Improving lint percentage (LP) is a key breeding target for Sea Island cotton (Gossypium barbadense), yet its genetic basis remains poorly understood. Here, we identify GbNAC072C as a positive regulator of LP that promotes fiber cell protrusions by directly activating the transcription of GbHOX3. We find that GbNAC072C is inhibited by GbDEAH12G, and crucially, the strength of this interaction is haplotype-dependent. The GbDEAH12G protein binds GbNAC072C with higher affinity than the GbDEAH12C variant, leading to stronger suppression of GbHOX3 activation and consequently lower LP. This explains why the GbDEAH12C-GbNAC072C allele combination gives improved LP. Our work elucidates how haplotype-specific protein interactions modulate a key transcriptional cascade and proposes a disinhibition strategy for breaking yield limits in Sea Island cotton breeding.

Fiber cell initiation and development affect cotton fiber yield and quality. Cotton fiber develops from the ovular epidermis of a seed, and approximately 25% to 30% of protodermal cells in each cotton ovule develop into fiber. However, the molecular basis for fiber cell development remains elusive. Here, we analyzed single-cell RNA-seq (scRNA-seq) data from over 40,000 cells during early stages of fiber cell development in Upland and Pima cotton and in a naked seed mutant. We found concerted expression changes of 900 to 1,700 genes in fiber-cell clusters involving gene expression, translation, and peptide biosynthesis, which were substantially delayed or absent in the mutant. Expression of ∼500 and ∼300 genes in Upland and Pima cotton, respectively, was distinguishably different and consistent with overrepresentation of the genes in transcriptional and translational regulation, implying their roles in fiber yield and quality traits. Gene coexpression network analysis of scRNA-seq along with scATAC-seq data revealed two modules of fiber gene coexpression networks. One module of the fiber coexpressed genes was associated with elevated chromatin accessibility for transcriptional regulation, whereas the other module of the genes was related to translational regulation and ribosome biogenesis. Indeed, expression of cotton putative translation factor genes was elevated in fiber cell clusters in both Upland and Pima cotton. Finally, cotton transgenic plants expressing promoter::GFP confirmed expression patterns of fiber-expressed GhRDL2_D5 during fiber cell initiation. These single-cell genomic resources provide insights into fiber cell development for breeding and biotechnological improvement of fiber yield and quality in Upland and Pima cotton.

High temperatures can hinder stand establishment, seedling growth, and photosynthetic processes in cotton. Yet, interpretations of thermotolerance in thylakoid processes often depend on whether measurements follow chronic or acute heat exposure, and species-level differences in these responses remain poorly characterized. This study evaluated the effects of chronic high temperatures (40°C/30°C) on key thylakoid processes in four-week-old Upland and Pima cotton seedlings and assessed their acclimation potential using rapid induction chlorophyll fluorescence across a range of incubation temperatures. As these processes were inferred from OJIP parameters rather than direct measurements of photosystem activity, they are interpreted as fluorescence-based indicators of thylakoid function. Chronic heat enhanced photosystem I (PSI)-related parameters in both species, with Upland exhibiting larger increases (44%-46%) compared to Pima (39%-40%), whereas photosystem II (PSII) photochemistry remained largely stable under chronic heat, declining by less than 2% at 40°C and by 6%-8% at 45°C under acute exposure. Acute temperature responses closely mirrored chronic patterns, and Upland showed higher thermal optima for PSI quantum yield and overall performance (40°C) than Pima (35°C), suggesting greater PSI electron-sink capacity. Collectively, these fluorescence-derived results suggest that PSI-related processes distinguish species-level thermotolerance in cotton. Upland's stronger enhancement of PSI acceptor-side capacity under both sustained and transient heat exposure points to a more robust acclimation strategy, whereas Pima shows limited PSI adjustment despite maintaining PSII efficiency. These findings clarify how thylakoid processes respond to heat across timescales and may help guide the development of heat-resilient cotton as growing-season temperatures rise.

The soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum race 4 (FOV4) poses a risk to U.S. cotton (Gossypium spp.) following detection in California, Texas, and New Mexico. This study evaluated the influence of cotton cultivar resistance on relative variation in soil FOV4 DNA quantity, a proxy for inoculum density, in a naturally infested field over two years. Field trials included Upland (G. hirsutum) and Pima (G. barbadense) cotton cultivars and measured plant mortality, root necrosis, and lint yield. Bulk soil FOV4 DNA was quantified by qPCR at three timepoints each year: planting, midseason (first flower), and late season (crop maturity). Susceptible Pima cultivars exhibited the highest mortality, most severe necrosis, and lowest yields, whereas resistant Pima and Upland cultivars had lower necrosis with variable mortality and yield. Commercial Upland cultivars with differing degrees of susceptibility showed intermediate mortality and necrosis yet high yields. Midseason soil FOV4 DNA levels varied among cultivars in both years (p=0.011, 0.028), with elevated levels in a subset of susceptible cultivars. Late season DNA levels varied among cultivars in 2021 (p=0.017) but not in 2020 (p=0.080) and did not correspond to resistance designations. Within cultivars, mortality correlated with FOV4 DNA levels at planting (p<0.001, McFadden's pseudo-R2 [R2MF]=0.810) and late season (p<0.001, R2MF=0.802), necrosis with late season DNA levels (p<0.001, R2=0.849), and yield showed no correlation with FOV4 DNA at any timepoint. These findings relate host response to DNA-based soil pathogen quantification and emphasize resistance variation as a determinant of FOV4 disease ecology and management success.

The textile dyeing sector contributes significantly to excessive water and energy use and environmental pollution. Managing yarn tension during the rewinding process is a crucial challenge in textile dyeing, as it has a direct impact on yarn quality, resource consumption, and overall efficiency. Traditional tension control techniques ignore how tension variation affects the production of wastewater and the need for chemical treatment. Using a digital signal processor (TMS320F28335), this study introduces a novel event-driven yarn tension control method for soft winding machines that maintains ideal, constant tension across fine, medium, and thick cotton yarn counts. The suggested method dramatically reduces tension variance, as demonstrated by experimental validation conducted at a leading Egyptian cotton yarn producer. This decreases yarn defects by 35% and allows for a 27% increase in machine speed without sacrificing yarn quality. Most significantly, liquor ratio data show that optimized tension management reduces water consumption during dyeing by 65–70%, thereby lowering chemical use and wastewater generation. Additionally, energy use dropped by almost 20%, improving process sustainability. This integrated strategy promotes the triple bottom line of social, economic, and environmental advantages and is consistent with cleaner manufacturing principles. The results provide a scalable methodology for environmentally friendly textile production, especially appropriate for developing nations with limited resources.

Sea Island cotton (Gossypium barbadense) produces premium-quality fibres, yet the genetic basis underlying its fibre development remains elusive. Here, we identify two key non-synonymous single nucleotide polymorphisms (SNPs, G/C and G/A) in the gene Gbar_D13G024080, which encodes the TRANSMEMBRANE PROTEIN 209 (TMEM209). These SNPs resulted in amino acid changes (V/L and R/K), and are significantly correlated with the fibre length in Sea Island cotton. CRISPR-Cas9-mediated knockout of GbTMEM209 significantly enhanced fibre length and fibre strength in both G. hirsutum and G. barbadense. Conversely, overexpression of GbTMEM209 in G. hirsutum led to reduced fibre length. Further mechanistic investigation revealed that GbTMEM209 competitively interacts with GbHOX3 to impair its transcriptional activation on cell wall-loosening genes GbEXPA1 and GbRDL1. Moreover, during the elongation stage of the fibres, GbTMEM209 and GbHOX3 exhibit an antagonistic relationship, which jointly regulate the development of cotton fibres. Virus-induced gene silencing (VIGS) of GbHOX3, GbEXPA1, or GbRDL1 consistently resulted in shortened fibres in Sea Island cotton, validating their critical roles in fibre development. Our findings establish GbTMEM209 as a novel negative regulator of fibre elongation and uncover a protein competition-mediated transcriptional control mechanism in cotton fibre morphogenesis. These findings provide valuable genetic targets and conceptual insights for molecular breeding programs aimed at improving cotton fibre quality.

