Jie Zheng

Cotton ( Gossypium hirsutum L.) is an important fiber crop, but its yield and overall fiber quality are constrained by biotic and abiotic factors. Under certain conditions, moderate rises in temperature and elevated atmospheric CO₂ levels may enhance cotton growth and productivity. However, these benefits are often constrained by heat and water stress. This review critically synthesizes the research on the contribution of soil amendments and agronomic practices to improving soil structure, nutrient retention, rhizosphere functionality, and plant stress resilience in cotton systems. Organic, mineral, and microbial amendments, including biochar formulations, can improve soil properties and microbial activity, especially under arid and saline conditions. Nevertheless, their effectiveness is highly context-dependent. Cotton exhibits physiological plasticity through changes in rooting patterns, osmotic adjustment, and antioxidant defense mechanisms, but its reproductive system is highly sensitive to heat stress. Phenological evidence suggests that warming accelerates crop development and increases the risk of heat and water stress during sensitive growth stages. Based on this synthesis, we propose the Climate-resilient cotton production model (CR-CPM), which conceptualizes cotton resilience as a threshold-based outcome emerging from interactions among soil, microbial, physiological, phenological, and management processes, where physiological thresholds determine the transition from effective management to system-level stress under extreme conditions. This framework emphasizes the need for integrated, site-specific strategies to sustain cotton productivity and soil health under increasing climatic stress.

Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its specific role within the F. oxysporum secretome during PBD pathogenesis remains poorly understood. In this study, we conducted a comprehensive analysis of the lysine acetylome across the F. oxysporum secretome. Utilizing highly sensitive immunoaffinity purification coupled with high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 291 acetylation sites within 85 potentially secreted proteins. Bioinformatics analysis revealed that these acetylated proteins are involved in a wide array of biological functions and exhibit diverse subcellular localizations. Notably, these secreted proteins represent a valuable resource for identifying novel effectors; specifically, eight upregulated genes encoding Kac proteins were identified as potential players during the initial asymptomatic stages of infection. Collectively, these findings provide a global overview of the F. oxysporum secretome acetylome and offer a foundational resource for elucidating the functional significance of lysine acetylation in sugarcane PBD pathogenesis.

In this study, a comprehensive genome-wide identification and analysis of the aldo–keto reductase (AKR) gene family was performed to explore the role of Gossypium hirsutumAKR40 under salt stress in cotton. A total of 249 AKR genes were identified with uneven distribution on the chromosomes in four cotton species. The diversity and evolutionary relationship of the cotton AKR gene family was identified using physio-chemical analysis, phylogenetic tree construction, conserved motif analysis, chromosomal localization, prediction of cis-acting elements, and calculation of evolutionary selection pressure under 300 mM NaCl stress. The real-time qPCR showed that genes encoding members of the aldo–keto reductase (AKR) family in Gossypium hirsutum displayed distinct expression patterns various stress treatments. Specifically, the expression levels of certain genes were significantly upregulated under drought and salt stress. Notably, the role of GhAKR40 gene in salt stress tolerance was validated using virus-induced gene silencing (VIGS) technology in cotton. The GhAKR40-silenced plants experienced leaf wilting under salt stress compared with wild-type and null-control plants. In addition, a series of physio-biochemical such as DAB staining and measurement of RWCL (relative water content in leaves) indexes also indicated that silencing of the AKR40 gene reduced the salt tolerance in cotton. Transcriptome sequencing and analysis of the VIGS-silenced lines suggest that GhAKR40 may enhance salt tolerance in cotton plants by potentially participating in plant-pathogen interactions and the MAPK signaling pathway, thereby modulating both pathways. These data demonstrate that GhAKRs play a significant role in salt stress tolerance. GhAKR40 functions as a positive regulator with a significant impact on stress tolerance. This study not only establishes a theoretical foundation for the comprehensive utilization of resistant germplasm resources in cotton but also paves the way for further exploration of resistance genes in the species.

