High-throughput imaging of fresh-frozen plant reproductive samples in a variable pressure SEM

Conventional light and electron microscopy are the most widely used techniques for examining plant reproductive tissues; however, they are time-consuming or expensive. The anther is the male part of the plant reproductive system. Structural changes drive development, and any structural defect may lead to an increase in fertility or cause sterility; thus, quick detection of structural changes is crucial in reproductive biology. We optimized an existing low-temperature SEM alternative to examine the internal structure of hydrated, fresh-frozen anthers. In contrast with the original technique, our method does not require precooling adhesion (ethanol to fix the specimen), and the cryo-sectioning can be conducted at atmospheric pressure. In addition to enabling the differentiation between aerial and liquid-filled intercellular spaces, this method is expected to facilitate the detection of quick (during a day) developmental changes in plant reproductive tissues, which is a current challenge using conventional approaches.•

This method allows the high-throughput imaging of fresh-frozen plant reproductive samples collected every 10 min, which is important for developmental studies.

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The cryo-images of samples with thickness ranging from 0.2 to 3 mm can be well-preserved at 800X magnification.

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This method does not require chemical processing, critical point drying, customized cryo-accessories, controlled temperature cold stages, or metal coating. This simplified method does not require highly skilled personnel, and it is suitable in most microscopy laboratories.

Estimation of nitrate nitrogen content in cotton petioles under drip irrigation based on wavelet neural network approach using spectral indices

BACKGROUND

Estimation of nitrate nitrogen (NO3--N) content in petioles is one of the key approaches for monitoring nitrogen (N) nutrition in crops. Rapid, non-destructive, and accurate evaluation of NO3--N contents in cotton petioles under drip irrigation is of great significance.

METHODS

In this study, we discussed the use of hyperspectral data to estimate NO3--N contents in cotton petioles under drip irrigation at different N treatments and growth stages. The correlations among trilateral parameters and six vegetation indices and petiole NO3--N contents were first investigated, after which a traditional regression model for petioles NO3--N content was established. A wavelet neural network (WNN) model for estimating petiole NO3--N content was also established. In addition, the performance of WNN was compared to those of random forest (RF), radial basis function neural network (RBF) and back propagation neural network (BP).

RESULTS

Between the blue edge amplitude (Db) and blue edge area (SDb) of the blue edge parameters was the optimal index for the estimation model of petiole NO3--N content. We found that the prediction results of the blue edge parameters and WNN were 7.3% higher than the coefficient of determination (R2) of the first derivative vegetation index and WNN. Root mean square error (RMSE) and mean absolute error (MAE) were 25.2% and 30.9% lower than first derivative vegetation, respectively, and the performance was better than that of RF, RBF and BP.

CONCLUSIONS

An inexpensive approach consisting of the WNN algorithm and blue edge parameters can be used to enhance the accuracy of NO3--N content estimation in cotton petioles under drip irrigation.

Discrimination of cellulose fabrics using infrared spectroscopy and newly developed discriminant analysis

Identifying cellulose fibers in fabric products is necessary for quality control and appropriate distribution but can be difficult because of their similarities. A novel technique to identify cellulose fabrics has been developed that uses infrared spectroscopy with the attenuated total reflection (ATR) method, evaluated with an improved Fisher's discriminant analysis including regularization coefficients and orthogonal decompositions. Sequential discrimination of six different types of cellulose fibers -cotton, ramie, and linen, which are natural fibers, and rayon, cupra, and lyocell, which are regenerated fibers- was achieved using the new technique.