The high fiber strength (FS) of a Upland cotton cultivar bred by interspecific cross was found to be associated with a D11 QTL and the identification of a candidate gene, and a genetic variant provides a potential tool for molecular breeding of high FS cotton cultivars. Fiber strength (FS) is one of the critical determinants of cotton fiber quality. Despite many quantitative trait loci (QTLs) associated with FS have been documented, many more are yet to be uncovered. In this study, an F2 population was constructed by crossing Huiyuan720 (Gossypium hirsutum) with Shida26-22, a high FS G. hirsutum cultivar bred by introgressing the high FS trait of G. barbadense cultivar Xinhai53 into Huiyuan720 via multiple backcrosses. Bulked segregant analysis sequencing of the F2 population identified six FS QTLs, including a major locus on chromosome D11 spanning 3.38Mb containing 121 annotated genes. By integrating transcriptome sequencing of developing fibers, analyzing gene co-expression network, and profiling genetic variants of annotated genes, GH_D11G2131, annotated to encode an armadillo repeat/tetratricopeptide repeat-like protein, was identified as a strong candidate gene potentially regulating FS. GH_D11G2131 harbored a non‑synonymous mutation and a promoter indel between the two parents, belonged to a co‑expression gene module highly correlated with cell wall development, and was significantly highly expressed in 20days post‑anthesis fibers of high FS cultivars. Virus-induced gene silencing demonstrated that knockdown of GH_D11G2131 resulted in thinner secondary cell walls and a significant reduction in lignin content, thanks to the marked downregulation of genes related to lignin biosynthesis. Collectively, this study uncovered a major FS QTL and a strong candidate gene associated with SCW development, providing a potential molecular tool for breeding elite cotton cultivars with high fiber quality.

Biofortification Approach for Enhancing Growth of Egyptian Cotton via Foliar Application of Zinc and Boron

Among cotton species, Gossypium barbadense produces the strongest fibers. Examining cytoskeletal dynamics in single epidermal cells of G. barbadense ovules offers a direct approach to investigating fiber quality. Microtubules are major cytoskeletal components whose organization and dynamics are precisely regulated by microtubule-associated proteins (MAPs). However, information on the TPX2 family remains limited, and characterizing its features in G. barbadense is critical to clarifying the role of TPX2 family members in fiber strength formation. Using the Arabidopsis thaliana TPX2 sequence as a reference, 40, 49, 26, and 26 TPX2 family members were identified in the genomes of G. barbadense, Gossypium hirsutum, Gossypium arboreum, and Gossypium raimondii, respectively. We further analyzed the expression pattern of GbTPX2-35 and validated its function via virus-induced gene silencing (VIGS). In G. barbadense, GbTPX2-35 (Gbar_D11G59825.1) was significantly upregulated in fiber samples of the parental lines at 25 days post-anthesis, and this expression pattern was further validated in G. barbadense lines with extreme fiber strength phenotypes. Next, VIGS-mediated silencing of GbTPX2-35 downregulated the transcript levels of cellulose synthase and microtubule-related protein genes, a finding further validated by mature fiber strength phenotypic data. This study preliminarily validated a pathway in which GbTPX2-35 regulates fiber strength by coordinating cellulose biosynthesis with microtubule cytoskeleton dynamics, providing valuable candidate genes and theoretical support for molecular breeding of high-strength cotton fibers.

