This study reveals genetic factors influencing macronutrient content in cottonseeds, identifying key loci and candidate genes for breeding strategies to improve seed nutrition. Macronutrients such as potassium (K), calcium (Ca), and magnesium (Mg) are essential for crop growth, seed quality, and nutrition and health of humans and animals. Insufficient levels of these macronutrients in cottonseeds can lead to malnutrition in animals consuming cottonseed meal-based products. However, the variation and genetic basis of macronutrient content in cottonseeds remain unclear. Here, we investigated the content of K, Ca, and Mg in cottonseeds from 276 cotton accessions grown across diverse ecological regions in China. All three macronutrients exhibited continuous and considerable large variation in the population, with broad-sense heritability values of 70.14

Potassium (K+), an essential macronutrient for plant growth and stress adaptation, becomes physiologically stressful when overaccumulated in soil. While K fertilization enhances cotton (Gossypium hirsutum) fiber quality and yield, the consequential KCl-induced ionic stress has emerged as a critical agricultural challenge demanding molecular-level resolution. This study unveils the previously unexplored epigenetic mechanisms mediated by histone H3 lysine 27 trimethylation (H3K27me3) in cotton's adaptation to KCl stress. Through integrated cleavage under targets and tagmentation (CUT&Tag) chromatin profiling and transcriptome sequencing, we demonstrate that KCl stress triggers genome-wide attenuation of H3K27me3 deposition, concomitant with characteristic stress phenotypes in cotton seedlings. Suppression of H3K27me3 using RDS 3434 significantly ameliorated KCl-induced physiological damage, thereby supporting a functional correlation between this epigenetic mark and stress tolerance. Mechanistic analyses revealed 48 genes exhibiting inverse correlation between H3K27me3 enrichment and transcriptional activation, including 2 that encode pivotal salt-tolerance regulators: Glutathione Synthase1 (GhGSH1) and Salt-Related MYB1 (GhSRM1). Virus-induced gene silencing validation confirmed these H3K27me3-associated genes as essential components of cotton's ionic stress response network. Our findings delineate the epigenetic landscape associated with KCl stress adaptation and highlight H3K27me3-mediated chromatin remodeling as a critical regulatory layer in plant abiotic stress responses. This work provides insights into epigenetic engineering strategies for developing stress-resilient cotton cultivars.

Cotton fiber elongation is a complex developmental process regulated by hormonal and metabolic signals. Auxin (indole-3-acetic acid, IAA) and brassinosteroid (BR) play crucial roles in cotton fiber development, but the mechanism by which they coordinate to regulate fiber elongation remains unclear. In this study, we determined that IAA levels gradually increase during fiber development and are higher in long-fiber varieties. In vitro ovule culture experiments revealed that IAA promotes fiber elongation in a dose-dependent manner. Transcriptome analysis showed that IAA activates BR biosynthesis and the BR signaling pathway, implying crosstalk between the two hormones. Interestingly, IAA could partially rescue fiber elongation caused by BR deficiency due to brassinazole treatment and in pag1 mutants, and BR supplementation partially alleviated fiber inhibition resulting from impaired IAA transport or IAA deficiency. However, neither hormone fully compensated for the absence of the other, indicating that both serve non-redundant roles in fiber elongation. Additionally, inhibiting glucose signaling by suppressing hexokinase activity through N-acetylglucosamine impaired fiber growth, but this could be rescued by exogenous application of either IAA or BR, suggesting that glucose acts upstream of IAA and BR, which cooperatively regulate the elongation of cotton fibers.

SWEET (sugars will eventually be exported transporter) proteins are vital for sugar transport in plants, mediating the movement of glucose, fructose, and sucrose, and playing key roles in growth, development, and stress responses. This study identified 1246 SWEET proteins across 59 plant species, spanning from chlorophytes to eudicots. Phylogenetic analysis revealed that SWEET proteins originated in chlorophytes and diverged into four clades (I-IV). Chlorophyte SWEETs, classified in clade II, lacked transport activity and were localized on the vacuolar membrane. In charophytes, clade I SWEETs acquired the ability to transport glucose and fructose, marking a significant adaptation during the transition to terrestrial plants. In bryophytes, clade II SWEETs transport glucose and fructose, localized on the vacuolar membrane. In vascular plants, clade IV SWEETs, which emerged in lycophytes, exhibited fructose transport activity and localized to the plasma or vacuolar membranes. Clade III SWEETs, exclusive to seed plants, are specialized in sucrose transport, which is crucial for long-distance sugar distribution. Sequence and structural analysis revealed that the highly conserved transmembrane regions form the triple-helix bundle essential for sugar transport. In contrast, the N-terminal and C-terminal regions contribute to substrate specificity and structural folding. Functional assays confirmed that removal of these non-conserved regions abolishes transport activity. In conclusion, this study provides a comprehensive analysis of the evolutionary origins, functional diversification, and structural significance of SWEET proteins, underscoring their pivotal roles in carbohydrate metabolism and plant diversification. These findings offer valuable insights into the molecular mechanisms underlying sugar transport and its evolutionary adaptations in plants.

