Cotton Species Research Articles

Convergence and divergence of diploid and tetraploid cotton genomes.

Polyploidy is an important driving force in speciation and evolution; however, the genomic basis for parallel selection of a particular trait between polyploids and ancestral diploids remains unexplored. Here we construct graph-based pan-genomes for diploid (A2) and allotetraploid (AD1) cotton species, enabled by an assembly of 50 genomes of genetically diverse accessions. We delineate a mosaic genome map of tetraploid cultivars that illustrates genomic contributions from semi-wild forms into modern cultivars. Pan-genome comparisons identify syntenic and hyper-divergent regions of continued variation between diploid and tetraploid cottons, and suggest an ongoing process of sequence evolution potentially linked to the contrasting genome size change in two subgenomes. We highlight 43% of genetic regulatory relationships for gene expression in diploid encompassing sequence divergence after polyploidy, and specifically characterize six underexplored convergent genetic loci contributing to parallel selection of fiber quality. This study offers a framework for pan-genomic dissection of genetic regulatory components underlying parallel selection of desirable traits in organisms.

Introgression and Mapping of Cotton Leaf Curl Disease (CLCuD) Resistance from Wild Gossypium armourianum Kearney into Upland Cotton (G. hirsutum L.).

Cotton leaf curl disease (CLCuD), caused by the whitefly transmitted geminivirus complex (Cotton leaf curl virus - CLCuV and their satellite molecules), is a serious threat to successful upland cotton production in northwest India, Pakistan, and China. The disease causes significant losses in fibre yield and the quality of cotton. Owing to the regular emergence of resistance breaking strains of CLCuV, all the previously available CLCuD resistant germplasms of upland cotton have become compromised and none of the extant upland cotton cultivars is resistant to this disease. Therefore, alternate sources of CLCuD resistance need to be explored, as genetic resistance is the only pragmatic and tenable management strategy to combat this malady. Here, we report for the first time the introgression and mapping of CLCuD resistance from a related non-progenitor wild diploid D-genome cotton species, G. armourianum into upland cotton. A backcross population (G. hirsutum/G. armourianum/G. hirsutum) was developed for this purpose. A single major QTL was found to be associated with resistance to CLCuD and was located on chromosome D01 through the genotyping-by-sequencing technique.

Genome-Wide Identification and Functional Validation of Actin Depolymerizing Factor (ADF) Gene Family in Gossypium hirsutum L.

The Actin Depolymerizing Factor (ADF) protein, highly conserved among eukaryotes, is essential for plant growth, development, and stress responses. Cotton, a vital economic crop with applications spanning oilseed, textiles, and military sectors, has seen a limited exploration of its ADF gene family. This research has identified 118 unique ADF sequences across four principal cotton species: Gossypium hirsutum L., Gossypium barbadense Linn, Gossypium raimondii, and Asiatic cotton. The study found that the structural domains and physicochemical properties of these proteins are largely uniform across species. The ADF genes were classified into four subfamilies with a notable expansion in groups III and IV due to tandem and chromosomal duplication events. A thorough analysis revealed a high degree of conservation in gene structure, including exon counts and the lengths of introns and exons, with the majority of genes containing three exons, aligning with the characteristics of the ADF family. RNA-seq analysis uncovered a spectrum of responses by GhADFs to various abiotic stresses with GhADF19 showing the most significant reaction. Virus-induced gene silencing (VIGS) experiments were conducted to assess the role of GhADF19 in plant growth under abiotic stress. The results demonstrated that plants with silenced GhADF19 exhibited significantly slower growth rates and lower dry weights when subjected to cold, salt, and drought stress compared to the control group. This marked reduction in growth and dry weight under stress conditions highlights the potential importance of GhADF19 in stress tolerance mechanisms.

A Genome-Wide Alternative Splicing Analysis of Gossypium arboreum and Gossypium raimondii During Fiber Development

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that contributes to proteome complexity and versatility in different plant species. However, detailed AS exploration in diploid cotton during fiber development has not been reported. In this study, we comparatively analyzed G. arboreum and G. raimondii AS events during fiber development using transcriptome data and identified 9690 and 7617 AS events that were distributed in 6483 and 4859 genes, respectively. G. arboreum had more AS genes and AS events than G. raimondii, and most AS genes were distributed at both ends of all 13 chromosomes in both diploid cotton species. Four major AS types, including IR, SE, A3SS, and A5SS, were all experimentally validated through RT-PCR assays. G. arboreum and G. raimondii had only 1888 AS genes in common, accounting for one-third and one-half of the total number of AS genes, respectively. Furthermore, we found a lysine-specific demethylase coding gene with a different AS mechanism in G. arboreum and G. raimondii, in which AS isoforms lacked part of a key conserved domain. Our findings may provide new directions for the discovery of functional genes involved in cotton species differentiation.