To investigate the correlation of cell-surface and intracellular immune receptor genes, 29 cotton tribe species that include 28 Gossypium species and Gossypium sister genus Gossypioides kirkii were selected to identify the PRR (LRR-RLK and LysM-RLK) and NLR (NB-ARC) protein gene families. In total, we identified 10,654 LRR-RLKs, 374 LysM-RLKs, and 9,524 NB-ARCs from 29 cotton tribe species. Compared to A. thaliana, almost all the cotton tribe species showed a slight expansion of the LysM-RLK family, but Gossypium D group species had a significant expansion of the LRR-RLK family. Among them, the LRR-RLK-I subfamily showed dramatic contraction, while two LRR-RLK (XI-1 and XII) subfamilies exhibited significant expansion in Gossypieae species. In addition, %LRR-RLKs showed a strong positive linear correlation (Pearson’s r = 0.8363), but %LysM-RLKs showed no correlation with %NB-ARC (Pearson’s r = -0.1837). Two subfamilies, LRR-RLK-VIII_2 and LRR-RLK-XII, formed the two most positive correlations with %NB-ARCs (Pearson’s r = 0.8156 and 0.7485), indicating that LRR-RLK-VIII_2 and LRR-RLK-XII gene families co-expand or co-contract with NB-ARC gene families in Gossypieae species. In addition, members of LRR-RLK-VIII_2, LRR-RLK-XII, LysM-RLK and NB-ARC family genes showed high expression levels in the leaves or roots of Upland cotton and Sea Island cotton based on the transcriptome data. The low correlations of the expression levels between root and leaf in LRR-RLK-VIII_2 and LRR-RLK-XII family genes indicated that LRR-RLK genes may be involved in the local immune response process in cotton. On the contrary, the high correlations of expression levels between root and leaf tissues in LysM-RLK and NB-ARC family genes suggested they might be involved in global immune response. Our results provided new insights into correlation and expression pattern analyses and narrowed the range of immune receptor genes that may be involved in pathogen recognition in cotton plants.

Estimation of Heterosis and Combining Ability Using Diallel Analysis for Quantitative Traits in Egyp-tian Cotton (Gossypium barbadense L.)

The WRKY transcription factor is a key regulatory protein involved in defence hormone signalling and plays a pivotal role in plant hormone-mediated disease resistance. However, the specific mechanism by which WRKY transcription factors regulate the jasmonic acid (JA) pathway to confer resistance against Verticillium wilt in cotton remains poorly understood. In this study, we demonstrated that GbWRKY11 expression in Gossypium barbadense was induced by both Verticillium dahliae and methyl jasmonate (MeJA), and its encoded protein functioned as a nuclear transcription activator. Functional analyses revealed that GbWRKY11 enhances Verticillium wilt resistance by modulating JA pathway-related gene expression in both cotton and Arabidopsis. Exogenous MeJA application restored resistance in GbWRKY11-silenced plants, further supporting its role in JA-mediated immunity. Mechanistically, GbWRKY11 directly binds to the W-box motif in the promoter of GbLOX5, a key JA biosynthesis gene, and activates its transcription. Silencing GbLOX5 compromised cotton resistance to Verticillium wilt, confirming the importance of JA synthesis in this defence response. Our findings elucidate the molecular mechanism by which GbWRKY11 mediates immune responses against Verticillium wilt, providing novel insights into the genetic resources associated with disease resistance in G. barbadense.

Genome-wide identification of the ProteinArginineMethyltransferase (PRMT) gene family and functional exploration of GhPRMT5 in cotton.