Histone methylation is pivotal in regulating the expression of numerous essential functional genes in plants. However, its specific function and mechanism in cotton fiber cell initiation remain poorly understood. The upland cotton (Gossypium hirsutum L.) variety Xuzhou142 (Xu142) and its fuzzless-lintless mutant Xu142 fl are ideal model materials for studying cotton fiber cell development. In vitro ovule culture analysis showed that the histone H3 lysine 27 trimethylation (H3K27me3) inhibitor RDS 3434 could inhibit fiber cell initiation and development. Cleavage under targets and tagmentation (CUT&Tag) and RNA sequencing (RNA-seq) data of-1, 0, and 1 day post-anthesis (DPA) ovules showed that H3K27me3 regulates fiber cell initiation by highly accumulating in Xu142 than in Xu142 fl. It was also found that H3K27me3 was negatively correlated with gene transcription, as 227 expressed genes showed an opposite trend to the H3K27me3 modification level and were identified to participate in multiple signaling pathways. Furthermore, the expression levels often potential genes related to fiber development were confirmed to correlate with H3K27me3 levels. The results demonstrate the critical role of H3K27me3 in fiber development process and present evidence supporting its involvement in cotton fiber cell initiation. The study lays the foundation and provides genetic resources for further investigations into genes related to fiber development.

Cottonseed is rich in microelements that are beneficial for human health. However, research on microelement concentrations in cottonseed remains limited. The distributions of manganese (Mn), copper (Cu), and zinc (Zn) concentrations in cottonseeds were analyzed across multiple years and locations using a genetic population of 276 cotton accessions. The results revealed that cottonseed microelement concentrations were primarily influenced by genetic factors. Correlation analysis indicated significant relationships among Mn, Cu, and Zn, although the strengths of these correlations varied across regions and years. In addition, Mn, Cu, and Zn play distinct roles in cotton production; Cu is positively correlated with fiber yield, whereas Zn is predominantly negatively associated with fiber quality traits. A GWAS identified 34 significant SNPs on 15 chromosomes distributed within 22 QTLs that potentially influenced microelement concentrations in cottonseeds. Notably, the SNP locus i14125Gh was found to be associated with both Cu and Zn, and the candidate gene Gh_A12G1265 was screened, suggesting its potential role in co-regulating their concentrations. In addition, the candidate gene Gh_D07G0953 was related to Cu concentration. This study provides valuable SNP information, candidate genes, and new insights to support the development of cotton varieties with enhanced microelement concentrations.

We characterized the WAK gene family in Gossypium barbadense and revealed the potential function of GbWAK5 in regulating salt tolerance by modulating ion homeostasis. Soil salinization is one of the main factors restricting cotton production. Although the role of the wall-associated kinases (WAKs) in plants has been extensively studied, its response to salt stress in sea-island cotton (Gossypium barbadense L.) has not been reported. Here, we conducted a whole-genome analysis of the WAK gene family in G. barbadense, identifying a total of 70 GbWAK genes, which were classified into five clades. Segmental and tandem duplication events have contributed to the expansion of the GbWAK gene family. A large number of cis-acting elements were predicted in the GbWAK promoter region. Through RNA sequencing, 37 GbWAKs that potentially play a role in cotton's response to salt stress were screened out, among which 10 genes with sustained up-regulated expression were confirmed by quantitative real-time PCR (qRT-PCR). GbWAK5, a member of Clade II, was significantly up-regulated following NaCl treatment and exhibited a typical WAK structure. Subcellular localization indicated that GbWAK5 is localized on the plasma membrane. Virus-induced gene silencing (VIGS) experiments revealed that the knockdown of GbWAK5 resulted in more severe dehydration and wilting in plants compared to the control under NaCl treatment. RNA-seq analysis revealed that several ion transport-related genes were down-regulated in TRV:GbWAK5 plants under salt stress, while TRV:GbWAK5 plants accumulated more Na+ and exhibited a higher Na+/K+ ratio compared to TRV:00 plants. These results offer a comprehensive analysis of the G. barbadense WAK gene family for the first time, and conclude that GbWAK5 is a promising gene for improving cotton's resistance to salt stress.