The analysis and identification of the genetic diversity of plant germplasm resources and varieties are crucial for plant breeding. DNA fingerprinting using genomic molecular markers is crucial for precisely identifying germplasm resources. In this study, the SLAF-seq was performed using 47 germplasm resources of the Wanzhou tea plant population and 5 common cultivated varieties from the Yunnan, Sichuan, and Fujian provinces. A total of 7,447,940 SNPs were identified from 1,641,569 SLAF tags with an averaged sequencing depth of 11.73 (Q30 94.93% and GC 41.37%), which were used to analyze the population composition and genetic diversity. Results showed a large degree of genetic diversity and genetic variation among the samples. The cluster analysis showed that the tea plant population was categorized into three groups, indicating that these germplasms could not be fully classified by their geographical origin, and the linkage disequilibrium analysis indicates that the population resources of the XJ production area are more modern in evolution. A total of 371 uniformly distributed SNP loci were selected and successfully employed to construct the first SNP fingerprint and quick response code (QR code) for tea resources in Wanzhou. These findings offer new insights for genotyping, classifying, and identifying germplasm and genetic resources in the breeding of the Wanzhou tea population.

Gossypium hirsutum is a key fiber crop that is sensitive to environmental factors, particularly drought stress, which can reduce boll size, increase flower shedding, and impair photosynthesis. The aminotransferase (AT) gene is essential for abiotic stress tolerance. A total of 3 Gossypium species were analyzed via genome-wide analysis, and the results unveiled 103 genes in G. hirsutum, 47 in G. arboreum, and 53 in G. raimondii. Phylogenetic analysis, gene structure examination, motif analysis, subcellular localization prediction, and promoter analysis revealed that the GhAT genes can be classified into five main categories and play key roles in abiotic stress tolerance. Using RNA-seq expression and KEGG enrichment analysis of GhTAT2, a coexpression network was established, followed by RT-qPCR analysis to identify hub genes. The RT-qPCR results revealed that the genes Gh_A13G1261, Gh_D13G1562, Gh_D10G1155, Gh_A10G1320, and Gh_D06G1003 were significantly upregulated in the leaf and root samples following drought stress treatment, with Gh_A13G1261 identified as the hub gene. The GhTAT2 genes were considerably enriched for tyrosine, cysteine, methionine, and phenylalanine metabolism and isoquinoline alkaloid, tyrosine, tryptophan, tropane, piperidine, and pyridine alkaloid biosynthesis. Under drought stress, KEGG enrichment analysis manifested significant upregulation of amino acids such as L-DOPA, L-alanine, L-serine, L-homoserine, L-methionine, and L-cysteine, whereas metabolites such as maleic acid, p-coumaric acid, quinic acid, vanillin, and hyoscyamine were significantly downregulated. Silencing the GhTAT2 gene significantly affected the shoot and root fresh weights of the plants compared with those of the wild-type plants under drought conditions. RT-qPCR analysis revealed that GhTAT2 expression in VIGS-treated seedlings was lower than that in both wild-type and positive control plants, indicating that silencing GhTAT2 increases sensitivity to drought stress. In summary, this thorough analysis of the gene family lays the groundwork for a detailed study of the GhTAT2 gene members, with a specific focus on their roles and contributions to drought stress tolerance.

Cytoplasmic male sterile (CMS) systems have great potential in hybrid seed production in many plants. However, the incompatibility between the cytoplasmic and nuclear genes and the availability of fewer CMS lines limit the system’s application in cotton heterosis. Therefore, the present study sequenced the mitochondrial (mt) genomes of a novel cotton (Gossypium hirsutum L.) CMS line J4A and its cytoplasmic nuclear homologous maintainer line J4B to investigate the mechanism underlying CMS and improve its application. A novel CMS gene, orf116b, was identified in the CMS line. Ectopic expression of orf116b in Escherichia coli suppressed growth, while its overexpression in Arabidopsis, rice, tobacco, and cotton led to complete or partial male sterility. Further analysis of anthers revealed mt disruption in J4A with higher levels of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), but lower levels of ATP and ribosomal protein (RP) than in J4B. Finally, a membrane-based yeast two-hybrid (MYTH) assay and bimolecular fluorescence complementation (BiFC) assays demonstrated that orf116b probably interacts with an anther-specific protein, LAT52. These observations collectively proved that orf116b is associated with early and stable pollen abortion in cotton, providing a foundation for further research on cotton fertility restoration and heterosis breeding.