The genetic basis of leaf hair development in upland cotton (Gossypium hirsutum).

Trichomes, which originate from the epidermal cell of aerial organs, provide plants with defense and secretion functions. Although numerous genes have been implicated in trichome development, the molecular mechanisms underlying trichome cell formation in plants remain incompletely understood. Here, we using genome-wide association study (GWAS) across 1037 diverse accessions in upland cotton (Gossypium hirsutum) to identify three loci associated with leaf pubescence (hair) amount, located on chromosome A06 (LPA1), A08 (LPA2) and A11 (LPA3), respectively. GhHD1, a previously characterized candidate gene, was identified on LPA1 and encodes an HD-Zip transcription factor. For LPA2 and LPA3, we identified two candidate genes, GhGIR1 and GhGIR2, both encoding proteins with WD40 and RING domains that act as inhibitors of leaf hair formation. Expression analysis revealed that GhHD1 was predominantly expressed in hairy accessions, whereas GhGIR1 and GhGIR2 were expressed in hairless accessions. Silencing GhHD1 or overexpressing GhGIR1 in hairy accessions induced in a hairless phenotype, whereas silencing GhGIR2 in hairless accessions resulted in a hairy phenotype. We also demonstrated that GhHD1 interact with both GhGIR1 and GhGIR2, and GhGIR1 can interact with GhGIR2. Further investigation indicated that GhHD1 functions as a transcriptional activator, binding to the promoters of the GhGIR1 and GhGIR2 to active their expression, whereas GhGIR1 and GhGIR2 can suppress the transcriptional activation of GhHD1. Our findings shed light on the intricate regulatory network involving GhHD1, GhGIR1 and GhGIR2 in the initiation and development of plant epidermal hairs in cotton.

GhMAX2 Contributes to Auxin-Mediated Fiber Elongation in Cotton (Gossypium hirsutum).

Strigolactones (SLs) represent a new group of phytohormones that play a pivotal role in the regulation of plant shoot branching and the development of adventitious roots. In cotton (Gossypium hirsutum, Gh), SLs play a crucial role in the regulation of fiber cell elongation and secondary cell wall thickness. However, the underlying molecular mechanisms of SL signaling involved in fiber cell development are largely unknown. In this study, we report two SL-signaling genes, GhMAX2-3 and GhMAX2-6, which positively regulate cotton fiber elongation. Further protein-protein interaction and degradation assays showed that the repressor of the auxin cascade GhIAA17 serves as a substrate for the F-box E3 ligase GhMAX2. The in vivo ubiquitination assay suggested that GhMAX2-3 and GhMAX2-6 ubiquitinate GhIAA17 and coordinately degrade GhIAA17 with GhTIR1. The findings of this investigation offer valuable insights into the roles of GhMAX2-mediated SL signaling in cotton and establish a solid foundation for future endeavors aimed at optimizing cotton plant cultivation.

An insight into heat stress response and adaptive mechanism in cotton.

The growing worldwide population is driving up demand for cotton fibers, but production is hampered by unpredictable temperature rises caused by shifting climatic conditions. Numerous research based on breeding and genomics have been conducted to increase the production of cotton in environments with high and low-temperature stress. High temperature (HT) is a major environmental stressor with global consequences, influencing several aspects of cotton plant growth and metabolism. Heat stress-induced physiological and biochemical changes are research topics, and molecular techniques are used to improve cotton plants' heat tolerance. To preserve internal balance, heat stress activates various stress-responsive processes, including repairing damaged proteins and membranes, through various molecular networks. Recent research has investigated the diverse reactions of cotton cultivars to temperature stress, indicating that cotton plant adaptation mechanisms include the accumulation of sugars, proline, phenolics, flavonoids, and heat shock proteins. To overcome the obstacles caused by heat stress, it is crucial to develop and choose heat-tolerant cotton cultivars. Food security and sustainable agriculture depend on the application of genetic, agronomic, and, biotechnological methods to lessen the impacts of heat stress on cotton crops. Cotton producers and the textile industry both benefit from increased heat tolerance. Future studies should examine the developmental responses of cotton at different growth stages, emphasize the significance of breeding heat-tolerant cultivars, and assess the biochemical, physiological, and molecular pathways involved in seed germination under high temperatures. In a nutshell, a concentrated effort is required to raise cotton's heat tolerance due to the rising global temperatures and the rise in the frequency of extreme weather occurrences. Furthermore, emerging advances in sequencing technologies have made major progress toward successfully se sequencing the complex cotton genome.