SINA (Seven in absentia) E3 ligases are critical components of the ubiquitin-proteasome system (UPS). They are responsible for ubiquitination and are involved in numerous cellular processes. The functional mechanisms of SINAs have been extensively studied in a few angiosperms. However, our understanding of the origin and evolution of plant SINA genes remain limited. Here we performed a large-scale comprehensive analysis of SINA proteins from various plant lineages. The plant SINA family genes likely originated from a common ancestral gene prior to the divergence of bryophyte and gave rise to two clades. Within clade I, subsequent parallel innovations in lycophytes and ferns resulted in the formation of two branches. All SINA proteins contain an N-terminal cysteine-rich really interesting new gene (RING) domain for ubiquitination, two zinc-finger motifs, and a C-terminal domain required for substrate-binding and dimerization. The SINA genes gains and losses occurred in angiosperms, resulting in an increase in the number of gene copies in eudicots and monocots. The Gossypium genus SINAs showed a tendency for expansion via whole-genome duplication and polyploidy. Finally, global expression patterns revealed the functional diversification of SINA genes in developmental stage and response to hormones and abiotic stresses in Arabidopsis and rice. These findings provide an insight into the evolution and diversification of SINA E3 ligases in plants and enhance our understanding of the role they play in determining substrate specificity and environment stress adaptations in angiosperms.

Protein ubiquitination is essential for plant growth and responses to the environment. The SEVEN IN ABSENTIA (SINA) ubiquitin ligases have been extensively studied in plants, but information on their roles in fiber development is limited. Here, we identified GhSINA1 in Upland cotton (Gossypium hirsutum), which has a conserved RING finger domain and SINA domain. Quantitative real-time PCR (qRT-PCR) analysis showed that GhSINA1 was preferentially expressed during fiber initiation and elongation, especially during initiation in the fuzzless-lintless cotton mutant. Subcellular localization experiments indicated that GhSINA1 localized to the nucleus. In vitro ubiquitination analysis revealed that GhSINA1 has E3 ubiquitin ligase activity. Ectopic overexpression of GhSINA1 in Arabidopsis thaliana reduced the number and length of root hairs and trichomes. Yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), and bimolecular fluorescence complementation (BiFC) assays demonstrated that the GhSINA1 proteins could interact with each other to form homodimers and heterodimers. Overall, these results suggest that GhSINA1 may act as a negative regulator in cotton fiber development through homodimerization and heterodimerization.

Verticillium wilt (VW), Fusarium wilt (FW) and Root-knot nematode (RKN) are the main diseases affecting cotton production. However, many reported quantitative trait loci (QTLs) for cotton resistance have not been used for agricultural practices because of inconsistencies in the cotton genetic background. The integration of existing cotton genetic resources can facilitate the dis-covery of important genomic regions and candidate genes involved in disease resistance. Here, an improved and comprehensive meta-QTL analysis was conducted on 487 disease resistant QTLs from 31 studies in the last two decades. A consensus linkage map with genetic overall length of 3006.59 cM containing 8650 markers was constructed. A total of 28 Meta-QTLs (MQTLs) were discovered, among which nine MQTLs were identified as related to resistance to multiple diseases. Candidate genes were predicted based on public transcriptome data and enriched in pathways related to disease resistance. This study used a method based on the integration of Meta-QTL, known genes and transcriptomics to reveal major genomic regions and putative candidate genes for resistance to multiple diseases, providing a new basis for marker-assisted selection of high disease resistance in cotton breeding.

Salinity is a major abiotic stress that restricts cotton growth and affects fiber yield and quality. Although studies on salt tolerance have achieved great progress in cotton since the completion of cotton genome sequencing, knowledge about how cotton copes with salt stress is still scant. S-adenosylmethionine (SAM) plays important roles in many organelles with the help of the SAM transporter, and it is also a synthetic precursor for substances such as ethylene (ET), polyamines (PAs), betaine, and lignin, which often accumulate in plants in response to stresses. This review focused on the biosynthesis and signal transduction pathways of ET and PAs. The current progress of ET and PAs in regulating plant growth and development under salt stress has been summarized. Moreover, we verified the function of a cotton SAM transporter and suggested that it can regulate salt stress response in cotton. At last, an improved regulatory pathway of ET and PAs under salt stress in cotton is proposed for the breeding of salt-tolerant varieties.

