Cotton photosynthetic efficiency and the root–shoot relationship are two important physiological indexes affecting the final yield, but the interactive effects of plastic film mulching and planting density on the cotton photosynthetic efficiency and root–shoot relationship have rarely been reported. We aimed to investigate the optimal plant density with or without plastic film mulching for improved seed cotton yield in southern Xinjiang. Therefore, a two-year field experiment was conducted to investigate the effects of plastic film mulching (with or without plastic film mulching) and planting density (D1: 9 × 10⁴ plants ha⁻¹; D2: 18 × 10⁴ plants ha⁻¹; D3, 22 × 10⁴ plants ha⁻¹, local conventional planting density; D4, 27 × 10⁴ plants ha⁻¹) on the cotton root–shoot relationship, photosynthetic parameters, and seed cotton yield. Our results showed that the seed cotton yield was improved under plastic film mulching at all planting densities, but economic income was significantly lower in comparison to without plastic film mulching in 2023. Compared with D3, seed cotton yield and economic income at D2 increased by 6.9% and 12.2%, either with or without plastic film mulching, respectively. The highest increase in the seed cotton yield in D2 under plastic film mulching was due to the greatest improvements in the root production capacity and photosynthesis. The boll capacity of the root system (BCR) and boll loading of the root system (BLR) in D2 were the highest among all treatments with film mulching, being 9.0% and 16.9% higher than that in D3 in 2022 and 2023. However, the root–shoot ratio (R/S) was 7.1% and 6.9% lower in D2 than D3, under film mulching, in 2022 and 2023. Moreover, moderate plant density (D2) improved the SPAD value, chlorophyll fluorescence (F_v/F_m and PI_abs), and photosynthetic parameter (Pn, Tr, and Gs) and decreased Ci compared with other planting density treatments in both years. Further analyses with correlation analysis showed that the seed cotton yield was highly positive correlated with BLR, BCR, and the photosynthetic parameter. In summary, suitable planting density (18 × 10⁴ plants ha⁻¹) combined with plastic film mulching has the potential to obtain high yields by enhancing the efficiency of photosynthetic assimilates, improving the capacity of cotton root production, providing a reference for suitable planting density under plastic film mulching.

Cotton is an important natural fiber crop. The RF2 gene family is a member of the bZIP transcription factor superfamily, which plays an important role in plant resistance to environmental stresses. In this paper, the RF2 gene family of four cotton species was analyzed genome-wide, and the key gene RF2-32 was cloned for functional verification. A total of 113 RF2 genes were identified in the four cotton species, and the RF2 family was relatively conserved during the evolution of cotton. Chromosome mapping and collinear analysis indicated that fragment replication was the main expansion mode of RF2 gene family during evolution. Cis-element analysis showed that there were many elements related to light response, hormone response and abiotic stress response in the promoters of RF2 genes. The transcriptome and qRT-PCR analysis of RF2 family genes in upland cotton showed that RF2 family genes responded to salt stress and drought stress. GhRF2-32 protein was localized in the cell nucleus. Silencing the GhRF2-32 gene showed less leaf wilting and increased total antioxidant capacity under drought and salt stress, decreased malondialdehyde content and increased drought and salt tolerance. This study revealed the evolutionary and functional diversity of the RF2 gene family, which laid a foundation for the further study of stress-resistant genes in cotton.

Cotton is one of the most economically important crops worldwide. Seed size is a vital trait for plants connected with yield and germination. GW2 encodes a RING_Ubox E3 ubiquitin ligase that controls seed development by affecting cell growth. Here, are few reports on GW2-like genes in cotton, and the function of GW2 in cotton is poorly understood. In the present study, a genome-wide analysis identified 6 and 3 GW2-like genes in each of the two cultivated tetraploids (Gossypium hirsutum and G. barbadense) and each of their diploid ancestral species (G. arboreum, G. raimondii), respectively. GhGW2-2D has the same functional domain and high sequence similarity with AtDA2 in Arabidopsis. Overexpression of GhGW2-2D in Arabidopsis significantly reduced seed and seedling size, suggesting GhGW2-2D is a potential target for regulating cotton seed size. These results provided information on the genetic and molecular basis of GW2-like genes in cotton, thus establishing a foundation for functional studies of cotton seeds.

Verticillium wilt (VW) caused by Verticillium dahliae (Vd) is a devastating fungal cotton disease characterized by high pathogenicity, widespread distribution, and frequent variation. It leads to significant losses in both the yield and quality of cotton. Identifying key non-synonymous single nucleotide polymorphism (SNP) markers and crucial genes associated with VW resistance in Gossypium hirsutum and Gossypium barbadense, and subsequently breeding new disease-resistant varieties, are essential for VW management. Here, we sequenced the transcriptome and metabolome of roots of TM-1 (G. hirsutum) and Hai7124 (G. barbadense) after 0, 1, and 2 days of V991 inoculation. Transcriptome analysis identified a total of 72,752 genes, with 5814 differentially expressed genes (DEGs) determined through multiple group comparisons. KEGG enrichment analysis revealed that the key pathways enriched by DEGs obtained from both longitudinal and transverse comparisons contained the glutathione metabolism pathway. Metabolome analysis identified 995 metabolites, and 22 differentially accumulated metabolites (DAMs), which were correlated to pathways including glutathione metabolism, degradation of valine, leucine, and isoleucine, and biosynthesis of terpenoids, alkaloids, pyridine, and piperidine. The conjoint analysis of transcriptomic and metabolomic sequencing revealed DAMs and DEGs associated with the glutathione metabolism pathway, and the key candidate gene GH_D11G2329 (glutathione S-transferase, GSTF8) potentially associated with cotton response to VW infection was selected. These findings establish a basis for investigating the mechanisms underlying the cotton plant’s resistance to VW.

Saline-alkali stress is one of the major abiotic stresses threatening crop growth. Cotton, as a “pioneer crop” that can grow in saline and alkali lands, is of great significance for understanding the regulatory mechanisms of plant response to stresses. Upland cotton has thus become a model plant for researchers to explore plant responses to saline-alkali stresses. In this study, RNA sequencing was employed to analyze tissue-specific expression of root tissues of TM-1 seedlings 20 min after exposure to compound saline-alkali stress. The RNA-Seq results revealed significant molecular differences in the responses of different root regions to the stress treatment. A total of 3939 differentially expressed genes (DEGs) were identified from pairwise comparisons between the non-root tip and root tip samples, which were primarily enriched in pathways including plant hormone signal transduction, MAPK signaling, and cysteine and methionine metabolism. Combined with the expression pattern investigation by quantitative real-time PCR (qRT-PCR) experiments, a key gene, GhERF2 (GH_A08G1918, ethylene-responsive transcription factor 2-like), was identified to be associated with saline-alkali tolerance. Through virus-induced gene silencing (VIGS), the GhERF2-silenced plants exhibited a more severe wilting phenotype under combined salt-alkali stress, along with a significant reduction in leaf chlorophyll content and fresh weights of plants and roots. Additionally, these plants showed greater cellular damage and a lower ability to scavenge reactive oxygen species (ROS) when exposed to the stress. These findings suggest that the GhERF2 gene may play a positive regulatory role in cotton responses to salt-alkali stress. These findings not only enhance our understanding of the molecular mechanisms underlying cotton response to compound saline-alkali stress, but also provide a foundation for future molecular breeding efforts aimed at improving cotton saline-alkali tolerance.