The strigolactone-gibberellin crosstalk mediated by a distant silencer fine-tunes plant height in upland cotton.

The optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most crucial fiber crop globally, but the knowledge of the genetic basis underlying plant height still needs to be discovered. Here we conducted a genome-wide association study (GWAS) to identify the major locus controlling plant height (PH1) in upland cotton. The locus encodes gibberellin 2-oxidase 1A (GhPH1), with a 1,133 bp-length structural variation (PAVPH1) located approximately 16 kb upstream of it. The presence or absence of PAVPH1 confers a differential expression of GhPH1, consequently leading to changes in plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes a specific 'CATTTG' motif on the GhPH1 promoter and PAVPH1. This binding event down-regulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that the critical repressor of the strigolactone (SL) signaling pathway, DWARF53 (D53), directly interacts with GhGARF and inhibits its binding to targets. Moreover, our study uncovers a previously unrecognized GA-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, crucial in regulating the plant height of upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height and provide valuable insights for developing semi-dwarf cotton varieties through precise modulation of GhPH1 expression.

Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton.

Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.

Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton.

Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.

Transcriptome dynamics of Gossypium purpurascens in response to abiotic stresses by Iso-seq and RNA-seq data.

Gossypium purpurascens is a member of the Malvaceae family, holds immense economic significance as a fiber crop worldwide. Abiotic stresses harm cotton crops, reduce yields, and cause economic losses. Generating high-quality reference genomes and large-scale transcriptomic datasets across diverse conditions can offer valuable insights into identifying preferred agronomic traits for crop breeding. The present research used leaf tissues to conduct PacBio Iso-seq and RNA-seq analysis. We carried out an in-depth analysis of DEGs using both correlations with cluster analysis and principal component analysis. Additionally, the study also involved the identification of both lncRNAs and CDS. We have prepared RNA-seq libraries from 75 RNA samples to study the effects of drought, salinity, alkali, and saline-alkali stress, as well as control conditions. A total of 454.06 Gigabytes of transcriptome data were effectively validated through the identification of differentially expressed genes and KEGG and GO analysis. Overwhelmingly, gene expression profiles and full-length transcripts from cotton tissues will aid in understanding the genetic mechanism of abiotic stress tolerance in G. purpurascens.

GhiPLATZ17 and GhiPLATZ22, zinc-dependent DNA-binding transcription factors, promote salt tolerance in upland cotton.

KEY MESSAGE: The utilization of transcriptome analysis, functional validation, VIGS, and DAB techniques have provided evidence that GhiPLATZ17 and GhiPLATZ22 play a pivotal role in improving the salt tolerance of upland cotton. PLATZ (Plant AT-rich sequences and zinc-binding proteins) are known to be key regulators in plant growth, development, and response to salt stress. In this study, we comprehensively analyzed the PLATZ family in ten cotton species in response to salinity stress. Gossypium herbaceum boasts 25 distinct PLATZ genes, paralleled by 24 in G. raimondii, 25 in G. arboreum, 46 in G. hirsutum, 48 in G. barbadense, 43 in G. tomentosum, 67 in G. mustelinum, 60 in G. darwinii, 46 in G. ekmanianum, and a total of 53 PLATZ genes attributed to G. stephensii. The PLATZ gene family shed light on the hybridization and allopolyploidy events that occurred during the evolutionary history of allotetraploid cotton. Ka/Ks analysis suggested that the PLATZ gene family underwent intense purifying selection during cotton evolution. Analysis of synteny and gene collinearity revealed a complex pattern of segmental and dispersed duplication events to expand PLATZ genes in cotton. Cis-acting elements and gene expressions revealed that GhiPLATZ exhibited salt stress resistance. Transcriptome analysis, functional validation, virus-induced gene silencing (VIGS), and diaminobenzidine staining (DAB) demonstrated that GhiPLATZ17 and GhiPLATZ22 enhance salt tolerance in upland cotton. The study can potentially advance our understanding of identifying salt-resistant genes in cotton.

Exploring the regulatory role of non-coding RNAs in fiber development and direct regulation of GhKCR2 in the fatty acid metabolic pathway in upland cotton.

