The β-amylase (BAM) gene family encodes important enzymes that catalyze the conversion of starch to maltose in various biological processes of plants and play essential roles in regulating the growth and development of multiple plants. So far, BAMs have been extensively studied in Arabidopsis thaliana (A. thaliana). However, the characteristics of the BAM gene family in the crucial economic crop, cotton, have not been reported. In this study, 27 GhBAM genes in the genome of Gossypium hirsutum L (G. hirsutum) were identified by genome-wide identification, and they were divided into three groups according to sequence similarity and phylogenetic relationship. The gene structure, chromosome distribution, and collinearity of all GhBAM genes identified in the genome of G. hirsutum were analyzed. Further sequence alignment of the core domain of glucosyl hydrolase showed that all GhBAM family genes had the glycosyl hydrolase family 14 domain. We identified the BAM gene GhBAM7 and preliminarily investigated its function by transcriptional sequencing analysis, qRT-PCR, and subcellular localization. These results suggested that the GhBAM7 gene may influence fiber strength during fiber development. This systematic analysis provides new insight into the transcriptional characteristics of BAM genes in G. hirsutum. It may lay the foundation for further study of the function of these genes.

Cotton is an important commercial crop whose growth and yield are severely affected by drought. S-adenosylmethionine (SAM) is widely involved in the plant stress response and growth regulation; however, the role of the S-adenosylmethionine synthase (SAMS) gene family in this process is poorly understood. Here, we systematically analyzed the expression of SAMS genes in Upland Cotton (Gossypium hirsutum L.). A total of 16 SAMS genes were identified, each with a similar predicted structure. A large number of cis-acting elements involved in the response to abiotic stress were predicted based on promoter analysis, indicating a likely important role in abiotic stress responses. The results of qRT-PCR validation showed that GhSAMS genes had different expression patterns after drought stress and in response to drought stress. Analysis of a selected subset of GhSAMS genes showed increased expression in cultivar Xinluzhong 39 (drought resistant) when compared to cultivar Xinluzao 26 (drought-sensitive) upland cotton. This study provides important relevant information for further study of SAMS genes in drought resistance research of upland cotton, which is helpful for drought-resistance improvement of upland cotton.

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.

Background: The B3-domain transcription factor ABI3 (ABSCISIC ACID INSENSITIVE 3) is a critical regulator of seed maturation, stress adaptation, and hormonal signaling in plants. However, its evolutionary dynamics and functional roles in cotton (Gossypium spp.) remain poorly characterized. Methods: We conducted a comprehensive genome-wide investigation of the ABI3 gene family across 26 plant species, with a focus on 8 Gossypium species. Analyses included phylogenetics, chromosomal localization, synteny assessment, gene duplication patterns, protein domain characterization, promoter cis-regulatory element identification, and tissue-specific/spatiotemporal expression profiling under different organizations of Gossypium hirsutum. Results: Phylogenetic and chromosomal analyses revealed conserved ABI3 evolutionary patterns between monocots and dicots, alongside lineage-specific expansion events within Gossypium spp. Syntenic relationships and duplication analysis in G. hirsutum (upland cotton) indicated retention of ancestral synteny blocks and functional diversification driven predominantly by segmental duplication. Structural characterization confirmed the presence of conserved B3 domains in all G. hirsutum ABI3 homologs. Promoter analysis identified key stress-responsive cis-elements, including ABA-responsive (ABRE), drought-responsive (MYB), and low-temperature-responsive (LTRE) motifs, suggesting a role in abiotic stress regulation. Expression profiling demonstrated significant tissue-specific transcriptional activity across roots, stems, leaves, and fiber developmental stages. Conclusions: This study addresses a significant knowledge gap by elucidating the evolution, structure, and stress-responsive expression profiles of the ABI3 gene family in cotton. It establishes a foundational framework for future functional validation and targeted genetic engineering strategies aimed at developing stress-resilient cotton cultivars with enhanced fiber quality.

Background: Genetic diversity and genetic differentiation between Gossypium hirsutum-Gossypium barbadense introgression lines (ILs) and early-maturing upland cotton lines are critical for resolving the core breeding contradiction in Xinjiang cotton region: narrow genetic basis of early-maturing cultivars and late maturity of ILs with superior fiber quality. Xinjiang is one of the major cotton-producing regions in China, and breeding high-quality early-maturing upland cotton adapted to local ecological conditions is essential for improving cotton yield and quality. However, the genetic relationship and differentiation between the two types of cotton germplasm remain unclear, which hinders the efficient utilization of germplasm resources in breeding. Therefore, this study aimed to clarify the genetic diversity and differentiation between the two germplasm types and identify key candidate loci related to early maturity and fiber quality, providing support for cotton breeding. Results: Here, we used a 40K Single Nucleotide Polymorphism chip to genotype core cotton germplasm in northern Xinjiang, and analyzed their population structure, genetic diversity and functional SNP loci associated with early maturity and fiber quality. The tested materials were clearly divided into two subgroups (ILs and early-maturing lines). Genetic diversity analysis revealed a significantly narrow genetic basis in the early-maturing subgroup, while the IL subgroup had higher genetic diversity. Specifically, the early-maturing subgroup showed lower nucleotide diversity and polymorphism information content compared with the IL subgroup, indicating that the genetic variation of early-maturing cotton germplasm in northern Xinjiang is relatively limited. A total of 25 non-synonymous SNPs were identified, among which the c.A613G:p.T205A mutation in GH_D09G1484 (mRNA-decapping enzyme 1, DCP1) was a characteristic variation of early-maturing cotton, and a possible non-synonymous mutation in GH_A09G2400 (Heat shock transcription factor A6b, HSFA6B) was associated with fiber development. These two candidate genes were annotated to be involved in plant growth and development, further supporting their potential roles in regulating cotton early maturity and fiber quality. Conclusions: This study clarified the genetic differentiation between the two types of germplasms and identified key candidate loci for early maturity and fiber quality, providing precise molecular markers and theoretical support for breeding high-quality early-maturing upland cotton adapted to Xinjiang’s ecological conditions. The results also highlight the value of Gossypium hirsutum–Gossypium barbadense introgression lines in enriching the genetic basis of early-maturing cotton, which can be further utilized to solve the core breeding contradiction in the Xinjiang cotton region.