[Objective] A disease that damages cotton fiber has been found in the Xinjiang cotton fields in recent years. The infected cotton fiber turned into mouse-gray and failed to fluff as the boll opens, losing all commercial value. The purpose of this study was to identify the pathogen causing lint rot in Xinjiang cotton fields, and to explore the relationship between mite and disease transmission. [Methods] A total of 161 diseased boll samples were collected from 25 cotton-growing units across northern and southern Xinjiang in 2021 and 2023. The strains were isolated and purified using the tissue isolation method. The pathogen was identified based on morphological characteristics, molecular biological analysis, and pathogenicity test. Different tissues and organs of cotton plants were artificially inoculated in the field to determine the infection sites of the pathogen. The correlation between cotton boll rot and mite was investigated by examining the occurrence frequency of the mite in diseased bolls in cotton field, and combining with the experiment of artificially inoculating healthy detached cotton bolls with mites carrying conidia. [Results] The cotton Nigrospora lint rot is widespread in Xinjiang cotton fields, and the damage is gradually worsening. A total of 146 Nigrospora strains were isolated from diseased samples collected from cotton fields in Xinjiang. The morphological characteristics of the strains were consistent with N. gorlenkoana. The DNA sequences of the internal transcribed spacer in eukaryotic ribose rDNA-ITS, translation elongation factor TEF1-α, and β-tubulin TUB2 in 27 representative strains exhibited high homology with N. gorlenkoana. Field and laboratory pathogenicity tests of 5 representative strains showed that the lint displayed extensive black-gray rot. Therefore, the pathogen causing cotton Nigrospora lint rot in Xinjiang was identified as N. gorlenkoana. The pathogen exclusively infected cotton fiber and did not affect seed, leaf, stem, bud, and flower of cotton. Siteroptes reniformis was closely associated with cotton Nigrospora lint rot. Adult mites or their physogastric females were found in all the diseased bolls, and they can carry the conidia of N. gorlenkoana into the bolls to spread the disease. [Conclusion] The cotton lint rot caused by N. gorlenkoana in Xinjiang in recent years is a disease specifically targeting cotton fiber, with S. reniformis as the primary transmission vector.

[Objective] This study aimed to investigate the role of sucrose in cotton resistance against Verticillium wilt and verify the function of GhSWEET55, providing a theoretical basis for revealing the molecular mechanism of cotton resistance to Verticillium wilt. [Methods] Cotton were inoculated with Verticillium dahliae using the root-wounding method. Sucrose content in cotton roots was determined by spectrophotometry. Differentially expressed genes were obtained by transcriptome sequencing. The enrichment of differentially expressed genes was studied by KEGG pathway analysis. Differentially expressed genes and SWEET family expression patterns were analyzed by transcriptome sequencing, and validated by quantitative real-time polymerase chain reaction (qRT-PCR). Bioinformatics analysis was performed to characterize the protein sequence features and phylogenetic relationships of GhSWEET55, and its expression pattern was analyzed by qRT-PCR. The function of GhSWEET55 was verified by virus-induced gene silencing (VIGS). [Results] Sucrose content in cotton roots increased significantly at 12 h and 48 h after V. dahliae infection, and decreased significantly at 96 h after V. dahliae infection. Some differentially expressed genes were enriched in sucrose-related energy metabolism pathways and defense response pathways. Most members of the SWEET family were differentially expressed, and GhSWEET55 from Clade III was significantly up-regulated. GhSWEET55 was predominantly expressed in cotton leaves, and the encoded protein was localized to the plasma membrane. Silencing of GhSWEET55 enhanced cotton resistance to Verticillium wilt. [Conclusion] Sucrose is involved in cotton resistance against Verticillium wilt. The SWEET gene family responds to V. dahliae infection. GhSWEET55 negatively regulates cotton resistance to V. dahliae.