Cotton fiber holds immense importance as the primary raw material for the textile industry. Consequently, comprehending the regulatory mechanisms governing fiber development is pivotal for enhancing fiber quality. Our study aimed to construct a regulatory network of competing endogenous RNAs (ceRNAs) and assess the impact of non-coding RNAs on gene expression throughout fiber development. Through whole transcriptome data analysis, we identified differentially expressed genes (DEGs) regulated by non-coding RNA (ncRNA) that were predominantly enriched in phenylpropanoid biosynthesis and the fatty acid elongation pathway. This analysis involved two contrasting phenotypic materials (J02-508 and ZRI015) at five stages of fiber development. Additionally, we conducted a detailed analysis of genes involved in fatty acid elongation, including KCS, KCR, HACD, ECR, and ACOT, to unveil the factors contributing to the variation in fatty acid elongation between J02-508 and ZRI015. Through the integration of histochemical GUS staining, dual luciferase assay experiments, and correlation analysis of expression levels during fiber development stages for lncRNA MSTRG.44818.23 (MST23) and GhKCR2, we elucidated that MST23 positively regulates GhKCR2 expression in the fatty acid elongation pathway. This identification provides valuable insights into the molecular mechanisms underlying fiber development, emphasizing the intricate interplay between non-coding RNAs and protein-coding genes.

Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.).

KEY MESSAGE: One major gene controlling primary root length (PRL) in Gossypium arboreum is identified and this research provides a theoretical basis for root development for cotton. Primary root elongation is an essential process in plant root system structure. Here, we investigated the primary root length (PRL) of 215 diploid cotton (G. arboreum) accessions at 5, 8, 10, 15 days after sowing. A Genome-wide association study was performed for the PRL, resulting in 49 significant SNPs associated with 32 putative candidate genes. The SNP with the strongest signal (Chr07_8047530) could clearly distinguish the PRLs between accessions with two haplotypes. GamurG is the only gene that showed higher relative expression in the long PRL genotypes than the short PRL genotypes, which indicated it was the most likely candidate gene for regulating PRL. Moreover, the GamurG-silenced cotton seedlings showed a shorter PRL, while the GamurG-overexpressed Arabidopsis exhibited a significantly longer PRL. Our findings provide insight into the regulation mechanism of cotton root growth and will facilitate future breeding programs to optimize the root system structure in cotton.

Impact of salinity stress on cotton and opportunities for improvement through conventional and biotechnological approaches.

Excess salinity can affect the growth and development of all plants. Salinization jeopardizes agroecosystems, induces oxidative reactions in most cultivated plants and reduces biomass which affects crop yield. Some plants are affected more than others, depending upon their ability to endure the effects of salt stress. Cotton is moderately tolerant to salt stress among cultivated crops. The fundamental tenet of plant breeding is genetic heterogeneity in available germplasm for acquired characteristics. Variation for salinity tolerance enhancing parameters (morphological, physiological and biochemical) is a pre-requisite for the development of salt tolerant cotton germplasm followed by indirect selection or hybridization programs. There has been a limited success in the development of salt tolerant genotypes because this trait depends on several factors, and these factors as well as their interactions are not completely understood. However, advances in biochemical and molecular techniques have made it possible to explore the complexity of salt tolerance through transcriptomic profiling. The focus of this article is to discuss the issue of salt stress in crop plants, how it alters the physiology and morphology of the cotton crop, and breeding strategies for the development of salinity tolerance in cotton germplasm.

Genomic loci associated with leaf abscission contribute to machine picking and environmental adaptability in upland cotton (Gossypium hirsutum L.).

INTRODUCTION: Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood. OBJECTIVES: In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability. METHODS: Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed. RESULTS: Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (HapRDR7 and HapRDR13) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment. CONCLUSION: Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

Epigenetic insight into floral transition and seed development in plants.

Seasonal changes are crucial in shifting the developmental stages from the vegetative phase to the reproductive phase in plants, enabling them to flower under optimal conditions. Plants grown at different latitudes sense and interpret these seasonal variations, such as changes in day length (photoperiod) and exposure to cold winter temperatures (vernalization). These environmental factors influence the expression of various genes related to flowering. Plants have evolved to stimulate a rapid response to environmental conditions through genetic and epigenetic mechanisms. Multiple epigenetic regulation systems have emerged in plants to interpret environmental signals. During the transition to the flowering phase, changes in gene expression are facilitated by chromatin remodeling and small RNAs interference, particularly in annual and perennial plants. Key flowering regulators, such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT), interact with various factors and undergo chromatin remodeling in response to seasonal cues. The Polycomb silencing complex (PRC) controls the expression of flowering-related genes in photoperiodic flowering regulation. Under vernalization-dependent flowering, FLC acts as a potent flowering suppressor by downregulating the gene expression of various flower-promoting genes. Eventually, PRCs are critically involved in the regulation of FLC and FT locus interacting with several key genes in photoperiod and vernalization. Subsequently, PRCs also regulate Epigenetical events during gametogenesis and seed development as a driving force. Furthermore, DNA methylation in the context of CHG, CG, and CHH methylation plays a critical role in embryogenesis. DNA glycosylase DME (DEMETER) is responsible for demethylation during seed development. Thus, the review briefly discusses flowering regulation through light signaling, day length variation, temperature variation and seed development in plants.

