Summary: Despite the established significance of WRKY proteins and phenylpropanoid metabolism in plant immunity, how WRKY proteins modulate aspects of the phenylpropanoid pathway remains undetermined. To understand better the role of WRKY proteins in plant defence, we identified a cotton (Gossypium hirsutum) protein, GhWRKY41, that is, universally and rapidly induced in three disease‐resistant cotton cultivars following inoculation with the plant pathogenic fungus, Verticillium dahliae. We show that overexpression of GhWRKY41 in transgenic cotton and Arabidopsis enhances resistance to V. dahliae, while knock‐down increases cotton more susceptibility to the fungus. GhWRKY41 physically interacts with itself and directly activates its own transcription. A genome‐wide chromatin immunoprecipitation and high‐throughput sequencing (ChIP‐seq), in combination with RNA sequencing (RNA‐seq) analyses, revealed that 43.1% of GhWRKY41‐binding genes were up‐regulated in cotton upon inoculation with V. dahliae, including several phenylpropanoid metabolism master switches, receptor kinases, and disease resistance‐related proteins. We also show that GhWRKY41 homodimer directly activates the expression of GhC4H and Gh4CL, thereby modulating the accumulation of lignin and flavonoids. This finding expands our understanding of WRKY‐WRKY protein interactions and provides important insights into the regulation of the phenylpropanoid pathway in plant immune responses by a WRKY protein.

Cotton is the most widely planted fiber crop in the world, and improving cotton fiber quality has long been a research hotspot. The development of cotton fibers is a complex process that includes four consecutive and overlapping stages, and although many studies on cotton fiber development have been reported, most of the studies have been based on cultivars that are promoted in production or based on lines that are used in breeding. Here, we report a phenotypic evaluation of Gossypium hirsutum based on immature fiber mutant (xin w 139) and wild-type (Xin W 139) lines and a comparative transcriptomic study at seven time points during fiber development. The results of the two-year study showed that the fiber length, fiber strength, single-boll weight and lint percentage of xin w 139 were significantly lower than those of Xin W 139, and there were no significant differences in the other traits. Principal component analysis (PCA) and cluster analysis of the RNA-sequencing (RNA-seq) data revealed that these seven time points could be clearly divided into three different groups corresponding to the initiation, elongation and secondary cell wall (SCW) synthesis stages of fiber development, and the differences in fiber development between the two lines were mainly due to developmental differences after twenty days post anthesis (DPA). Differential expression analysis revealed a total of 5131 unique differentially expressed genes (DEGs), including 290 transcription factors (TFs), between the 2 lines. These DEGs were divided into five clusters. Each cluster functional category was annotated based on the KEGG database, and different clusters could describe different stages of fiber development. In addition, we constructed a gene regulatory network by weighted correlation network analysis (WGCNA) and identified 15 key genes that determined the differences in fiber development between the 2 lines. We also screened seven candidate genes related to cotton fiber development through comparative sequence analysis and qRT–PCR; these genes included three TFs (GH_A08G1821 (bHLH), GH_D05G3074 (Dof), and GH_D13G0161 (C3H)). These results provide a theoretical basis for obtaining an in-depth understanding of the molecular mechanism of cotton fiber development and provide new genetic resources for cotton fiber research.

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