The lincRNA XH123 is involved in cotton cold-stress regulation

We characterize a functional lincRNA, XH123 in cotton seedling in defense of cold stress. The silencing of XH123 leads to increased sensitivity to cold stress and the decay of chloroplast. Cotton, which originated from the arid mid-American region, is one of the most important cash crops worldwide. Cultivated cotton is now widely spread throughout high-altitude regions such as those in the far northwest of Asia. In such areas, spring temperatures below 12 ℃ impose cold stress on cotton seedlings, with concomitant threat of lost yield and productivity. It is documented that cold stress can induce differential expression of long noncoding RNAs (lncRNAs) in cotton; however, it is not yet clear if these cold-responsive lncRNAs are actively involved with tolerance of cold stress at the molecular level. Here, we select ten long intergenic non-coding RNAs as candidate genes and use virus-induced gene silencing and additional cold treatments to examine their roles in the response to cold stress during the cotton seedling stage. One such gene, XH123, was revealed to be involved in tolerance of cold stress. Specifically, XH123-silenced plants demonstrated sensitivity to cold stress, exhibiting chloroplast damage and increased endogenous levels of reactive oxygen species. The transcriptome profile of XH123-silenced seedlings was similar to that of cold-stressed seedlings having the known cold stress gene PIF3 silenced. These results imply that the lincRNA XH123 is actively involved with cold stress regulation in cotton during the seedling stage.

Genetic modification of Gossypium arboreum universal stress protein (GUSP1) improves drought tolerance in transgenic cotton (Gossypium hirsutum)

Cotton crop suffers shortage of irrigation water at reproductive stage which reduces the yield and fibre quality. Universal stress proteins belong to Pfam00582 which enables several plants to cope with multiple stresses via ATP binding. GUSP1 (Gossypium arboreum USP) is one of such proteins; its amino acids were mutated after in silico simulations including homology modeling and molecular docking analysis. Transgenic cotton plants were developed through Agrobacterium mediated genetic transformation by using mutated pmGP1 and non mutated pGP1 constructs under CaMV35S promoter. PCR and semi-quantitative PCR analyses confirmed the amplification and expression of transgene in transgenic plants. It was revealed that leaf relative water content, total chlorophyll content, CO₂ assimilation as net photosynthesis, stomatal conductance, total soluble sugars and proline content was significantly increased at P ≤ 0.0001 and P ≤ 0.001 in both the pmGP1 and pGP1 transgenic plants as compared to non transgenic control plants. Moreover, relative membrane permeability and the transpiration rate were reduced significantly at P ≤ 0.0001 and P ≤ 0.001 respectively in transgenic plants under drought stress. Furthermore, the T1 transgenic seedlings containing pmGP1 mutated construct showed longer roots under desiccation stress imposed by 5% PEG. Transgene inheritance into the T1 progeny plants was confirmed by amplification through PCR and integration through Southern blot. Hence, our results pave the way to utilize the mutagenized known genes for increasing endurance of plants under drought stress. This will help to increase our understanding of drought tolerance/ sensitivity in cotton plants at the molecular level.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01048-5.

Elevation of GhDREB1B transcription by a copy number variant significantly improves chilling tolerance in cotton

The elevation of transcript levels of GhDREB1B causes the accumulation of osmoregulants and mitigation of reactive oxygen species, which contributes to the enhanced resistance to chilling stress in AiSheng98 cotton. Low temperature is one of the key environmental stresses that impairs cotton growth and restricts fiber productivity. Dehydration responsive element binding (DREB) transcription factors play an important role in cold response in plants by modulating the transcription level of cold-responsive genes to protect the plants from low-temperature stress. Here, we showed that GhDREB1B, a copy number variant in the AiSheng98 (AS98) cotton mutant, significantly improved chilling tolerance in cotton seedlings, while silencing of GhDREB1B made transgenic cotton sensitive to chilling stress in AS98 cotton compared with control plants. Elevated GhDREB1B transcript level activated the expression of major cold-responsive genes. Genome-wide expression profiling by RNA sequencing revealed the upregulation of genes related to fatty acids, lipid proteins, osmoprotection, and anti-oxidative enzymes in AiSheng98. Excessive accumulation of malondialdehyde (MDA) and higher ion leakage rates occurred in wild-type LFH10 plants when compared to those of Aisheng98 during chilling stress, signifying lower chilling tolerance in the wild-type than in Aisheng98. Furthermore, the Aisheng98 mutant under chilling stress accumulated higher levels of free proline and soluble sugar than LFH10 accumulated. These results suggest that GhDREB1B is a positive regulator and its variant can alter the expression patterns of major low-temperature stress-related genes and enhance chilling tolerance in cotton.