Evolutionary comparison of lncRNAs in four cotton species and functional identification of LncR4682-PAS2-KCS19 module in fiber elongation.

Long non-coding RNAs (lncRNAs) play an important role in various biological processes in plants. However, there have been few reports on the evolutionary signatures of lncRNAs in closely related cotton species. The lncRNA transcription patterns in two tetraploid cotton species and their putative diploid ancestors were compared in this paper. By performing deep RNA sequencing, we identified 280 429 lncRNAs from 21 tissues in four cotton species. lncRNA transcription evolves more rapidly than mRNAs, and exhibits more severe turnover phenomenon in diploid species compared to that in tetraploid species. Evolutionarily conserved lncRNAs exhibit higher expression levels, and lower tissue specificity compared with species-specific lncRNAs. Remarkably, tissue expression of homologous lncRNAs in Gossypium hirsutum and G. barbadense exhibited similar patterns, suggesting that these lncRNAs may be functionally conserved and selectively maintained during domestication. An orthologous lncRNA, lncR4682, was identified and validated in fibers of G. hirsutum and G. barbadense with the highest conservatism and expression abundance. Through virus-induced gene silencing in upland cotton, we found that lncR4682 and its target genes GHPAS2 and GHKCS19 positively regulated fiber elongation. In summary, the present study provides a systematic analysis of lncRNAs in four closely related cotton species, extending the understanding of transcriptional conservation of lncRNAs across cotton species. In addition, LncR4682-PAS2-KCS19 contributes to cotton fiber elongation by participating in the biosynthesis of very long-chain fatty acids.

Predicting Cold-Stress Responsive Genes in Cotton with Machine Learning Models

Machine Learning (ML) serves as a potent tool for data mining and predictive analytics in genomic research. However, its application in identifying stress-responsive genes remains underexplored. This study identified distinct variations in the expression patterns of one-to-one homologous genes responding to cold stress in three cotton species: Gossypium hirsutum, Gossypium barbadense, and Gossypium arboreum. To better understand cold-responsive genes, we developed ML predictive models (LightGBM, XGBoost, and Random Forest) utilizing 121 biochemical features. The incorporating of these features significantly enhanced model accuracy. Moreover, incorporating evolutionary information further refined the models, achieving an impressive 80.80% accuracy in predicting cold-stress responsive genes. Notably, models trained on sequence features from G. hirsutum showed transferability to the closely related species of G. barbadense, with accuracies ranging from 78.65% to 83.04%. This research presents a promising workflow for identifying candidate genes for experimental exploration of cold stress responses and establishes a systematic framework for predicting cold-stress related genes using ML methodologies.

Pan-genome analysis of GT64 gene family and expression response to Verticillium wilt in cotton

BackgroundThe GT64 subfamily, belonging to the glycosyltransferase family, plays a critical function in plant adaptation to stress conditions and the modulation of plant growth, development, and organogenesis processes. However, a comprehensive identification and systematic analysis of GT64 in cotton are still lacking.ResultsThis study used bioinformatics techniques to conduct a detailed investigation on the GT64 gene family members of eight cotton species for the first time. A total of 39 GT64 genes were detected, which could be classified into five subfamilies according to the phylogenetic tree. Among them, six genes were found in upland cotton. Furthermore, investigated the precise chromosomal positions of these genes and visually represented their gene structure details. Moreover, forecasted cis-regulatory elements in GhGT64s and ascertained the duplication type of the GT64 in the eight cotton species. Evaluation of the Ka/Ks ratio for similar gene pairs among the eight cotton species provided insights into the selective pressures acting on these homologous genes. Additionally, analyzed the expression profiles of the GT64 gene family. Overexpressing GhGT64_4 in tobacco improved its disease resistance. Subsequently, VIGS experiments conducted in cotton demonstrated reduced disease resistance upon silencing of the GhGT64_4, may indicate its involvement in affecting lignin and jasmonic acid biosynthesis pathways, thus impacting cotton resistance. Weighted Gene Co-expression Network Analysis (WGCNA) revealed an early immune response against Verticillium dahliae in G. barbadense compared to G. hirsutum. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT-PCR) analysis indicated that some GT64 genes might play a role under various biotic and abiotic stress conditions.ConclusionsThese discoveries enhance our knowledge of GT64 family members and lay the groundwork for future investigations into the disease resistance mechanisms of this gene in cotton.