Key message The study of the origin, evolution, and diversification of the wall-associated kinase gene family in plants facilitates their functional investigations in the future. Abstract Wall-associated kinases (WAKs) make up one subfamily of receptor-like kinases (RLKs), and function directly in plant cell elongation and responses to biotic and abiotic stresses. The biological functions of WAKs have been extensively characterized in angiosperms; however, the origin and evolutionary history of the WAK family in green plants remain unclear. Here, we performed a comprehensive analysis of the WAK family to reveal its origin, evolution, and diversification in green plants. In total, 1061 WAK genes were identified in 37 species from unicellular algae to multicellular plants, and the results showed that WAK genes probably originated before bryophyte differentiation and were widely distributed in land plants, especially angiosperms. The phylogeny indicated that the land plant WAKs gave rise to five clades and underwent lineage-specific expansion after species differentiation. Cis -acting elements and expression patterns analyses of WAK genes in Arabidopsis and rice demonstrated the functional diversity of WAK genes in these two species. Many gene gains and losses have occurred in angiosperms, leading to an increase in the number of gene copies. The evolutionary trajectory of the WAK family during polyploidization was uncovered using Gossypium species. Our results provide insights into the evolution of WAK genes in green plants, facilitating their functional investigations in the future.

In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.

The wall-associated kinases (WAKs) and WAK-like kinases (WAKLs) form a group of receptor-like kinases (RLKs) with extracellular domains tightly linked to the cell wall. The WAKs/WAKLs have been known to be involved in plant growth, development, and stress responses. However, the functions of WAKs/WAKLs are less well known in cotton. In this study, 58, 66, and 99 WAK/WAKL genes were identified in Gossypium arboreum, G. raimondii, and G. hirsutum, respectively. Phylogenetic analysis showed they were classified into five groups, with two groups specific to cotton. Collinearity analysis revealed that segmental and tandem duplications resulted in expansion of the WAK/WAKL gene family in cotton. Moreover, the Ka/Ks ratios indicated this family was exposed to purifying selection pressure during evolution. The structures of the GhWAK/WAKL genes and encoded proteins suggested the functions of WAKs/WAKLs in cotton were conserved. Transient expression of four WAK/WAKL-GFP fusion constructs in Arabidopsis protoplasts indicated that they were localized on the plasma membrane. The cis-elements in the GhWAK/WAKL promoters were responsive to multiple phytohormones and abiotic stresses. Expression profiling showed that GhWAK/WAKL genes were induced by various abiotic stresses. This study provides insights into the evolution of WAK/WAKL genes and presents fundamental information for further analysis in cotton.

以6个陆地棉品种(系)为亲本,采用NCⅡ交配设计配制9个杂交组合,对杂交组合F1、F2的表型性状、产量性状以及纤维品质性状进行比较分析.结果表明:大部分组合F1和F2在单株果枝数和单株结铃数存在一定竞争优势,F2铃重和衣分存在竞争衰退现象,导致F2皮棉产量较F1明显降低.但有些强优势组合的杂种优势在F2中仍能很好延续,其中组合5的F2籽棉和皮棉产量较F1提高,说明组合5的F2在产量方面具有一定杂种优势,可以利用其F2的杂种优势.

Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.

>Dear Editor,Sources of genetic variations in genomes include small-scale sources (such as single-nucleotide polymorphisms (SNPs),insertions/deletions (InDels), and simple sequence repeats and larger-scale structural variations (mainly presence-absence variants (PAVs)) and copy number variants). PAVs are sequences that are either inserted or missing in genomes in comparison with a reference sequence or genome. PAVs can

Background Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. To better understand the genetic mechanisms responsible for fiber quality traits, we conducted a genome-wide association study to identify and mine fiber-quality-related quantitative trait loci (QTLs) and genes. Results In total, 42 single nucleotide polymorphisms (SNPs) and 31 QTLs were identified as being significantly associated with five fiber quality traits. Twenty-five QTLs were identified in previous studies, and six novel QTLs were firstly identified in this study. In the QTL regions, 822 genes were identified and divided into four clusters based on their expression profiles. We also identified two pleiotropic SNPs. The SNP locus i52359Gb was associated with fiber elongation, strength, length and uniformity, while i11316Gh was associated with fiber strength and length. Moreover, these two SNPs were nonsynonymous and located in genes Gh_D09G2376 and Gh_D06G1908 , respectively. RT-qPCR analysis revealed that these two genes were preferentially expressed at one or more stages of cotton fiber development, which was consistent with the RNA-seq data. Thus, Gh_D09G2376 and Gh_D06G1908 may be involved in fiber developmental processes. Conclusions The findings of this study provide insights into the genetic bases of fiber quality traits, and the identified QTLs or genes may be applicable in cotton breeding to improve fiber quality.

机采棉品种中棉所99001于2019年5月通过湖南省农作物品种审定.本文介绍了中棉所99001的特征特性、产量表现、纤维品质、抗性和栽培技术要点等.

Additional file 1: Table S1. Analysis of variance (ANOVA) of the cotton fiber quality traits. Table S2. Significant SNPs detected for cotton fiber quality traits by a GWAS. Table S3. Comparisons of the QTLs identified in this study with those identified in previous studies. Table S4. Annotation information of these genes in the QTL regions. Table S5. Primer sequences for RT-qPCR in this study.