[Objective] Forkhead box protein G1 (FOXG1), as a transcription factor, plays a crucial role in cell proliferation and differentiation. At present, the FOXG1 gene family has not been systematically studied in cotton. This research aimed to identify and analyze FOXG1 gene family in cotton. [Methods] FOXG1 gene family members were identified in cotton using bioinformatic approaches. Analyses were performed on the physicochemical properties, conserved motifs, and phylogenetic relationships of the corresponding proteins. The expression patterns of FOXG1 genes in Gossypium hirsutum and G. barbadense were investigated using transcriptome data. Preliminary functional exploration of the FOXG1 genes was conducted through association analysis between haplotypes of G. hirsutum FOXG1 genes and fiber quality traits, as well as via transgenic overexpression of GhFOXG1-4 gene in Arabidopsis thaliana. [Results] A total of 6, 5, 3, 3, 6, 6, 6, and 3 FOXG1 genes were identified in G. hirsutum, G. barbadense, G. raimondii, G. arboreum, G. tomentosum, G. mustelinum, G. darwinii, and G. herbaceum, respectively. These 38 FOXG1 proteins and 3 FOXG1 proteins of A. thaliana could be divided into 4 clades. GhFOXG1-1 was highly expressed in anther and ovule. GhFOXG1-2, GbFOXG1-1 and GbFOXG1-2 were highly expressed in anther, ovule and fiber. GhFOXG1-4 was highly expressed in ovule. GhFOXG1-4 and GhFOXG1-5 had 2 and 3 haplotypes, respectively. Significant differences in upper half mean length, breaking strength, and micronaire were observed among these haplotypes. The stem cell width of A. thaliana overexpressing GhFOXG1-4 gene was significantly larger than that of wild type. [Conclusion] A total of 38 FOXG1 genes were identified in 8 cotton species. The excellent haplotypes of some GhFOXG1 genes have the potential to synergistically improve fiber quality. GhFOXG1-4 positively regulates the stem cell width in A. thaliana, which lays a foundation for further study the function of FOXG1 family genes.

[Objective] To address the issues of idle field in winter and spring, low utilization efficiency of cotton straw, and declining profitability in cotton production in the Yellow River Basin, a cotton-Stropharia rugosoannulata double cropping system was proposed, which utilize crushed cotton straw for S. rugosoannulata cultivation in the winter fallow field, followed by S. rugosoannulata residue returning to field. The objective was to investigate the comprehensive effects of this system on productivity, economic benefit, and soil fertility, aiming to provide technical support for the green and sustainable development in the local cotton-growing region. [Methods] Field experiments were conducted from 2022 to 2024 in Linqing City, Shandong Province. Using monocropped spring cotton (MFC) and monocropped short-season cotton (MSC) as controls, the annual yield, economic returns, and soil nutrient content dynamics of two double cropping patterns, intercropping of spring cotton with S. rugosoannulata (FC+SR), short-season cotton followed by S. rugosoannulata in succession planting (SC+SR), were systematically compared. [Results] Compared with MFC treatment, the seed cotton yields of FC+SR and SC+SR treatments significantly decreased by 7.7% and 14.2%, respectively. However, by harvesting S. rugosoannulata (fresh yield: 20.80-21.53 t·hm^-2), the system's net profit was significantly increased to 216 700-244 100 yuan·hm^-2, which was 43.3-48.8 times that of MFC treatment. The net profit of SC+SR pattern was 12.6% higher than that of the FC+SR pattern. Compared with monocropped cotton, the double cropping patterns combined with straw and S. rugosoannulata residue returning significantly increased the contents of alkali-hydrolyzable nitrogen, available phosphorus, and available potassium in the 0-20 cm, 20-40 cm, and 40-60 cm soil layers. And the improvement effect of the SC+SR pattern was generally superior to that of FC+SR. [Conclusion] The cotton-S. rugosoannulata double cropping system is feasible in the Yellow River Basin, with the short-season cotton followed by S. rugosoannulata in succession planting (SC+SR) being the preferred choice. This pattern achieved the recycling of field straw resources and synergistic enhancement of economic benefits and soil fertility, serving as an effective pathway for promoting high-quality agricultural development in the cotton-growing regions of the Yellow River Basin.