Genome‑wide analysis of cotton SCAMP genes and functional characterization of GhSCAMP2 and GhSCAMP4 in salt tolerance

BackgroundSecretory carrier membrane proteins (SCAMPs) form a family of integral membrane proteins and play a crucial role in mediating exocytosis in both animals and plants. While SCAMP genes have been studied in several plant species, their functions in cotton, particularly in response to abiotic stress, have not yet been reported.ResultsIn this study, a total of 53 SCAMP genes were identified in G. arboreum, G. raimondii, G. hirsutum, and G. barbadense. These genes were classified into five groups based on a phylogenetic analysis with SCAMPs from Arabidopsis thaliana. The main factor driving the expansion of the SCAMP gene family in G. hirsutum is tandem and segmental duplication events. Using MEME, in addition to the conserved SCAMP domain, we identified 3–13 other domains in each GhSCAMP. The cis-element analysis suggested that GhSCAMPs were widely involved in cotton growth and development, and responses to abiotic stresses. RNA sequencing (RNA-Seq) and reverse transcription-quantitative polymerase chain reaction (RT-qPCR) results showed that most GhSCAMPs were expressed highly in many tissues and had differential expression responses to drought, cold, and heat stresses. Knock-down of GhSCAMP2 and GhSCAMP4 by virus-induced gene silencing (VIGS) lead to a salt-sensitive phenotype and had a lower content of CAT, POD, and SOD.ConclusionsThis study identified SCAMP genes in four cotton species, enhancing our understanding of the potential biological functions of SCAMPs. Additionally, we demonstrated that GhSCAMP2 and GhSCAMP4 positively regulate cotton tolerance to salt stress.

Graph-based analysis of DNA sequence comparison in closed cotton species: A generalized method to unveil genetic connections.

Graph theory provides a systematic method for modeling and analysing complicated biological data as an effective bioinformatics tool. Based on current trends, the number of DNA sequences in the DNA database is growing quickly. To determine the origin of a species and identify homologous sequences, it is crucial to detect similarities in DNA sequences. Alignment-free techniques are required for accurate measures of sequence similarity, which has been one of the main issues facing computational biologists. The current study provides a mathematical technique for comparing DNA sequences that are constructed in graph theory. The sequences of each DNA were divided into pairs of nucleotides, from which weighted loop digraphs and corresponding weighted vectors were computed. To check the sequence similarity, distance measures like Cosine, Correlation, and Jaccard were employed. To verify the method, DNA segments from the genomes of ten species of cotton were tested. Furthermore, to evaluate the efficacy of the proposed methodology, a K-means clustering method was performed. This study proposes a proof-of-model that utilises a distance matrix approach that promises impressive outcomes with future optimisations to be made to the suggested solution to get the hundred percent accurate result. In the realm of bioinformatics, this paper highlights the use of graph theory as an effective tool for biological data study and sequence comparison. It's expected that further optimization in the proposed solution can bring remarkable results, as this paper presents a proof-of-concept implementation for a given set of data using the proposed distance matrix technique.

A computational analysis revealed BES1 transcription factor and β-amylase as crosstalk elements in Upland cotton species (Gossypium sp.)

Cotton is a resilient and multipurpose crop, meeting major of the world’s textile needs while also yielding byproducts like edible oil and animal feed. Starch plays a crucial role in cotton fabric production. It enhances fabric strength by forming a protective film around cotton fibers, making them more resistant to wear and tear. BES1 (brassinosteroid insensitive 1) is a key regulator in brassinosteroid signaling. It controls thousands of target genes involved in development processes. Interestingly, two β-amylase proteins (BAM7 and BAM8) are part of the BES1 family, despite their primary function as β-amylases. β-Amylase (BAM) and BES1 are two gene families with functional and regulatory roles in controlling shoot growth and development by mediating brassinosteroid effects. They share similar domains and participate in various biological processes, tolerance and responses to stresses like salt and drought. In a computational analysis comparing Arabidopsis and Gossypium species, BAM and BES1 were characterized. BES1 genes were grouped into four clusters based on the comparison of the two species. Two clusters corresponded to BAM7 and BAM8, while the other two clusters were associated with BES1. The conserved nucleotide domain sequence is GCTGGATGG. Short tandem repeats include TG and TTG, which can serve as molecular markers. BES1 is specifically linked to cellulose and fiber production and holds promise as a candidate for plant selection and breeding in Gossypium (cotton).

Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton.

Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3-79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi-locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non-introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression-mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber.

Integrative physiology and transcriptome sequencing reveal differences between G. hirsutum and G. barbadense in response to salt stress and the identification of key salt tolerance genes

BackgroundSoil salinity is one of the major abiotic stresses that threatens crop growth. Cotton has some degree of salt tolerance, known as the “pioneer crop” of saline-alkali land. Cultivation of cotton is of great significance to the utilization of saline-alkali land and the development of cotton industry. Gossypium hirsutum and G. barbadense, as two major cotton species, are widely cultivated worldwide. However, until recently, the regulatory mechanisms and specific differences of their responses to salt stress have rarely been reported.ResultsIn this study, we comprehensively compared the differences in the responses of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 to salt stress. The results showed that Hai7124 exhibited better growth than did TM-1 under salt stress, with greater PRO content and antioxidant capability, whereas TM-1 only presented greater K+ content. Transcriptome analysis revealed significant molecular differences between the two cotton species in response to salt stress. The key pathways of TM-1 induced by salt are mainly related to growth and development, such as porphyrin metabolism, DNA replication, ribosome and photosynthesis. Conversely, the key pathways of Hai7124, such as plant hormone signal transduction, MAPK signaling pathway-plant, and phenylpropanoid biosynthesis, are mainly related to plant defense. Further comparative analyses of differentially expressed genes (DEGs) revealed that antioxidant metabolism, abscisic acid (ABA) and jasmonic acid (JA) signalling pathways were more strongly activated in Hai7124, whereas TM-1 was more active in K+ transporter-related genes and ethylene (ETH) signalling pathway. These differences underscore the various molecular strategies adopted by the two cotton species to navigate through salt stress, and Hai7124 responded more strongly to salt stress, which explains the potential reasons for the greater salt tolerance of Hai7124. Finally, we identified 217 potential salt tolerance-related genes, 167 of which overlapped with the confidence intervals of significant SNPs identified in previous genome-wide association studies (GWASs), indicating the high reliability of these genes.ConclusionsThese findings provide new insights into the differences in the regulatory mechanisms of salt tolerance between G. hirsutum and G. barbadense, and identify key candidate genes for salt tolerance molecular breeding in cotton.

Application of mannitol as pre-treatment and sucrose supports callus induction through anther culture in Gossypium arboreum

Diploid or tree cotton (Gossypium arboreum) species may provide a breeding source for fiber quality and disease resistance. Developing homozygous lines of Gossypium arboreum through anther culture can be a successful strategy for breeding the parental lines needed for cotton hybrids. This study describes callus induction on four G. arboreum genoytypes under various concentrations of sucrose as well as plant growth regulators. Explant materials were derived from immature anther and grew on modified Murashige and Skoog (MS) media. Prior to main treatment, mannitol application were applied to anthers with concentration of 0.7 M and modified MS media consisted of 3%, 5%, and 7% sucrose, as well as an addition of IAA, NAA, BAP, 2,4-D and Kin. Optimum callus formation was observed in Marvi genotype, in a medium containg IAA as well as sucrose between 5-7%. Furthermore, combination of IAA and NAA with sucrose 7% indicates highest number of embryogenic calli. However, Marvi genotype showed decreased rate of callus formation when the amount of sucrose increased on MS supplemented with NAA medium. The results indicated that the best formula on each genotypes were different. However, MS media with IAA (1 mg/l) + kin (0.2 mg/l) + CM (70 ml/l) + sucrose 5% provided the best performance to produce embryogenic calli on each genotypes. Our report can be utilized as an opportunity and strategy to obtain double haploid lines as a parental source in hybrid production.

A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development.

Assembly of complete genomes can reveal functional genetic elements missing from draft sequences. Here we present the near-complete telomere-to-telomere and contiguous genome of the cotton species Gossypium raimondii. Our assembly identified gaps and misoriented or misassembled regions in previous assemblies and produced 13 centromeres, with 25 chromosomal ends having telomeres. In contrast to satellite-rich Arabidopsis and rice centromeres, cotton centromeres lack phased CENH3 nucleosome positioning patterns and probably evolved by invasion from long terminal repeat retrotransposons. In-depth expression profiling of transposable elements revealed a previously unannotated DNA transposon (MuTC01) that interacts with miR2947 to produce trans-acting small interfering RNAs (siRNAs), one of which targets the newly evolved LEC2 (LEC2b) to produce phased siRNAs. Systematic genome editing experiments revealed that this tripartite module, miR2947-MuTC01-LEC2b, controls the morphogenesis of complex folded embryos characteristic of Gossypium and its close relatives in the cotton tribe. Our study reveals a trans-acting siRNA-based tripartite regulatory pathway for embryo development in higher plants.