The allocation of carbon sources between cotton ovule and fibre significantly influences the yield and quality of seed and fibre. SWEET15 (Sugars Will Eventually be Exported Transporter 15) plays a key role in sucrose transport; however, the transcriptional regulation of SWEET15 in cotton remains unclear. Here, a SWEET15_A01, predominantly expressed during late ovule development (25-35 DPA), functions as a sucrose transporter between the ovule and fibre in cotton. Promoter variations between sea-island and upland cottons correlate with differential expression and cottonseed oil content. Overexpressing SWEET15_A01 in upland cotton reduces fibre length, seed size and oil content but increases lint percentage. Downregulation of SWEET15_A01 in upland cotton ovules upregulates other sugar transporters and cellulose synthase genes (CesAs) in fibres, indicating compensatory mechanisms. The R2R3-MYB transcription factor MYB44 directly binds to the SWEET15_A01 promoter, suppressing its expression, while bHLH3 interacts with MYB44 to weaken this repression. Overexpressing MYB44 increases fibre length but reduces seed size and oil content. This study reveals genetic variations for cottonseed oil improvement and elucidates how the MYB44/bHLH3-SWEET15_A01 module coordinates sugar allocation to balance seed and fibre development, offering strategies for enhancing cottonseed oil content.

Among the two allopolyploid cultivated species of cotton, Gossypium barbadense is known for its superior quality fiber compared to Gossypium hirsutum. Length and strength are key determinants of the fiber quality. Although mature fibers are composed of dried cell walls that mainly consist of cellulose, the dynamic remodeling of pectin, xyloglucan, and xylan polysaccharides during fiber growth significantly impacts the final fiber quality. Comprehensive knowledge of polysaccharides and their biosynthesis during fiber development in cultivated species is crucial for improving fiber quality. In this study, comparative large-scale glycome, transcriptome and proteome profiling were conducted daily on fibers of both cotton species, covering critical stages of fiber development spanning primary cell wall synthesis and the transition to secondary cell wall synthesis. Interspecific comparisons revealed that a delayed deposition of cellulose content, as well as the occurrence of lower levels and differential compositions of non-fucosylated/fucosylated xyloglucans, homogalacturonans, and highly branched rhamnogalacturonan-I polysaccharides, possibly contribute to longer elongation time and longer fiber phenotypes of G. barbadense relative to G. hirsutum. Our study also suggests that differential temporal compositions of arabinoxylans and glucuronoxylans might contribute to the variation in cellulose microfibril arrangement and the strength of fiber that exists between the two species of cotton. Comparative transcriptomic analysis identified differentially accumulated polysaccharide-synthesizing glycosyltransferases that may underlie differences in fiber quality between the two species. Transcripts encoding many cell wall-localized expansins were found to be more abundant in G. barbadense than in G. hirsutum, which could be a contributing factor for the longer fibers of G. barbadense. Overall, these findings expand our understanding of the molecular factors that contribute to fiber quality and provide insights for targeted cotton fiber improvement.

Cotton seeds oils have their potential biological activity and specific physicochemical properties, due to which they are playing vital role in human nutritional diet for health benefits. The aim of this study was to compare secondary metabolites, physicochemical properties and fatty acids composition of seeds oil extracts of Gossypium hirsutum L. and Gossypium barbadense L. Cotton seeds used in this study were obtained from the Agricultural Research and Technology Corporation (ARTC), Wad Medani, Sudan. Seed oils methanolic extracts of Gossypium hirsutum and Gossypium barbadense were screened for their accumulated secondary compounds. Results indicated that G. hirsutum seed oil has more alkaloid than G. barbadense, whereas no variation in the amount of saponins, tannins, phenolic compounds, flavonoids and steroids &amp; terpenoids in two mentioned species. Physicochemical properties analyses were carried out using standard analytical methods. Results of physical properties showed that the specific gravity and refractive index@25C0 were 6.73 and 1.470 for G. hirsutum compared to 6.87 and 1.475 for G. barbadense respectively. Density (g/c3) of seed oils in order were 0.935 and 0.939 whereas pH was 6.76 and 5.76. The chemical properties of oils of two studied species recorded acid values (mg KOH/ g), % of free fatty acids, peroxide values (meq/Kg fat), saponification value (mg KOH/g) and iodine value (I/g oil) were in order 7.1and 20.3; 3.3and 10.3; 0.00 and 0.00; 188.0 and 195.0; 113.6 and 110.4 for G. hirsutum and G. barbadense respectively. Fatty acids composition of seed oils of two species were revealed using the gas chromatography-mass spectrometry (GC-MS) technique. The dominant unsaturated fatty acids of G. hirsutum seed oils were oleic acid 13.11% and linoleic acid 44.25%, while the saturated fatty acids were palmitic acid 29.16 %, methyl stearate acid (stearic acid) 5.06%, methyl tetradecanoate (methyl myristate) 1.48% and arachidic acid 0.67%. Comparatively, the unsaturated fatty acids of G. barbadense were oleic acid 22.63 % and linoleic acid 9.65 %, whereas the saturated fatty acids were palmitic acid 40.12%, methyl stearate (stearic acid) 7.18%, methyl tetradecanote (methyl myristate) 1,71% and arachidic acid 1.51%. In conclusion, the study revealed that oils extracted from G. hirsutum and G. barbadense, grown in Sudan contain the main saturated and unsaturated fatty acids. Physicochemical properties showed standard values in most parameters especially for G. hirsutum. Secondary metabolites obtained indicated the presence of biological activities in the oils of these species.