Disruption of topologically associating domains by structural variations in tetraploid cottons

Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. We observed that approximately 16% of SVs occurred in TAD boundary regions that were called boundary affecting-structural variations (BA-SVs), and had a large effect on disrupting TAD organization. Nevertheless, SVs preferred occurring in TAD interior instead of TAD boundary, probably associated with the relaxed evolutionary selection pressure. We noticed the biased evolution of the At and Dt subgenomes of tetraploid cottons, in terms of SV-mediated disruption of 3D genome structure relative to diploids. In addition, we provide evidence showing that both SVs and TAD disruption could lead to expression difference of orthologous genes. This study advances our understanding of the effect of SVs on 3D genome organization and gene expression regulation in plants.

Genome-wide identification and molecular evolution analysis of the heat shock transcription factor (HSF) gene family in four diploid and two allopolyploid Gossypium species

Heat shock transcription factors (HSFs) can regulate plant development and stress response. The comprehensive evolutionary history of the HSF family remains elusive in cotton. In this study, each cotton species had 78 members in Gossypium barbadense and Gossypium hirsutum. The diploid species had 39 GaHSFs in Gossypium arboreum, 31 GrHSFs in Gossypium raimondii, 34 GtHSFs in Gossypium turneri, and 34 GlHSFs in Gossypium longicalyx. The HSF family in cotton can be classified into three subfamilies, with seven groups in subfamily A and five groups in subfamily B. Different groups exhibited distinct gene proportions, conserved motifs, gene structures, expansion rates, gene loss rates, and cis-regulatory elements. The paleohexaploidization event led to the expansion of the HSF family in cotton, and the gene duplication events in six Gossypium species were inherited from their common ancestor. The HSF family in diploid species had a divergent evolutionary history, whereas two cultivated tetraploids presented a highly conserved evolution of the HSF family. The HSF members in At and Dt subgenomes of the cultivated tetraploids showed a different evolution from their corresponding diploid donors. Some HSF members were regarded as key candidates for regulating cotton development and stress response. This study provided the comprehensive information on the evolutionary history of the HSF family in cotton.

Pyramiding of cry toxins and methanol producing genes to increase insect resistance in cotton

The idea of enhanced methanol production from cell wall by pectin methyl esterase enzymes (PME) combined with expression of cry genes from Bacillus thuringiensis as a strategy to improve insect pest control in cotton is presented. We constructed a cassette containing two cry genes (cry1Fa and Cry32Aa) and two pme genes, one from Arabidopsis thaliana (AtPME), and other from Aspergillus. niger (AnPME) in pCAMBIA1301 plant expression vector using CAMV-35S promoter. This construction was transformed in Eagle-2 cotton variety by using shoot apex-cut Agrobacterium-mediated transformation. Expression of cry genes and pme genes was confirmed by qPCR. Methanol production was measured in control and in the cry and pme transformed plants showing methanol production only in transformed plants, in contrast to the non-transgenic cotton plants. Finally, insect bioassays performed with transgenic plants expressing cry and pme genes showed 100% mortality for Helicoverpa armigera (cotton bollworm) larvae, 70% mortality for Pectinophora gossypiella (pink bollworm) larvae and 95% mortality of Earias fabia, (spotted bollworm) larvae, that was higher than the transgenic plants expressing only cry genes that showed 84%, 49% and 79% mortality, respectively. These results demonstrate that Bt. cry-genes coupled with pme genes are an effective strategy to improve the control of different insect pests.

Assessment of genetically modified cotton GHB614 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-018)

Following the submission of application EFSA-GMO-RX-018 under Regulation (EC) No 1829/2003 from BASF Agricultural Solutions Seed US LLC, the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the herbicide-tolerant genetically modified cotton GHB614, for food and feed uses, excluding cultivation within the European Union. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. The GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-018 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on cotton GHB614.