Molecular traits of MAPK kinases and the regulatory mechanism of GhMAPKK5 alleviating drought/salt stress in cotton.

Mitogen-activated protein kinase kinases (MAPKKs) play a critical role in the mitogen-activated protein kinase (MAPK) signaling pathway, transducing external stimuli into intracellular responses and enabling plant adaptation to environmental challenges. Most research has focused on the model plant Arabidopsis (Arabidopsis thaliana). The systematic analysis and characterization of MAPKK genes across different plant species, particularly in cotton (Gossypium hirsutum), are somewhat limited. Here, we identified MAPKK family members from 66 different species, which clustered into 5 different sub-groups, and MAPKKs from four cotton species clustered together. Through further bioinformatic and expression analysis, GhMAPKK5 was identified as the most responsive MAPKK member to salt and drought stress among the 23 MAPKKs identified in Gossypium hirsutum. Silencing GhMAPKK5 in cotton through virus-induced gene silencing (VIGS) led to quicker wilting under salt and drought conditions, while overexpressing GhMAPKK5 in Arabidopsis enhanced root growth and seed germination under these stresses, demonstrating GhMAPKK5's positive role in stress tolerance. Transcriptomics and Yeast-Two-Hybrid assays revealed a MAPK cascade signal module comprising GhMEKK (Mitogen-activated protein kinase kinase kinases)3/8/31-GhMAPKK5-GhMAPK11/23. This signaling cascade may play a role in managing drought and salt stress by regulating transcription factor genes, such as WRKYs, which are involved in the biosynthesis and transport pathways of ABA, proline, and RALF. This study is highly important for further understanding the regulatory mechanism of MAPKK in cotton, contributing to its stress tolerance and offering potential in targets for genetic enhancement.

Genome-wide analysis of HACD family genes and functional characterization of GhHACD2 for very long chain fatty acids biosynthesis in Gossypium hirsutum

Cotton (Gossypium spp.) not only serves as a primary textile fiber crop but also as a vital oilseed crop. It stands as the world’s fifth-largest oil crop and is rich in essential fatty acids. At present, the mechanisms underlying the biosynthesis of cottonseed oil have been extensively studied in cotton. 3-Hydroxyacyl-CoA dehydratase (HACD) is the third rate-limiting enzyme in the elongase complex, which plays a critical role in the biosynthesis of Very Long Chain Fatty Acids (VLCFA). However, the members of the HACD family and their roles in cottonseed oil remain uncharacterized in cotton. This study identified that G. arboreum and G. raimondii have two HACD genes, while four HACD genes exists in G. hirsutum, and G. barbadense. The phylogenetic relationships of the 12 HACD genes from the four cotton species further divided them into two subfamilies. Gene structure and conserved motif analysis revealed that members of the HACD family were relatively conserved during the evolution of cotton, but members within the same subfamily exhibited more similar structures. Homology and collinearity analysis suggest whole-genome duplication/segmental duplication may be a key factor in the amplification of the cotton HACD gene family. The qRT-PCR analysis of high-oil and low-oil genotype found significant differences in the expression levels of GhHACD1-4, which indicates GhHACD1-4 is expected to participate in the lipid oil biosynthesis process. Subcellular localization experiments confirmed the presence of the GhHACD2 inendoplasmic reticulum. The KEGG pathway enrichment analysis of co-expressed genes of GhHACD1 and GhHACD2 genes were conducted to confirm their potential involvement in fatty acid elongation and oil biosynthesis. Furthermore, transgenic overexpression analysis of GhHACD2 caused a 5.02% decrease in oil content compared with the control in yeast, while the levels of C28:0, C30:0, and VLCFAs were significantly improved. This study characterizes HACD gene family members in cotton and provides rich genetic resources for increasing cottonseed oil content and improving the nutritional value of cottonseed oil.

Genome-Wide Identification and Expression Analysis of ADK Gene Family Members in Cotton under Abiotic Stress.