Verticillium wilt (VW), caused by the soil-borne fungusVerticillium dahliae, stands as one of the most destructive diseases affecting cotton production world-wide. Developing and deploying VW-resistant cotton varieties represents the most effective and sustainable strategy for mitigating the impact of VW. However, breeding VW-resistant upland cotton (Gossypium hirsutum, Gh) varieties is constrained by the limited VW resistance in Gh. One strategy for improving VW resistance of Gh varieties is to introgress resistance alleles from sea-island cotton (Gossypium barbadense, Gb). Interspecific chromosome segment substitution lines (CSSLs) developed based on Gh x Gb offer materials not only for breeding VW-resistant Gh varieties but also for mapping and cloning VW resistance genes. In this study, we used 318 CSSLs derived from Emian-22 (Gh) × 3-79 (Gb) for mapping of VW-resistant QTLs based on phenotypic data collected from 3years of field disease-nursery based experiments and 1.3 million single nucleotide polymorphisms identified among the CSSLs. A genome-wide association study revealed 77 VW resistance QTLs, with only 12 of them overlapping with known VW resistance loci, suggesting that the CSSL population is a valuable resource for mining novel VW-resistant alleles. In the two VW-resistant QTLs on chromosomes A01 and D12, nonsynonymous mutations were found in several annotated genes related to biotic stress responses. Ghi_D12G018010 (GhHIR1) in the D12 locus was shown to positively contribute to VW resistance, as down-regulating the gene by virus-induced gene silencing led to reduction of VW resistance. The findings of this study provide candidate genes and markers for improving cotton VW resistance through molecular breeding.

Aim: The present study was conducted to analyse the adoption behavior of ELS cotton cultivation practices and to identify the factors influencing the adoption behavior of ELS cotton cultivation among the farmers. Place and Duration of Study: The study was conducted during 2022 in Chamarajanagar district of Karnataka, one of the important regions cultivating Extra Long Staple (ELS) cotton. Methodology: A total of 200 respondents were selected for the study using the Simple Random Sampling technique to ensure adequate representation of the farming population. To assess adoption behaviour, eleven key recommended practices related to ELS cotton cultivation were selected. Each respondent was presented with these practices individually and asked to indicate their level of adoption. Results: High adoption was observed in land preparation (summer ploughing and harrowing), seed rate and depth management, hand weeding, crop rotation, and chemical control based on ETL. Harvesting related practices such as frequent picking, selecting well burst bolls, and shade drying were also widely followed. Many recommended practices were adopted by ELS cotton farmers, though several were implemented with practical modifications to suit field realities, labour constraints, and resource availability. Key adjustments were observed in spacing, organic manure use, NPK top dressing, refuge crop planting, ridges &amp; furrow planting, and morning harvesting. In contrast, practices that required higher technical skill, greater cost, or specialized knowledge showed poor adoption. These included micronutrient and foliar nutrition, growth regulators, terminal growth arresting, seed treatment, trap cropping, bio-control agents, pheromone traps, and irrigation at critical stages. Conclusion: Overall, practices that were simple, low cost and clearly linked to immediate price benefits had high adoption, whereas those requiring additional labour, time, infrastructure, or specialized knowledge had lower adoption among farmers.