[Objective] This study aims to address the issues of impurity contamination in machine-picked seed cotton in Xinjiang and the low efficiency of manual sorting, we propose a highly efficient and precise method for detecting impurities in seed cotton to enhance cotton quality. [Methods] An improved CID-YOLO model is introduced based on YOLO v11. Firstly, a normalization-based attention mechanism module is introduced to enable the network to balance target channel features and pixel features while reducing parameter count and computational complexity, thereby improving detection accuracy. Secondly, according to the characteristics that the detected target is easy to appear at the edge, the lightweight adaptive convolution module is used to replace some convolution modules in the backbone network and neck network, which can better preserve the edge and structure information of the sampling phase, and effectively reduce the amount of parameters. Finally, an efficient layer aggregation network is used to replace the improved pyramid pooling module in the backbone network to enhance the ability of feature multi-scale extraction and information aggregation, so as to improve the perception performance of targets of different scale targets in complex background. [Results] Experimental results demonstrate that the CID-YOLO model achieves outstanding performance in seed cotton impurity detection, with a detection accuracy of 92.1%, recall of 89.5%, F₁ score of 90.8%, and mean average precision of 92.8%. Its overall recognition effectiveness significantly outperforms existing YOLO series models. [Conclusion] The proposed CID-YOLO method enables rapid and precise identification of drip irrigation tapes, colored impurities, cotton stalks, and plastic mulch in machine-picked seed cotton. It provides effective technical support for real-time seed cotton impurity detection and holds promising application prospects.

[Objective] Construct a yeast two-hybrid (Y2H) library of Gossypium barbadense, and screen for interacting proteins of GbbHLH130 using Y2H assays. [Methods] This study constructed a Y2H library of G. barbadense using the Gateway technique, and employed the Y2H system to screen for candidate proteins interacting with GbbHLH130. [Results] This study successfully constructed a G. barbadense Y2H library, with a second library capacity of 1.36 × 10⁷ CFU, and insert fragment length >1 000 bp, and a recombination rate of 100%. Using Y2H technology, 298 initial positive clones were screened, and the interaction between GbRAV1, GbHSFA1b, and GbbHLH130 was verified through Y2H assays. [Conclusion] This study successfully constructed a Y2H library of G. barbadense and preliminarily screened candidate interacting proteins for GbbHLH130. GbRAV1 and GbHSFA1b were verified to interact with GbbHLH130 through Y2H assays, suggesting that they may play a role in the biological process of response to drought stress mediated by GbbHLH130. However, their interaction mechanisms and specific roles in drought response need further research.

[Objective] This research aimed to investigate the effects of reclaimed water irrigation and different mulching methods on cotton growth, yield, and fiber quality. [Methods] A field experiment was conducted in Hutubi County, Changji Hui Autonomous Prefecture, Xinjiang in 2024. Six treatments were established: well water irrigation throughout the whole growth stage + straw mulching (T₁); reclaimed water irrigation throughout the whole growth stage + straw mulching (T₂); reclaimed water irrigation at critical water-demand stages (squaring stage and flowering and boll-setting stage) + straw mulching (T₃); reclaimed water irrigation throughout the whole growth stage + plastic film mulching (T₄); reclaimed water irrigation at critical water-demand stages + plastic film mulching (T₅); and well water irrigation throughout the whole growth stage + plastic film mulching (CK). Cotton plant height, stem diameter, leaf area index (LAI), yield traits, irrigation water use efficiency (IWUE), and fiber quality were compared across different treatments. The entropy-weighted technique for order preference by similarity to ideal solution (TOPSIS) method was used for comprehensive evaluation to select the optimal treatment. Meanwhile, the heavy metal contents in the soil and different cotton organs were determined and analyzed. [Results] During the flowering and boll-setting stage, and boll-opening stage, reclaimed water irrigation significantly increased plant height, stem diameter, and LAI compared with well water irrigation. The plant height, stem diameter, and LAI under straw mulching were greater than those under plastic film mulching; the T₂ treatment exhibited the maximum plant height, stem diameter, and LAI. T₂ also achieved the highest seed cotton yield, lint yield, and IWUE, and upper half mean length, breaking tenacity, breaking elongation, and micronaire of fiber of T₂ were superior to those of other treatments. Comprehensive evaluation using entropy-weighted TOPSIS showed that the T₂ treatment performed best. Compared with well water irrigation, reclaimed water irrigation significantly increased the contents of chromium (Cr) and lead (Pb) in the 0-60 cm soil layer and Cr content in cotton roots, stems, and leaves, while significantly reducing the arsenic (As) content in the 0-60 cm soil layer and cotton roots. However, the contents of mercury (Hg), cadmium (Cd), Cr, Pb, and As in soil and cotton plants under different treatments were all below the risk screening values. [Conclusion] Under the conditions of this experiment, the combination of reclaimed water irrigation throughout the whole growth stage and straw mulching showed the best comprehensive performance.