Adenosine kinase (ADK) is a key enzyme widely distributed in plants, playing an important role in maintaining cellular energy homeostasis and regulating plant growth, development, and responses to environmental stresses. However, research on ADK genes in cotton (Gossypium hirsutum), an economically significant crop, has been limited. This study identified 92 ADK genes from four cotton species (G. arboreum, G. raimondii, G. hirsutum, and G. barbadense) using HMMER and Local BLASTP methods and classified them into six groups. Chromosomal localization revealed a random distribution of ADK genes in G. hirsutum, with 13 genes located on the At subgenome and 14 genes on the Dt subgenome. Gene structure analysis showed consistency in exon-intron organization within subgroups, while conserved motif analysis identified subgroup-specific motifs, indicating functional diversity. Synteny and collinearity mapping analysis revealed that the primary expansion mechanisms of the ADK gene family in cotton are polyploidy and segmental duplication. Cis-regulatory elements in GhADK promoters were classified into light response, hormone response, developmental regulation, and stress response. We also analyzed the expression patterns of GhADK genes under a low temperature (4 °C) and drought conditions. Most GhADK genes responded to cold stress with different expression patterns, indicating their roles in rapid response and long-term cold adaptation. Under drought stress, expression patterns varied, with some genes showing sustained high expression levels. The qRT-PCR validation of transcriptomic data confirmed the stress-induced expression patterns of selected GhADK genes. Functional analysis through the VIGS silencing of GhADK25 demonstrated its importance in cold and drought stress responses, with silencing resulting in poor growth under stress, highlighting its significance in stress tolerance. This study provides a basis for further understanding the evolutionary relationships and functions of the cotton ADK gene family.

Physiological and structural traits contribute to thermotolerance in wild Australian cotton species.

Five species of cotton (Gossypium) were exposed to 38°C days during early vegetative development. Commercial cotton (Gossypium hirsutum) was contrasted with four wild cotton species (G. australe, G. bickii, G. robinsonii and G. sturtianum) that are endemic to central and northern Australia. Plants were grown at daytime maxima of 30°C or 38°C for 25 d, commencing at the four-leaf stage. Leaf areas and shoot biomass were used to calculate relative rates of growth and specific leaf areas. Leaf gas exchange measurements revealed assimilation and transpiration rates, as well as electron transport rates (ETR) and carboxylation efficiency (CE) in steady-state conditions. Finally, leaf morphological traits (mean leaf area and leaf shape were quantified), along with leaf surface decorations, imaged using scanning electron microscopy. Shoot morphology was differentially affected by heat, with three of the four wild species growing faster at 38°C than at 30°C, whereas early growth in G. hirsutum was severely inhibited by heat. Areas of individual leaves and leaf numbers both contributed to these contrasting growth responses, with fewer, smaller leaves at 38°C in G. hirsutum. CO2 assimilation and transpiration rates of G. hirsutum were also dramatically reduced by heat. Cultivated cotton failed to achieve evaporative cooling, contrasting with the transpiration-driven cooling in the wild species. Heat substantially reduced ETR and CE in G. hirsutum, with much smaller effects in the wild species. We speculate that leaf shape, as assessed by invaginations of leaf margins, and leaf size contributed to heat dispersal differentially among the five species. Similarly, reflectance of light radiation was also highly distinctive for each species. These four wild Australian relatives of cotton have adapted to hot days that are inhibitory to commercial cotton, deploying a range of physiological and structural adaptations to achieve accelerated growth at 38°C.

Advances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding.

Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation in cultivated cotton species. To enhance the genetic diversity crucial for this primary fiber crop, it is essential to augment current germplasm resources. High-throughput sequencing has significantly impacted cotton functional genomics, enabling the creation of diverse mutant libraries and the identification of mutant functional genes and new germplasm resources. Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy to enrich cotton germplasm resources, yielding stable and high-quality raw materials. In this paper, we discuss the good foundation laid by high-throughput sequencing of cotton genome for mutant identification and functional genome, and focus on the construction methods of mutant libraries and diverse sequencing strategies based on mutants. In addition, the important functional genes identified by the cotton mutant library have greatly enriched the germplasm resources and promoted the development of functional genomes. Finally, an innovative strategy for constructing a cotton CRISPR mutant library was proposed, and the possibility of high-throughput screening of cotton mutants based on a UAV phenotyping platform was discussed. The aim of this review was to expand cotton germplasm resources, mine functional genes, and develop adaptable materials in a variety of complex environments.

A super pan‐genome map provides genomic insights into evolution of diploid cotton species

A super pan‐genome map provides genomic insights into evolution of diploid cotton species