Diversity and Spatiotemporal Dynamics of Fungal Communities in the Rhizosphere Soil of Cotton in the Arid Region of Northwest China

This study aimed to investigate the fungal diversity and its temporal and spatial dynamics in the rhizosphere soil of healthy cotton by high-throughput sequencing. We studied species richness, composition, and distribution of cotton rhizosphere fungal community with respect to location (Alaer, Kuerle, Tumushuke, Hami, Shihezi, Wusu, and Jinghe) and plant growth period (seedling stage, bud stage, flowering stage, and boll-opening stage) using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. A total of 1,838,454 fungal nuclear ribosomal internal transcribed spacer region sequences (rRNA ITS) were obtained from all cotton plants sampled at different growth stages in the seven locations in Xinjiang. The most abundant fungal group in the cotton rhizosphere was the Ascomycota (78.72%), followed by the Zygomycota (9.56%) and Basidiomycota (2.77%). These sequences revealed an enormous number of operational taxonomic units (OTUs) in cotton (1802 unique OTUs), with 67-464 OTUs in a single cotton sample, at a 3% threshold and a sequencing depth of 30,000 sequences. We identified 33 classes and 389 genera from the resulting 1,800,714 sequences. Sordariomycetes was the most frequent class in all samples, followed by Leotiomycetes and Eurotiomycetes. There were some differences in OTUs among different growth stages, but the differences were not significant, with 382 OTUs (14.66%) being common to each of the stages. A marked difference in the diversity of fungi in the rhizosphere soil of cotton was evident among the different locations, with the highest number of OTUs being detected in Jinghe (1084 OTUs) and clusters of OTUs representative of northern and eastern Xinjiang being detected. There were significantly more tags of Mortierella in Jinghe and Wusu than in the other sampling sites. The dynamics of the rhizosphere fungal communities were influenced by sampling sites. To the best of our knowledge, the current study is the first application of PCR-based Illumina to characterize and compare the fungal biodiversity in multiple rhizosphere soil samples from cotton.

Genome wide analysis of IQD gene family in diploid and tetraploid species of cotton (Gossypium spp.)

Calmodulin (CaM) is considered as the most significant Ca²⁺ signaling messenger that mediate various biochemical and physiological reactions. IQ domain (IQD) proteins are plant specific CML/CaM calcium binding which are characterized by domains of 67 amino acids. 50, 50, 94, and 99 IQD genes were detected from G. arboreum (A2), G. raimondii (D5), G. barbadense (AD2) and G. hirsutum (AD1) respectively. Existence of more orthologous genes in cotton species than Arabidopsis, advocated that polyploidization produced new cotton specific orthologous gene clusters. Duplication of gene events depicts that IQD gene family of cotton evolution was under strong purifying selection. G. hirsutum exhibited high level synteny. GarIQD25 exhibited high expression in stem, root, flower, ovule and fiber in G. arboreum. In G. raimondii, GraIQD03 demonstrated upregulation across stem, ovule, fiber and seed. GbaIQD11 and GbaIQD62 exhibited upregulation in fiber development in G. barbadense. GhiIQD69 recognized as main candidate genes for plant parts, floral tissues, fiber and ovule development. Promotor analysis identified cis-regulatory elements were involved in plant growth and development. Overwhelmingly, present study paves the way to better understand the evolution of cotton IQD genes and lays a foundation for future investigation of IQD in cotton.

Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton

Cotton fiber mutants are valuable resources for studying functions of altered genes and their roles in fiber development. The n₄^t is a recessive tufted-fuzzless seed mutant created through chemical mutagenesis with ethyl methanesulfonate. Genetic analysis indicated that the tufted-fuzzless phenotype is controlled by a single recessive locus. In this study, we developed an F₂ population of 602 progeny plants and sequenced the genomes of the parents and two DNA bulks from F₂ progenies showing the mutant phenotype. We identified DNA sequence variants between the tufted-fuzzless mutant and wild type by aligning the sequence reads to the reference TM-1 genome and designed subgenome-specific SNP markers. We mapped the n₄^t locus on chromosome D04 within a genomic interval of about 411 kb. In this region, seven genes showed significant differential expression between the tufted-fuzzless mutant and wild type. Possible candidate genes are discussed in this study. The utilization of the n₄^t mutant along with other fiber mutants will facilitate our understanding of the molecular mechanisms of cotton fiber cell growth and development.

