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Salinity stress is one of the primary threats to agricultural crops resulting in impaired crop growth and development. Although cotton is considered as reasonably salt tolerant, it is sensitive to salt stress at some critical stages like germination, flowering, boll formation, resulting in reduced biomass and fiber production. The mechanism of partial ion exclusion (exclusion of Na+ and/or Cl–) in cotton appears to be responsible for the pattern of uptake and accumulation of harmful ions (Na+ and Cl) in tissues of plants exposed to saline conditions. Maintaining high tissue K+/Na+ and Ca2+/Na+ ratios has been proposed as a key selection factor for salt tolerance in cotton. The key adaptation mechanism in cotton under salt stress is excessive sodium exclusion or compartmentation. Among the cultivated species of cotton, Egyptian cotton (Gossypium barbadense L.) exhibit better salt tolerance with good fiber quality traits as compared to most cultivated cotton and it can be used to improve five quality traits and transfer salt tolerance into Upland or American cotton (Gossypium hirsutum L.) by interspecific introgression. Cotton genetic studies on salt tolerance revealed that the majority of growth, yield, and fiber traits are genetically determined, and controlled by quantitative trait loci (QTLs). Molecular markers linked to genes or QTLs affecting key traits have been identified, and they could be utilized as an indirect selection criterion to enhance breeding efficiency through marker-assisted selection (MAS). Transfer of genes for compatible solute, which are an important aspect of ion compartmentation, into salt-sensitive species is, theoretically, a simple strategy to improve tolerance. The expression of particular stress-related genes is involved in plant adaptation to environmental stressors. As a result, enhancing tolerance to salt stress can be achieved by marker assisted selection added with modern gene editing tools can boost the breeding strategies that defend and uphold the structure and function of cellular components. The intent of this review was to recapitulate the advancements in salt screening methods, tolerant germplasm sources and their inheritance, biochemical, morpho-physiological, and molecular characteristics, transgenic approaches, and QTLs for salt tolerance in cotton.

The changing climate is intensifying salt stress globally. Salt stress is a menace to cotton crop quality and yield. The seedling, germination, and emergence phases are more prone to the effects of salt stress than other stages. Higher levels of salt can lead to delayed flowering, a reduced number of fruiting positions, shedding of fruits, decreased boll weight, and yellowing of fiber, all of which have an adverse effect on the yield and quality of the seed cotton. However, sensitivity toward salt stress is dependent on the salt type, cotton growth phase, and genotype. As the threat of salt stress continues to grow, it is crucial to gain a comprehensive understanding of the mechanisms underlying salt tolerance in plants and to identify potential avenues for enhancing the salt tolerance of cotton. The emergence of marker-assisted selection, in conjunction with next-generation sequencing technologies, has streamlined cotton breeding efforts. This review begins by providing an overview of the causes of salt stress in cotton, as well as the underlying theory of salt tolerance. Subsequently, it summarizes the breeding methods that utilize marker-assisted selection, genomic selection, and techniques for identifying elite salt-tolerant markers in wild species or mutated materials. Finally, novel cotton breeding possibilities based on the approaches stated above are presented and debated.

Upland cotton is one of the main cultivated species of cotton, and salt stress is an important factor in its growth and development. Wall-associated receptor kinase galacturonan binding (GUB_WAK_bind) is an extracellular domain of wall-associated kinase (WAK), which can sense the environment and play a role in the response to plant stress.In this study, the GUB_WAK_bind gene in Gossypium hirsutum was identified and analyzed by bioinformatics at the whole genome level, including its physicochemical properties, evolutionary development, gene structure, chromosome positioning, cis-acting elements in the promoter, etc., and the expression of the GUB_WAK_bind genes under salt stress were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 22 GUB_WAK_bind gene members were identified in Gossypium hirsutum and divided into three subgroups by evolutionary development and motif analysis, most of which contained motif 5, which is similar to the motif pattern of subgroup members. The number of exons in this gene family is between 1 and 4, the number of introns is between 0 and 3, and 22 gene members are distributed on 14 chromosomes of Gossypium hirsutum. Almost all gene members have adverse stress response elements in their promoter region. The expression analysis in response to salt stress showed that the selected six genes were induced by NaCl stress with significant expression differences (P 0.05).The results of this study have a certain reference value for understanding the evolution and function of GUB_WAK_bind genes and studying the salt tolerance genes of Gossypium hirsutum.

Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton “Tongyan No. 1.” Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6–245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.

Background Cytoplasmic linker–associated proteins (CLASPs) are tubule proteins that can bind to microtubules and participate in regulating the structure and function of microtubules, which significantly affects the development and growth of plants. These proteins have been identified in Arabidopsis; however, little research has been performed in upland cotton. Methods In this study, the whole genome of the CLASP_N family was analyzed to provide theoretical support for the function of this gene family in the development of upland cotton fiber. Bioinformatics was used to analyze the family characteristics of CLASP_N in upland cotton, such as member identification, sequence characteristics, conserved domain structure and coevolutionary relationships. Real-time fluorescent quantitative PCR (qRT-PCR) was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber. Results At the genome-wide level, we identified 16 upland cotton CLASP_N genes. A chromosomal localization analysis revealed that these 16 genes were located on 13 chromosomes. The motif results showed that all CLASP_N proteins have the CLASP_N domain. Gene structure analysis showed that the structure and length of exons and introns were consistent in the subgroups. In the evolutionary analysis with other species, the gene family clearly diverged from the other species in the evolutionary process. A promoter sequence analysis showed that this gene family contains a large number of cis-acting elements related to a variety of plant hormones. qRT-PCR was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber and leaves, and Gh210800 was found to be highly expressed in the later stages of fiber development. The results of this study provide a foundation for further research on the molecular role of the CLASP_N genes in cotton fiber development.

Background Cytoplasmic linker–associated proteins (CLASPs) are tubule proteins that can bind to microtubules and participate in regulating the structure and function of microtubules, which significantly affects the development and growth of plants. These proteins have been identified in Arabidopsis; however, little research has been performed in upland cotton. Methods In this study, the whole genome of the CLASP_N family was analyzed to provide theoretical support for the function of this gene family in the development of upland cotton fiber. Bioinformatics was used to analyze the family characteristics of CLASP_N in upland cotton, such as member identification, sequence characteristics, conserved domain structure and coevolutionary relationships. Real-time fluorescent quantitative PCR (qRT-PCR) was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber. Results At the genome-wide level, we identified 16 upland cotton CLASP_N genes. A chromosomal localization analysis revealed that these 16 genes were located on 13 chromosomes. The motif results showed that all CLASP_N proteins have the CLASP_N domain. Gene structure analysis showed that the structure and length of exons and introns were consistent in the subgroups. In the evolutionary analysis with other species, the gene family clearly diverged from the other species in the evolutionary process. A promoter sequence analysis showed that this gene family contains a large number of cis-acting elements related to a variety of plant hormones. qRT-PCR was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber and leaves, and Gh210800 was found to be highly expressed in the later stages of fiber development. The results of this study provide a foundation for further research on the molecular role of the CLASP_N genes in cotton fiber development.