[Objective] This study aimed to analyze and clarify the biological function of Gossypium hirsutum GhVAS1, and to elucidate its regulatory mechanism underlying boll abscission. [Methods] Using the Arabidopsis thaliana VAS1 gene as a query sequence, two GhVAS1 homologs (GhVAS1-A05 and GhVAS1-D05) were identified and cloned from the upland cotton cultivar TM-1. Subsequently, phylogenetic analysis, conserved motif prediction and protein structure characterization of the cloned GhVAS1 genes were performed. The spatiotemporal expression patterns of GhVAS1 were analyzed by integrating RNA-sequencing (RNA-seq) data with quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The subcellular localization of GhVAS1 was determined using a transient expression system in Nicotiana benthamiana. To assess the role of GhVAS1 in boll abscission, cotton leaf crumple virus (CLCrV)-mediated virus-induced gene silencing (VIGS) was employed in cotton plants. Endogenous levels of auxin (indole-3-acetic acid, IAA) and 1-aminocyclopropane-1-carboxylic acid (ACC) in abscission layer tissues were quantified, and the transcriptional profiles of abscission-related genes were analyzed. In parallel, heterologous overexpression of GhVAS1 in A. thaliana was conducted to validate its conserved regulatory role in organ abscission across plant species. [Results] Phylogenetic analysis revealed that the two GhVAS1 share a close evolutionary relationship with AtVAS1 and encode highly conserved proteins in G. hirsutum. GhVAS1 transcripts exhibited preferential accumulation in the abscission layer and were significantly and consistently upregulated in response to abscission-inducing signals. Subcellular localization assays demonstrated that both GhVAS1 proteins are localized to the nucleus and plasma membrane. VIGS-mediated silencing of GhVAS1 resulted in a significant reduction in cotton boll abscission, which was accompanied by a marked increase in endogenous IAA content and a concurrent decrease in ACC levels in abscission layer tissues. Consistently, the transcriptional levels of key ethylene biosynthetic genes (GhACS and GhACO) and cell wall hydrolysis-related genes (GhPG and GhCEL) were significantly downregulated in GhVAS1-silenced plants. In parallel, heterologous overexpression of GhVAS1 in A. thaliana accelerated floral organ abscission compared with wild-type plants. [Conclusion] GhVAS1 positively regulates boll abscission in cotton by coordinating the IAA-ethylene metabolic balance in abscission layer tissues and upregulating the expression of cell wall degradation-related genes, thereby promoting abscission layer cell separation and subsequent organ shedding.

[Objective] This study aimed to investigate the function of the GhMLO6 gene in cotton Verticillium wilt resistance and identify a candidate gene for disease resistance breeding in cotton. [Methods] Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the expression pattern of GhMLO6. The virus-induced gene silencing (VIGS) technique was employed to transiently silence GhMLO6 in cotton to study its function in Verticillium wilt resistance. Agrobacterium-mediated transient expression technology was applied to Nicotiana benthamiana to explore the subcellular localization of GhMLO6. [Results] The qRT-PCR results revealed that GhMLO6 presented the highest expression level in cotton roots, followed by stems and leaves. Compared with the control, infection with Verticillium dahliae significantly increased the expression level of GhMLO6 in roots. Compared with the control plants in which empty vectors were used, GhMLO6-silenced plants displayed a significant decrease in disease index and relative fungal DNA content. After stem recovery and cultivation, the accumulation of hyphae was reduced, and the resistance of cotton to Verticillium wilt was significantly increased. Transient expression analysis indicated that GhMLO6 localizes on the cell membrane. [Conclusion] GhMLO6 is localized to the cell membrane and performs a negative regulatory function in cotton Verticillium wilt resistance. Therefore materials with Verticillium wilt resistance could be obtained via gene editing technology.