Ectopic expression of GhIQD14 (cotton IQ67 domain-containing protein 14) causes twisted organ and modulates secondary wall formation in Arabidopsis

In plants, although KNOX genes are known to regulate secondary cell wall (SCW) formation, their protein-regulating mechanisms remain largely unknown. Here, we showed that GhKNL1, which regulates SCW formation and fiber development in cotton, could interact with an IQ67 domain containing protein (GhIQD14) in yeast. Confocal observation showed that GhIQD14 was localized to the microtubules. In Arabidopsis, ectopic expression of GhIQD14 caused hypocotyls to be sensitive to microtubule depolymerization agent, organ twisting of seedlings, trichomes, rosette leaves, and capsules, as well as severely irregular xylem vessels and thicker interfascicular fiber cell walls in the inflorescence stem. Furthermore, we found that GhIQD14 interacted with AtKNAT7 in vivo, and instantaneous co-expression of GhIQD14 and AtKNAT7 in tobacco showed that GhIQD14 weakened the distribution of AtKNAT7 in the nucleus, bringing it into the microtubules, thus affecting the SCW formation related genes expression. Our results suggested that GhIQD14 might be involved in the morphological development and SCW formation in cotton.

Amination of cotton fiber using polyethyleneimine and its application as an adsorbent to directly remove a harmful cyanobacterial species, Microcystis aeruginosa, from an aqueous medium

In the present study, we applied an adsorption-based strategy for the removal of a harmful cyanobacterial species, Microcystis aeruginosa, using cotton fiber. Considering the negatively charged surface properties of M. aeruginosa cells in aqueous phases, aminated cotton fibers were prepared through polyethyleneimine (PEI) modification on the pristine cotton fibers. The aminated surface properties of PEI-modified cotton fiber (PEI-cotton) were confirmed by Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), and potentiometric titration analyses. The pristine cotton fiber could not remove the M. aeruginosa cells, but the PEI-cotton could efficiently remove 98.7% of M. aeruginosa cells from the aqueous medium. In addition, removed cells could be observed on the sorbent surface by field emission scanning electron microscopy (FE-SEM) analysis. PEI-cotton fabricated in 3% PEI solution could remove M. aeruginosa cells (97.9%) more efficiently compared to that fabricated in 1% (82.1%) and 2% (86.2%) of PEI solutions. From the toxicity assessment of the PEI-cotton using Daphnia magna, negligible toxicity of PEI-cotton was confirmed. Our results indicate that the application of PEI-cotton fibers for the removal of M. aeruginosa cells could be suggested as a feasible, effective, and eco-friendly method of harmful algal bloom (HAB) control in water resources.

Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress

Background

Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited.

Results

Our study was conducted based on the DUF668 gene family identified from cotton genome sequencing. Phylogenetic analysis showed that the DUF668 family genes can be classified into four subgroups in cotton. We identified 32 DUF668 genes, which are distributed on 17 chromosomes and most of them located in the nucleus of Gossypium hirsutum. Gene structure and motif analyses revealed that the members of the DUF668 gene family can be clustered in G. hirsutum into two broad groups, which are relatively evolutionarily conserved. Transcriptome data analysis showed that the GhDUF668 genes are differentially expressed in different tissues under various stresses (cold, heat, drought, salt, and Verticillium dahliae), and expression is generally increased in roots and stems. Promoter and expression analyses indicated that Gh_DUF668–05, Gh_DUF668–08, Gh_DUF668–11, Gh_DUF668–23 and Gh_DUF668–28 in G. hirsutum might have evolved resistance to adverse stress. Additionally, qRT-PCR revealed that these 5 genes in four cotton lines, KK1543 (drought resistant), Xinluzao 26 (drought sensitive), Zhongzhimian 2 (disease resistant) and Simian 3 (susceptible), under drought and Verticillium wilt stress were all significantly induced. Roots had the highest expression of these 5 genes before and after the treatment. Among them, the expression levels of Gh_DUF668–08 and Gh_DUF668–23 increased sharply at 6 h and reached a maximum at 12 h under biotic and abiotic stress, which showed that they might be involved in the process of adverse stress resistance in cotton.