Physiological and transcriptional analyses reveal formation of memory under recurring drought stresses in seedlings of cotton (Gossypium hirsutum).

Plants are frequently subjected to a range of environmental stresses, including drought, salinity, cold, pathogens, and herbivore attacks. To survive in such conditions, plants have evolved a novel adaptive mechanism known as 'stress memory'. The formation of stress memories necessitates coordinated responses at the cellular, genetic/genomic, and epigenetic levels, involving altered physiological responses, gene activation, hyper-induction and chromatin modification. Cotton (Gossypium spp.) is an important economic crop with numerous applications and high economic value. In this study, we establish G. hirsutum drought memory following cycles of mild drought and re-watering treatments and analyzed memory gene expression patterns. Our findings reveal the physiological, biochemical, and molecular mechanisms underlying drought stress memory formation in G. hirsutum. Specifically, H3K4me3, a histone modification, plays a crucial role in regulating [+ /+ ] transcriptional memory. Moreover, we investigated the intergenerational inheritance of drought stress memory in G. hirsutum. Collectively, our data provides theoretical guidance for cotton breeding.

Dissecting the major genetic components underlying cotton lint development.

Numerous genetic loci and several functionally characterized genes have been linked to determination of lint percentage (lint%), one of the most important cotton yield components, but we still know little about the major genetic components underlying lint%. Here, we first linked the genetic loci containing MYB25-like_At and HD1_At to the fiberless seed trait of 'SL1-7-1' and found that MYB25-like_At and HD1_At were very lowly expressed in 'SL1-7-1' ovules during fiber initiation. We then dissected the genetic components involved in determination of lint% using segregating populations derived from crosses of fuzzless mutants and intermediate segregants with different lint%, which not only confirmed the HD1_At locus but identified the HD1_Dt locus as being the major genetic components contributing to fiber initiation and lint%. The segregating populations also allowed us to evaluate the relative contributions of MYB25-like_At, MYB25-like_Dt, HD1_At, and HD1_Dt to lint%. Haplotype analysis of an Upland cotton (Gossypium hirsutum) population with 723 accessions (including 81 fuzzless seed accessions) showed that lint% of the accessions with the LP allele (higher lint%) at MYB25-like_At, MYB25-like_Dt, or HD1_At was significantly higher than that with the lp allele (lower lint%). The lint% of the Upland cotton accessions with 3 or 4 LP alleles at MYB25-like and HD1 was significantly higher than that with 2 LP alleles. The results prompted us to propose a strategy for breeding high-yielding cotton varieties, i.e. pyramiding the LP alleles of MYB25-like and HD1 with new lint% LP alleles without negative impact on seed size and fiber quality.

Transcriptomic analysis reveals the beneficial effects of salt priming on enhancing defense responses in upland cotton under successive salt stress.

Priming-mediated stress tolerance in plants stimulates defense mechanisms and enables plants to cope with future stresses. Seed priming has been proven effective for tolerance against abiotic stresses; however, underlying genetic mechanisms are still unknown. We aimed to assess upland cotton genotypes and their transcriptional behaviors under salt priming and successive induced salt stress. We pre-selected 16 genotypes based on previous studies and performed morpho-physiological characterization, from which we selected three genotypes, representing different tolerance levels, for transcriptomic analysis. We subjected these genotypes to four different treatments: salt priming (P0), salt priming with salinity dose at 3-true-leaf stage (PD), salinity dose at 3-true-leaf stage without salt priming (0D), and control (CK). Although the three genotypes displayed distinct expression patterns, we identified common differentially expressed genes (DEGs) under PD enriched in pathways related to transferase activity, terpene synthase activity, lipid biosynthesis, and regulation of acquired resistance, indicating the beneficial role of salt priming in enhancing salt stress resistance. Moreover, the number of unique DEGs associated with G. hirsutum purpurascens was significantly higher compared to other genotypes. Coexpression network analysis identified 16 hub genes involved in cell wall biogenesis, glucan metabolic processes, and ribosomal RNA binding. Functional characterization of XTH6 (XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE) using virus-induced gene silencing revealed that suppressing its expression improves plant growth under salt stress. Overall, findings provide insights into the regulation of candidate genes in response to salt stress and the beneficial effects of salt priming on enhancing defense responses in upland cotton.