Pima cotton (Gossypium barbadense) producing superior quality fibers used for premium fabrics and a source of valuable genetic diversity to improve Upland cotton (G. hirsutum). However, current Pima cultivars lack premium quality traits and have a narrow genetic base. Germplasm and genomic resources for population-scale genetic studies and targeted breeding in Pima cotton are limited in the US. Additionally, photoperiod sensitivity is a barrier to introgress beneficial alleles from the tropical G. barbadense germplasm into US cotton. A 473-member diversity panel, comprising photoperiod-insensitive and sensitive accessions from over 50 countries, was assembled to assess genetic and phenotypic diversity and genomic analyses of photoperiod response in Pima cotton. Population genetic analyses of the panel using array-based SNP markers showed genetic diversity was low, as indicated by Nei's genetic distance of 0.156 and identity by state of 0.759. A core set of 41 accessions captured 99% of total allelic diversity, with smaller core sets developed for each photoperiod group. Population structure analysis revealed six subpopulations, including Peruvian germplasm, diversified Peruvian lines, Sea-Island types, American Pima cultivars, Egyptian accessions, and accessions from Russia/former Soviet Union. Phenotypically, photoperiod-insensitive accessions showed broad variability in fiber length (22.85-41.40mm), strength (28.12-56.01g tex⁻¹), and elongation (5.70-10.29%). Sea-Island types had longer fibers, while American Pima lines had stronger fibers. Genome-wide association studies of photoperiod response under long-day conditions identified a major genomic region on chromosome D06, along with novel marker-trait associations on A10 and D10. Targeted genomic analysis revealed candidate genes for photoperiod sensitivity, including VOZ1 at the Gb_Ppd locus on D06. The diversity panel of Pima cotton assembled in the current study showed excellent phenotypic variation in fiber quality and morphological traits and could be used for population scale genetic studies. The identified structured sub-populations offer valuable parental lines for targeted cotton genetic improvement and core sets enable rapid trait discovery and breeding in cotton. GWAS uncovered three key genomic regions controlling photoperiod response, highlighting distinct genetic mechanisms for flowering time in Upland vs. Pima cotton. The VOZ1 at the Gb_Ppd locus on chromosome D06 was confirmed as a candidate gene for photoperiod sensitivity in tropical G. barbadense landraces laying the foundation for dissecting the molecular genetic architecture of flowering time in cotton.

Semigamy is a rare fertilization anomaly in plants that enables haploid induction (HI), a valuable strategy for accelerating crop breeding; however, its molecular basis remains largely unexplored. We investigated transcriptional and epigenetic mechanisms underlying semigamy mutant VSg in island cotton (Gossypium barbadense), which exhibits a high haploid induction rate during double fertilization. We combined cytological observations with time-resolved transcriptome profiling and whole-genome bisulfite sequencing across key fertilization stages. This integrative approach captured dynamic molecular changes associated with gamete nuclear fusion and early zygotic development. Compared with the wild-type, which displayed rapid polar nuclei fusion and normal free nuclear endosperm formation, the semigamy mutant showed delayed polar nuclei fusion and impaired sperm-egg nuclear fusion. Transcriptomic analyses identified differentially expressed genes enriched in membrane fusion processes, while epigenomic profiling revealed dynamic DNA methylation changes in genes encoding transmembrane proteins, cyclins, and kinesins, suggesting disrupted regulation of membrane dynamics and cell cycle progression. These results indicate that coordinated transcriptional and epigenetic regulation of nuclear fusion and cell cycle pathways underlie semigamy-induced developmental arrest and haploid induction. The study provides mechanistic insights into fertilization biology and highlights semigamy as a promising system for improving haploid breeding strategies in crops.