Conclusion

The significant changes in GhDUF668 expression in the roots after adverse stress indicate that GhDUF668 is likely to increase plant resistance to stress. This study provides an important theoretical basis for further research on the function of the DUF668 gene family and the molecular mechanism of adverse stress resistance in cotton.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07716-w.

Cerium oxide nanoparticles improve cotton salt tolerance by enabling better ability to maintain cytosolic K+/Na+ ratio

Background

Salinity is a worldwide factor limiting the agricultural production. Cotton is an important cash crop; however, its yield and product quality are negatively affected by soil salinity. Use of nanomaterials such as cerium oxide nanoparticles (nanoceria) to improve plant tolerance to stress conditions, e.g. salinity, is an emerged approach in agricultural production. Nevertheless, to date, our knowledge about the role of nanoceria in cotton salt response and the behind mechanisms is still rare.

Results

We found that PNC (poly acrylic acid coated nanoceria) helped to improve cotton tolerance to salinity, showing better phenotypic performance, higher chlorophyll content (up to 68% increase) and biomass (up to 38% increase), and better photosynthetic performance such as carbon assimilation rate (up to 144% increase) in PNC treated cotton plants than the NNP (non-nanoparticle control) group. Under salinity stress, in consistent to the results of the enhanced activities of antioxidant enzymes, PNC treated cotton plants showed significant lower MDA (malondialdehyde, up to 44% decrease) content and reactive oxygen species (ROS) level such as hydrogen peroxide (H₂O₂, up to 79% decrease) than the NNP control group, both in the first and second true leaves. Further experiments showed that under salinity stress, PNC treated cotton plants had significant higher cytosolic K⁺ (up to 84% increase) and lower cytosolic Na⁺ (up to 77% decrease) fluorescent intensity in both the first and second true leaves than the NNP control group. This is further confirmed by the leaf ion content analysis, showed that PNC treated cotton plants maintained significant higher leaf K⁺ (up to 84% increase) and lower leaf Na⁺ content (up to 63% decrease), and thus the higher K⁺/Na⁺ ratio than the NNP control plants under salinity stress. Whereas no significant increase of mesophyll cell vacuolar Na⁺ intensity was observed in PNC treated plants than the NNP control under salinity stress, suggesting that the enhanced leaf K⁺ retention and leaf Na⁺ exclusion, but not leaf vacuolar Na⁺ sequestration are the main mechanisms behind PNC improved cotton salt tolerance. qPCR results showed that under salinity stress, the modulation of HKT1 but not SOS1 refers more to the PNC improved cotton leaf Na⁺ exclusion than the NNP control.

Conclusions

PNC enhanced leaf K⁺ retention and Na⁺ exclusion, but not vacuolar Na⁺ sequestration to enable better maintained cytosolic K⁺/Na⁺ homeostasis and thus to improve cotton salt tolerance. Our results add more knowledge for better understanding the complexity of plant-nanoceria interaction in terms of nano-enabled plant stress tolerance.

Graphic abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-021-00892-7.

Genome-wide identification, evolutionary estimation and functional characterization of two cotton CKI gene types

BACKGROUND

Casein kinase I (CKI) is a kind of serine/threonine protein kinase highly conserved in plants and animals. Although molecular function of individual member of CKI family has been investigated in Arabidopsis, little is known about their evolution and functions in Gossypium.