[Objective] This study aims to analyze the effect of the Haloxylon ammodendron (C. A. Mey.) Bunge HaNAC12 gene on the fatty acid content and drought resistance of cotton, and to provide theoretical and technical guidance for cotton stress-resistant breeding. [Methods] The HaNAC12 gene was introduced into cotton through the cotton shoot apical meristem genetic transformation system. After molecular detection of T₀ and T₁ generation plants, the phenotypic and physiological indexes differences between transgenic and non-transgenic cotton were compared through drought stress experiments. [Results] After 30 days of natural drought stress (T30 treatment), the plant height of transgenic cotton was significantly increased by 11% compared with the non-transgenic control, and the degree of leaf wilting was less than that of the control. Physiological index analysis of cotton leaves under T30 treatment showed that the content of malondialdehyde in transgenic cotton was significantly 34% lower than that in the control, with less damage to the plasma membrane; the contents of soluble sugar, proline and chlorophyll were significantly 66%, 89% and 50% higher than those in the control, respectively, with stronger osmotic adjustment ability; the activities of superoxide, peroxidase and catalase dismutase were significantly 94%, 25% and 58% higher than those in the control, respectively, with stronger ability to scavenge reactive oxygen species. Under the T30 treatament, the expression levels of genes related to fatty acid metabolism, such as fatty acid synthase and desaturase, in transgenic cotton were significantly higher than those in the control after drought stress, and the content of free fatty acids in transgenic cotton was significantly 50% higher than that in non-transgenic cotton. There were no significant differences in leaf phenotypes and physiological and biochemical indexes between transgenic and non-transgenic cotton in the normal watering group. [Conclusion] The HaNAC12 may enhance the drought stress tolerance of cotton seedlings by promoting the synthesis and accumulation of fatty acids, providing new gene resources and material support for the genetic improvement of cotton drought resistance.

[Objective] The severe shortage of freshwater has severely restricted cotton production in the arid and semi-arid areas of Xinjiang, and water deficit during the key growth stages exerts an even more adverse effect on yield. Saline water supplemental irrigation can alleviate freshwater shortages, but its optimal salinity threshold remains unclear. This study investigated the effects of supplemental irrigation with saline water of different salinity levels on the photosynthetic characteristics and yield formation of cotton, aiming to determine the suitable salinity threshold for cotton supplemental irrigation in arid areas. [Methods] A two-year field experiment was conducted during the cotton growing seasons in 2023 and 2024. The conventional fresh water without supplemental irrigation was used as the control (CK, irrigation quota of 3 600 m³·hm^-2), and five saline water supplemental irrigation treatments were established: 3.5 g·L^-1 (S3.5), 5.0 g·L^-1 (S5), 6.5 g·L^-1 (S6.5), 8.0 g·L^-1 (S8), 9.5 g·L^-1 (S9.5). The saline supplemental irrigation regime consisted of one application at the bud stage (375 m³·hm^-2) and two applications at the boll-setting stage (375 m³·hm^-2 + 450 m³·hm^-2). The total irrigation amount was 4 800 m³·hm^-2 (including 1 200 m³·hm^-2 of saline water and 3 600 m³·hm^-2 of freshwater). Gas exchange parameters, chlorophyll fluorescence parameters in functional leaves after saline water irrigations, and yield components of cotton were measured. [Results] During the early boll-setting stage, the two-year average net photosynthetic rate (P_n) of treatments with salinity levels of S3.5, S5, and S6.5 increased by 6.89%-18.00% compared with CK, and the S3.5 treatment was significantly higher than CK. The transpiration rates (T_r) of the S3.5 and S5 treatments were significantly increased by 18.96% and 9.10%, respectively, compared with CK, and the stomatal conductances (G_s) were increased by 12.95% and 3.90%, respectively. After three saline water supplementary irrigations, the initial fluorescence (F₀) of the S9.5 treatment was significantly increased by 5.99% (in 2023) and 6.54% (in 2024) relative to CK, while the maximum photochemical efficiency (F_v/F_m) of the S3.5 treatment was significantly higher than that of the S9.5 treatment. The boll-leaf ratio of cotton was the lowest in the S3.5 treatment, with two-year values of 24.58 and 24.87, followed by the S5 treatment with values of 25.02 and 25.05. The two-year average seed cotton yield of treatments with salinity levels of 3.5-6.5 g·L^-1 significantly increased by 2.73%-12.67% compared with CK (5 721.00 kg·hm^-2). [Conclusion] Supplemental irrigation with saline water with a salinity level of 3.5-6.5 g·L^-1 can optimize the photosynthetic performance of cotton and achieve stable or increased yields. However, excessively high salinity level (>6.5 g·L^-1) is prone to cause photoinhibition, leading to a significant reduction in cotton yield. This study provides an important theoretical basis for determining the salinity threshold for saline water irrigation in arid areas.

