statistics. There is hand spinning and hand weaving for home uses and commercialization within and outside the traditional community, which contribute to the continuity of the in situ conservation of Gossypium barbadense. Medicinal use is more determinant than hand weaving in deciding to keep plants and seeds. Fabric handicraft is a predominantly female, low-income activity. Interviews with cotton hand spinners indicated that in situ maintenance may be favoured by access to weaving looms and improvement in the marketing and sale of their products. Policies valuing handicrafts can ensure the continuity of biodiversity and disseminate and vivify traditions in addition to maintaining an income for the artisans. Full article

Sea Island cotton is the best quality tetraploid cultivated cotton in the world, in terms of fiber quality. Glyphosate is a widely used herbicide in cotton production, and the improper use of herbicides has led to pollen abortion in sea island cotton and, consequently, to a dramatic decrease in yield; however, the mechanism remains unclear. In this study, different concentrations (0, 3.75, 7.5, 15, and 30 g/L) of glyphosate were applied to CP4-EPSPS transgenic sea island cotton Xinchang 5 in 2021 and 2022 at Korla, with 15 g/L glyphosate chosen as the suitable concentration. By comparing the paraffin sections of 2–24 mm anthers in the 15 g/L glyphosate treatment group with those in the water control group, we showed that the key period of anther abortion after glyphosate treatment was the formation and development of tetrads, which corresponded to 8–9 mm buds. Transcriptome sequencing analysis of the treated and control anthers revealed a significant enrichment of differentially expressed genes in phytohormone-related pathways, in particular abscisic acid response and regulation pathways. Additionally, after treatment with 15 g/L of glyphosate, there was a significant increase in the amount of abscisic acid in the anthers in the 8–9 mm buds. Further analysis of the differential expression of abscisic acid response and regulatory genes, an abscisic acid response gene GbTCP14 (Gbar_A11G003090) was identified, which was significantly upregulated in buds with 15 g/L glyphosate treatment than the control, and it could be a key candidate gene for the subsequent research involving male sterility induced by glyphosate in sea island cotton. Full article

Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations. Full article

Allotetraploid cotton (Gossypium hirsutum and Gossypium barbadense) are cultivated worldwide for its white fiber. For centuries, conventional breeding approaches increase cotton yield at the cost of extensive erosion of natural genetic variability. Sea Island cotton (G. barbadense) is known for its superior fiber quality, but show poor adaptability as compared to Upland cotton. Here, in this study, we use ethylmethanesulfonate (EMS) as a mutagenic agent to induce genome-wide point mutations to improve the current germplasm resources of Sea Island cotton and develop diverse breeding lines with improved adaptability and excellent economic traits. We determined the optimal EMS experimental procedure suitable for construction of cotton mutant library. At M₆ generation, mutant library comprised of lines with distinguished phenotypes of the plant architecture, leaf, flower, boll, and fiber. Genome-wide analysis of SNP distribution and density in yellow leaf mutant reflected the better quality of mutant library. Reduced photosynthetic efficiency and transmission electron microscopy of yellow leaf mutants revealed the effect of induced mutations at physiological and cellular level. Our mutant collection will serve as the valuable resource for basic research on cotton functional genomics, as well as cotton breeding. Full article