Quantitative trait loci and candidate genes for yield-related traits of upland cotton revealed by genome-wide association analysis under drought conditions.

BACKGROUND: Due to the influence of extreme weather, the environment in China's main cotton-producing areas is prone to drought stress conditions, which affect the growth and development of cotton and lead to a decrease in cotton yield. RESULTS: In this study, 188 upland cotton germplasm resources were phenotyped for data of 8 traits (including 3 major yield traits) under drought conditions in three environments for two consecutive years. Correlation analysis revealed significant positive correlations between the three yield traits. Genetic analysis showed that the estimated heritability of the seed cotton index (SC) under drought conditions was the highest (80.81%), followed by that of boll weight (BW) (80.64%) and the lint cotton index (LC) (70.49%) With genome-wide association study (GWAS) analysis, a total of 75 quantitative trait loci (QTLs) were identified, including two highly credible new QTL hotspots. Three candidate genes (Gh_D09G064400, Gh_D10G261000 and Gh_D10G254000) located in the two new QTL hotspots, QTL51 and QTL55, were highly expressed in the early stage of fiber development and showed significant correlations with SC, LC and BW. The expression of three candidate genes in two extreme materials after drought stress was analyzed by qRT-PCR, and the expression of these two materials in fibers at 15, 20 and 25 DPA. The expression of these three candidate genes was significantly upregulated after drought stress and was significantly higher in drought-tolerant materials than in drought-sensitive materials. In addition, the expression levels of the three candidate genes were higher in the early stage of fiber development (15 DPA), and the expression levels in drought-tolerant germplasm were higher than those in drought-sensitive germplasm. These three candidate genes may play an important role in determining cotton yield under drought conditions. CONCLUSIONS: This study is helpful for understanding the regulatory genes affecting cotton yield under drought conditions and provides germplasm and candidate gene resources for breeding high-yield cotton varieties under these conditions.

Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton (Gossypium purpurascens).

Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton.

Genome-wide analysis of the serine carboxypeptidase-like protein family reveals Ga09G1039 is involved in fiber elongation in cotton.

The Gossypium is a model genus for understanding polyploidy and the evolutionary pattern of inheritance. This study aimed to investigate the characteristics of SCPLs in different cotton species and their role in fiber development. A total of 891 genes from one typical monocot and ten dicot species were naturally divided into three classes based on phylogenetic analysis. The SCPL gene family in cotton has undergone intense purifying selection with some functional variation. Segmental duplication and whole genome duplication were shown to be the two main reasons for the increase in the number of genes during cotton evolution. The identification of Gh_SCPL genes exhibiting differential expression in particular tissues or response to environmental stimuli provides a new measure for the in-depth characterization of selected genes of importance. Ga09G1039 was involved in the developmental process of fibers and ovules, and it is significantly different from proteins from other cotton species in terms of phylogenetic, gene structure, conserved protein motifs and tertiary structure. Overexpression of Ga09G1039 significantly increased the length of stem trichomes. Ga09G1039 may be a serine carboxypeptidase protein with hydrolase activity, according to functional region, prokaryotic expression, and western blotting analysis. The results provide a comprehensive overview of the genetic basis of SCPLs in Gossypium and further our knowledge in understanding the key aspects of SCPLs in cotton with their potential role in fiber development and stress resistance.

Transcriptome and proteome profiling revealed the key genes and pathways involved in the fiber quality formation in brown cotton.

Colored cotton is also called eco-cotton because of its natural color fiber. It is inferior in yield and quality than white cotton. The underlying regulatory genes involved in fiber quality and pigment synthesis are not well understood. This study aimed to investigate the transcriptomic and proteomic changes during fiber development in a brown cotton cultivar (Z161) and a white cotton cultivar. The differential proteins with the same expression trend as genes were significantly and positively correlated with corresponding fold changes in expression. Enrichment analysis revealed that Z161, enriched in fiber elongation genes related to flavonoid biosynthesis, phenylalanine metabolism, glutathione metabolism, and many more genes (proteins) are up-regulated. Moreover, 164 glycosyltransferases genes, 15 MYB-bHLH-WD40 genes, and other transcription factors such as C2H2 (12), ERF (11), and NAC (7) were preferentially expressed in Z161. Weighted correlation network analysis identified fatty acid synthesis and energy metabolism as the principal metabolic pathways in both cotton genotypes during fiber development. Identified 15 hub genes will provide important insights for genetic manipulation of fiber quality and pigment deposition balance in brown cotton fibers.