Abscission is a process that allows plants to shed tissues or organs via cell separation, and occurs throughout the life cycle. Removal of leaves through the use of chemical defoliants is very important for mechanical harvesting of cotton (Gossypium hirsutum). However, our knowledge of the molecular mechanisms of the defoliation response involved is limited. In this study, RNA-seq was conducted in order to profile the differentially expressed genes (DEGs) between cultivars X50 (sensitive to chemical defoliants) and X33 (relatively insensitive) at different time points after treatment with thidiazuron and ethephon (TE). A total of 2434 DEGs were identified between the two cultivars across the different time-points. Functional categories according to GO and KEGG analyses revealed that plant hormone signal transduction and zeatin biosynthesis were involved in the response to TE. Cytokinin oxidase/dehydrogenase (CKX) genes and ethylene-related genes were up-regulated following TE treatment, and were associated with increased level of ethylene, especially in cultivar X50. Down-regulation of GhCKX3 resulted in delayed defoliation and a reduced ethylene response. The results show that crosstalk between cytokinin and ethylene regulates cotton defoliation, and provide new insights into the molecular mechanisms underlying the mode of action of defoliants in cotton.

Background: Sea island cotton (Gossypium barbadense) has markedly superior high quality fibers, which plays an important role in the textile industry and acts as a donor for upland cotton (G. hirsutum) fiber quality improvement. The genetic characteristics analysis and the identification of key genes will be helpful to understand the mechanism of fiber development and breeding utilization in sea island cotton. Results: In this study, 279 sea island cotton accessions were collected from different origins for genotyping and phenotyping fiber quality traits. A set of 6303 high quality single nucleotide polymorphisms (SNPs) were obtained by high-density CottonSNP80K array. The population characteristics showed that the sea island cotton accessions had wide genetic diversity and were clustered into three groups, with Group1 closely related to Menoufi, an original sea island cotton landrace, and Group2 and Group3 related to widely introduced accessions from Egypt, USA and Former Soviet Union. Further, we used 249 accessions and evaluated five fiber quality traits under normal and salt environments over 2 years. Except for fiber uniformity (FU), fiber length (FL) and fiber elongation (FE) were significantly decreased in salt conditions, while fiber strength (FS) and fiber micronaire (MIC) were increased. Based on 6303 SNPs and genome-wide association study (GWAS) analysis, a total of 34 stable quantitative trait loci (QTLs) were identified for the five fiber quality traits with 25 detected simultaneously under normal and salt environments. Gene Ontology (GO) analysis indicated that candidate genes in the 25 overlapped QTLs were enriched mostly in “cellular and biological process”. In addition, “xylem development” and “response to hormone” pathways were also found. Haplotype analyses found that GB_A03G0335 encoding an E3 ubiquitin-protein ligase in QTL TM6004 had SNP variation (A/C) in gene region, was significantly correlated with FL, FS, FU, and FE, implying a crucial role in fiber quality. Conclusions: The present study provides a foundation for genetic diversity of sea island cotton accessions and will contribute to fiber quality improvement in breeding practice.

(1) Background: This study aims to analyze the defoliation and boll opening performance of 123 upland cotton germplasm resources after spraying defoliant, using multispectral data to select relevant vegetation indices and identify germplasm resources sensitive to defoliants, providing methods for cotton variety improvement and high-quality parental resources. (2) Methods: 123 historical upland cotton germplasm resources from Xinjiang were selected, and the defoliation and boll opening of cotton leaves were investigated at 0, 4, 8, 12, 16, and 20 days after defoliant application. Simultaneously, multispectral digital images were collected using drones to obtain 12 vegetation indices. Based on defoliation rate, the optimal vegetation index was selected, and defoliant-sensitive germplasm resources were identified. (3) Results: The most significant difference in defoliation rate of cotton germplasm resources occurred 16 days after application. Cluster analysis grouped the 123 breeding materials into three categories, with Class I showing the best defoliation effect. Among the 12 vegetation indices, the Plant Senescence Reflectance Index (PSRI) has the highest correlation coefficient with the defoliation rate; and when the PSRI value is higher, the defoliation effect of the material is better. By comparing the traditional investigation method with the unmanned aerial vehicle multispectral technology, 15 cotton materials sensitive to defoliants were determined, with a defoliation rate of over 85%, a lint percentage ranging from 76.67% to 98.04%, and a PSRI value ranging from 0.1607 to 0.1984. (4) Conclusions: The study found that the vegetation index with sensitive response can be used as an effective indicator to evaluate the sensitivity of cotton breeding materials to defoliants. Using an unmanned aerial vehicle (UAV) equipped with vegetation indices for screening shows a high consistency with the manual investigation and screening method in screening excellent defoliation materials; it proves that it is feasible to screen cotton breeding materials with excellent defoliation effects using UAV multispectral technology.