[Objective] This study aims to establish a rapid quantitative detection method for Rhizoctonia solani, the causal agent of cotton seedling damping-off in soil, and to investigate the correlation between pathogen abundance and disease occurrence, providing a scientific basis for effective disease control. [Methods] A quantitative detection method for R. solani AG-4 HGⅢ in soil was developed using internal reference strain correction and quantitative real-time polymerase chain reaction (qPCR). Pot experiments and field trials were conducted to study the relationship between R. solani abundance in soil and the incidence of cotton seedling damping-off. [Results] A qPCR-based quantitative detection method incorporating internal reference stain correction was successfully established, with high specificity and a sensitivity of 10 copies·μL^-1. The critical threshold of R. solani in soil for severe disease occurrence and seedling mortality risk was determined to be 10⁶ copies·g^-1. [Conclusion] A rapid quantitative detection method for R. solani in cotton field soil was successfully developed, enabling accurate quantification of the pathogen and the early disease risk warning.

[Objective] This study aims to investigate the effects of different tillage practices combined with straw returning on cotton growth, yield, and rhizosphere soil bacterial communities in a potato-cotton rotation system, so as to provide a scientific basis for optimizing farmland management and improving soil microecological health in this system. [Methods] The cotton cultivar Xiang X1107 was used as material. Four treatments were designed: no-tillage (NT), no-tillage with straw returning (NTS), rotary tillage (T), and rotary tillage with straw returning (TS). Growth-related traits and biomass of cotton plant at key growth stages, as well as yield and its components were measured. High-throughput sequencing of the 16S rRNA gene was used to analyze the diversity and composition of rhizosphere soil bacterial communities at the boll-opening stage of cotton, and functional prediction was performed using the Functional Annotation of Prokaryotic Taxa (FAPROTAX). [Results] Straw returning and tillage practice had no significant effect on cotton emergence rate. Compared with no-tillage treatments (NT and NTS), rotary tillage treatments (T and TS) significantly increased plant height, stem diameter, and biomass at the seedling stage, and significantly increased boll weight. Whereas no significant differences in seed cotton yield and boll number were detected among all treatments. Straw returning treatments (NTS and TS) significantly elevated the Shannon Wiener's diversity index, Chao1 index, and evenness index of rhizosphere bacterial communities, with NTS showing the highest values for all indices except the Shannon Wiener's diversity index. Principal coordinates analysis (PCoA) revealed that tillage practice was the primary factor driving the differentiation of bacterial community structure. Proteobacteria was the dominant phylum across all treatments. Straw returning (NTS and TS) significantly decreased the relative abundance of Proteobacteria, while significantly increased the relative abundances of Acidobacteriota and Actinobacteriota. At the genus level, no-tillage treatments (NTS and TS) enriched nitrogen-fixing-related genera including Burkholderia_Caballeronia_Paraburkholderia, Klebsiella, Bradyrhizobium, and Allorhizobium_Neorhizobium_Pararhizobium_Rhizobium complex, and FAPROTAX prediction confirmed a significant enhancement of nitrogen fixation function. Treatment enriched Pantoea and Pseudomonas, and increased the abundances of chemoheterotrophy and human pathogen all related functional groups, whereas TS treatment effectively reduced the risk of pathogenic bacteria. [Conclusion] NTS is conducive to maintaining soil microbial diversity, enhancing nitrogen fixation function, and reducing pathogenic bacteria risk, and is thus the recommended tillage mode in the potato-cotton rotation system. TS can serve as an alternative to promote early-stage growth and regulate microbial functions. Appropriate combination modes can be selected according to local soil conditions, ecological and economic objectives in agricultural production.