RESULTS

In this study, five cotton species were applied to study CKI gene family in cotton, twenty-two species were applied to trace the origin and divergence of CKI genes. Four important insights were gained: (i) the cotton CKI genes were classified into two types based on their structural characteristics; (ii) two types of CKI genes expanded with tetraploid event in cotton; (iii) two types of CKI genes likely diverged about 1.5 billion years ago when red and green algae diverged; (iv) two types of cotton CKI genes which highly expressed in leaves showed stronger response to photoperiod (circadian clock) and light signal, and most two types of CKI genes highly expressed in anther showed identical heat inducible expression during anther development in tetraploid cotton (Gossypium hirsutum).

CONCLUSION

This study provides genome-wide insights into the evolutionary history of cotton CKI genes and lays a foundation for further investigation of the functional differentiation of two types of CKI genes in specific developmental processes and environmental stress conditions.

Cotton DMP gene family: characterization, evolution, and expression profiles during development and stress

Members of DOMAIN OF UNKNOWN FUNCTION 679 membrane protein (DMP) gene family, a type of plant-specific membrane proteins, have been proposed to function in various physiological processes such as reproductive development and senescence in plants. Here, a total of 174 DMP genes were identified and analyzed in 16 plant species (including 58 DMPs in four cotton species). Phylogenetic analysis showed that these DMPs could be clustered into five subfamilies (I-V). 137 duplicated cotton gene pairs were identified and most duplicate events were formed by whole-genome duplication (WGD)/segmental duplications. Expression analysis revealed that most of cotton DMPs were mainly expressed in the reproductive organs (the sepal, petal, pistil and anther) and the fiber of secondary cell wall stage. GhDMPs promoter regions containing the different cis-elements also showed different responses to abiotic stress. In addition, gene interaction networks showed that DMPs, as an endomembrane system, were involved in plant senescence process and flower reproductive development. We speculated GhDMP8-A/-D, GbDMP8-A/-D could be used as some candidate gene for inducing cotton haploid. This genome-wide study provides a systematic analysis of the cotton DMP gene family, and further insights towards understanding the potential functions of candidate genes.

Genome-wide identification, characterization and expression profiles of the CCD gene family in Gossypium species

Carotenoid cleavage dioxygenases (CCDs) are a group of enzymes that catalyze the selective oxidative cleavage steps from carotenoids to apocarotenoids, which are essential for the synthesis of biologically important molecules such as retinoids, and the phytohormones abscisic acid (ABA) and strigolactones. In addition, CCDs play important roles in plant biotic and abiotic stress responses. Till now, a comprehensive characterization of the CCD gene family in the economically important crop cotton (Gossypium spp.) is still missing. Here, we performed a genome-wide analysis and identified 33, 31, 16 and 15 CCD genes from two allotetraploid Gossypium species, G. hirsutum and G. barbadense, and two diploid Gossypium species, G. arboreum and G. raimondii, respectively. According to the phylogenetic tree analysis, cotton CCDs are classified as six subgroups including CCD1, CCD4, CCD7, CCD8, nine-cis-epoxycarotenoid dioxygenase (NCED) and zaxinone synthase (ZAS) sub-families. Evolutionary analysis shows that purifying selection dominated the evolution of these genes in G. hirsutum and G. barbadense. Predicted cis-acting elements in 2 kb promoters of CCDs in G. hirsutum are mainly involved in light, stress and hormone responses. The transcriptomic analysis of GhCCDs showed that different GhCCDs displayed diverse expression patterns and were ubiquitously expressed in most tissues; moreover, GhCCDs displayed specific inductions by different abiotic stresses. Quantitative reverse-transcriptional PCR (qRT-PCR) confirmed the induction of GhCCDs by heat stress, salinity, polyethylene glycol (PEG) and ABA application. In summary, the bioinformatics and expression analysis of CCD gene family provide evidence for the involvement in regulating abiotic stresses and useful information for in-depth studies of their biological functions in G. hirsutum.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02805-9.