(1) Background: This study aims to analyze the defoliation and boll opening performance of 123 upland cotton germplasm resources after spraying defoliant, using multispectral data to select relevant vegetation indices and identify germplasm re-sources sensitive to defoliants, providing methods for cotton variety improvement and high-quality parental resources. (2) Methods: 123 historical upland cotton germplasm resources from Xinjiang were selected, and the defoliation and boll opening of cotton leaves were investigated at 0, 4, 8, 12, 16, and 20 days after defoliant application. Sim-ultaneously, multispectral digital images were collected using drones to obtain 12 vegetation indices. Based on defoliation rate, the optimal vegetation index was selected, and defoliant-sensitive germplasm resources were identified. (3) Results: The most significant difference in defoliation rate of cotton germplasm resources occurred 16 days after application. Cluster analysis grouped the 123 breeding materials into three categories, with Class I showing the best defoliation effect. Among the 12 vegetation indices, the Plant Senescence Reflectance Index (PSRI) has the highest correlation coef-ficient with the defoliation rate; and when the PSRI value is higher, the defoliation ef-fect of the material is better. Using drone multispectral technology, 15 defoli-ant-sensitive cotton materials were identified, with defoliation rates exceeding 85%, boll opening rates ranging from 76.67% to 98.04%, and PSRI values between 0.1607 and 0.1984.(4) Conclusions: The study found that vegetation indices with sensitive re-sponses can serve as effective indicators for evaluating the sensitivity of cotton breed-ing materials to defoliants. The combined analysis of traditional survey methods and PSRI classification demonstrates that using drone multispectral technology as a sub-stitute for manual methods in large-scale, rapid monitoring and selection of cotton breeding materials with excellent defoliation effects is feasible.

The glycosyltransferase 92 (GT92) gene belongs to the glycosyltransferase gene family. In the plant genome, it is one of the numerous genes involved in sugar metabolism and glycosylation modification. Nonetheless, the GT92 sub-family assumes a vital function in facilitating plants’ adaptation to adverse environments and modulating plant growth, development, and the processes of organogenesis. To date, comprehensive characterization and systematic investigation of GT92 in cotton remain underexplored. In this study, we systematically analyzed the structural features, phylogenetic tree, gene architecture, expression profiles, evolutionary relationships, and selective pressures of GT92 gene family members across four Gossypium species using bioinformatics approaches for the first time. Collectively, 44 GT92 genes were identified, including 14 in G. hirsutum. Based on the phylogenetic tree, GT92 protein sequences from the four cotton species were clustered into five distinct subfamilies. Chromosomal mapping of these genes was performed, and their structural details were visualized. We further predicted cis-acting elements in G. hirsutum GT92 genes and characterized duplication patterns across the four Gossypium species. Ka/Ks ratios of orthologous gene pairs were calculated to investigate selective pressures among the species. RNA-seq data from G. hirsutum and G. barbadense revealed GT92 expression patterns. WGCNA (Weighted Gene Co-expression Network Analysis) identified GhGT92_5 and GhGT92_6 as members of the MEtan module, which was significantly negatively correlated with the 6-hour time point post-drought stress. Mfuzz trend analysis classified GhGT92_5 and GhGT92_6 into Cluster13 and Cluster14, respectively. qRT-PCR validated their roles under drought and salt stress conditions. Subcellular localization showed GhGT92_5 primarily distributed in the plasma membrane and chloroplasts, while GhGT92_6 was localized in the endoplasmic reticulum and chloroplasts. All of these findings have expanded our understanding of the GT92 family members, establishing a basis for more in-depth exploration of the stress-tolerance mechanisms of this gene in cotton.

Fruit branch length in cotton is a key trait influencing plant architecture and suitability for mechanisation; elucidating its molecular regulatory mechanisms is crucial for breeding varieties with desirable plant architecture. In this study, an F₂ segregating population was established using the long-fruit-branch upland cotton line L16 and the short-fruit-branch line S14 as parents. By integrating morphological, cytological, and omics approaches, we systematically analysed the underlying mechanisms of variation in fruit branch length. Phenotypic analysis indicated that the inter-node elongation rate of the first fruit branch in L16 was significantly higher than that in S14. Tissue section observations revealed that the length of cortical parenchyma cells in L16 was significantly greater than that in S14, suggesting that the difference in fruit branch length primarily stems from variations in the extent of cortical parenchyma cell elongation. BSA-Seq analysis identified five QTL regions significantly associated with fruit branch length, encompassing 82 coding genes. Further RNA-Seq analysis of the fruit branch initiation stage (T0) and rapid elongation stage (T1) identified 3106 differentially expressed genes common to both stages. GO and KEGG enrichment analyses revealed that these genes were significantly enriched in pathways related to plant hormone signalling, the cytoskeleton, and microtubule organisation. By integrating BSA-Seq and RNA-Seq data, three candidate genes were screened that simultaneously harboured non-synonymous mutations and were significantly highly expressed in the short fruit branch line S14. Combined with bioinformatics analysis, GH_D02G0744 was predicted to be the most likely key candidate gene regulating cotton fruit branch length. This study provides important genetic resources to elucidate the molecular regulatory mechanisms of cotton fruit branch length and lays a theoretical foundation for molecular breeding to improve cotton plant architecture.