Relationship between imidacloprid residues and control effect on cotton aphids in arid region

In this case, the dissipation and residues of imidacloprid as well as its control efficacy against aphids (Aphis gossypii Glover) in cotton cropping system were reported. After the final spray at the rates of 10.5-42.5 g a.i. ha^-1, the initial deposits were 0.59-2.25 mg kg^-1 with half-lives of 2.12-2.84 days on leaves and 0.06-0.21 mg kg^-1 with half-lives of 1.51-4.20 days in soil, respectively. The initial residues were significantly higher with longer persistence in the upper position of the leaf than in middle and lower positions. The different application dosages could induce a significant difference in the initial deposits, but not show consistent correlation with the dissipation rate. The repeated applications of imidacloprid could alter its residue levels and dissipation rates. The long-term residue concentrations of imidacloprid (60 days after the final application) reached to the nondetectable level in soil. Combined with the control efficacy results, it was considered that the recommended dose of imidacloprid on cotton could be used effectively and safe in this arid area from the view of crop protection and environmental contamination.

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection

BACKGROUND

Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.

RESULTS

We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.

CONCLUSIONS

This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

The water footprint of irrigation-supplemented cotton and mung-bean crops in Northern Ethiopia

Global freshwater resources are getting scarcer and scarcer due to the ever-increasing population, climate change, and other human activities. Hence, assessing the consumption of freshwater by different consumers is a key to efficiently utilize the resource. In this study, the Water Footprint Assessment (WFA) tool was used to determine the water footprint (WF) of Center Pivot (CP) irrigated cotton and mung-bean production using two approaches, namely, CROPWAT and field-data based methods. Based on the CROPWAT-based estimates, the average total WF of cotton was found to be 2745 m³/ton. Out of this, the green and blue WF contributed to an average of 35% and 65 %, respectively. For mung-bean, the total WF was 6561m³/ton, of which blue WF covered around 93 %. Comparison of the blue WF from CROPWAT and field-data based estimates showed a good agreement (nRMSE = 4.5 %, nMBE = 10.7 % and relative error/RE/ranging from 0.8 to 17% for cotton and 12.6% for mung-bean) and no significant difference (p = 0.456) was obtained between the two estimates. The effect of planting date on the WF estimation also showed a small variation of 0.7%–6.6 % for cotton and up to 12% for mung-bean. However, major reductions were obtained on the blue WF of cotton and mung-bean as a result of changing planting dates by about two months prior to the baseline planting dates. In this study, it is concluded that WF assessment could be satisfactorily estimated using CROPWAT model if supported with field obtained information such as soil, crop, and weather data. Another finding of the present study was that, changing planting dates close to the major rainy months could substantially contribute to reducing the blue WF in similar climates.

An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid 'Huaza Mian H318', as revealed by genome-wide gene expression analysis

Background

Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton.

Results

The elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4–5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318.

Conclusion

The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07580-8.

A novel synthetic approach to produce cellulose-based woven scaffolds impregnated with bioactive glass for bone regeneration

Tissue-engineering has become the best alternative solution for replacing the damaged tissues. However, the cost of scaffold materials is still a big challenge, so the development of cost-effective scaffolds is highly encouraged. In this research, different types of cotton textile-scaffolds as a cellulosic material were developed to be utilized as a substrate for cells proliferation. They were loaded with bioactive glass (BG) doped with silver nanoparticles (AgNPs). The effect of the loaded materials on the physicochemical and mechanical characteristics of the cellulosic textile scaffolds was investigated by means of FTIR, contact angle, physical and mechanical properties of the cotton fabrics, in addition to assessing their antimicrobial activity. Moreover, the biomineralization was evaluated after soaking in Simulated Body Fluid (SBF) using ICP and SEM accessorized with EDX. Cells proliferation capacities of the developed cellulosic woven-scaffolds were assessed against MG63 cell line at different incubation times. The physicochemical and mechanical features of these fabrics demonstrated a positive influence for the existence of BG impregnation, especially those doped with AgNPs. The antimicrobial features were also affirmed for the cellulosic scaffolds. More pronounced influence was observed on the biomineralization of the scaffold impregnated with BG doped with 0.5% Ag. The percentages of proliferated cells were very close to negative control (100% ± 10). This approach offers a novel and affordable alternative cellulosic woven-scaffolds for bone regeneration.