Integrative analyses of long and short-read RNA sequencing reveal the spliced isoform regulatory network of seedling growth dynamics in upland cotton.

The polyploid genome of cotton has significantly increased the transcript complexity. Recent advances in full-length transcript sequencing are now widely used to characterize the complete landscape of transcriptional events. Such studies in cotton can help us to explore the genetic mechanisms of the cotton seedling growth. Through long-read single-molecule RNA sequencing, this study compared the transcriptomes of three yield contrasting genotypes of upland cotton. Our analysis identified different numbers of spliced isoforms from 31,166, 28,716, and 28,713 genes in SJ48, Z98, and DT8 cotton genotypes, respectively, most of which were novel compared to previous cotton reference transcriptomes, and showed significant differences in the number of exon structures and coding sequence length due to intron retention. Quantification of isoform expression revealed significant differences in expression in the root and leaf of each genotype. An array of key isoform target genes showed protein kinase or phosphorylation functions, and their protein interaction network contained most of the circadian oscillator proteins. Spliced isoforms from the GIGANTEA (GI) protien were differentially regulated in each genotype and might be expected to regulate translational activities, including the sequence and function of target proteins. In addition, these spliced isoforms generate diurnal expression profiles in cotton leaves, which may alter the transcriptional regulatory network of seedling growth. Silencing of the novel spliced GI isoform Gh_A02G0645_N17 significantly affected biomass traits, contributed to variable growth, and increased transcription of the early flowering pathway gene ELF in cotton. Our high-throughput hybrid sequencing results will be useful to dissect functional differences among spliced isoforms in the polyploid cotton genome.

Defect Engineering in CuS1- x Nanoflowers Enables Low-Overpotential and Long-Cycle-Life of Lithium-Oxygen Batteries.

The defect engineering is essential for the development of efficient cathode catalysts for lithium-oxygen batteries. Herein, CuS1 -x nanoflowers are fabricated by microwave hydrothermal method. Through theoretical and experimental analysis, the S vacancies are observed, which result in augmented charge around Cu, improved adsorption of LiO2, and reduced overpotential. On the one hand, the generated electronic defects cause the Fermi level to shift toward the conduction band, which enhances the electronic conductivity and ion transfer. On the other hand, the increased S vacancies provide a large number of Cu active sites, which increase the charge transfer from Cu to LiO2, which improves the stability of the intermediate adsorption. Interactively, CuS1- x catalyst obtains a capacity of 23,227 mAh g-1 and a cycle life of 225 at 500 mA g-1. This work will be helpful for obtaining an efficient cathode catalyst by providing a deep understanding of vacancy modulation in advanced catalysts.

The SUMO ligase MMS21 profoundly influences maize development through its impact on genome activity and stability.

The post-translational addition of SUMO plays essential roles in numerous eukaryotic processes including cell division, transcription, chromatin organization, DNA repair, and stress defense through its selective conjugation to numerous targets. One prominent plant SUMO ligase is METHYL METHANESULFONATE-SENSITIVE (MMS)-21/HIGH-PLOIDY (HPY)-2/NON-SMC-ELEMENT (NSE)-2, which has been connected genetically to development and endoreduplication. Here, we describe the potential functions of MMS21 through a collection of UniformMu and CRISPR/Cas9 mutants in maize (Zea mays) that display either seed lethality or substantially compromised pollen germination and seed/vegetative development. RNA-seq analyses of leaves, embryos, and endosperm from mms21 plants revealed a substantial dysregulation of the maize transcriptome, including the ectopic expression of seed storage protein mRNAs in leaves and altered accumulation of mRNAs associated with DNA repair and chromatin dynamics. Interaction studies demonstrated that MMS21 associates in the nucleus with the NSE4 and STRUCTURAL MAINTENANCE OF CHROMOSOMES (SMC)-5 components of the chromatin organizer SMC5/6 complex, with in vitro assays confirming that MMS21 will SUMOylate SMC5. Comet assays measuring genome integrity, sensitivity to DNA-damaging agents, and protein versus mRNA abundance comparisons implicated MMS21 in chromatin stability and transcriptional controls on proteome balance. Taken together, we propose that MMS21-directed SUMOylation of the SMC5/6 complex and other targets enables proper gene expression by influencing chromatin structure.

The prevalence and characteristics of alexithymia in stroke patients: a systematic review and meta-analysis.

BACKGROUND: Previous studies have indicated the potential occurrence of alexithymia among stroke patients, yet the prevalence of alexithymia in this population remains disparate across different investigations without a synthesized overview. AIM: To systematically evaluate the prevalence and characteristics of alexithymia in stroke patients. METHODS: A systematic review and meta-analysis was conducted following the PRISMA guidelines. PubMed, Embase, Web of Science, The Cochrane Library, CINAHL, China Knowledge Resource Integrated Database (CNKI), Wanfang Database, Chinese Biomedical Database, and Weipu Database (VIP) were searched from inception to December 31,2022, two independent researchers extracted data and evaluated article quality. RESULTS: Seventeen studies were included, reporting on the prevalence of alexithymia or Toronto Alexithymia Scale-20 (TAS-20) scores among stroke patients. The pooled prevalence was found to be 35.0% (95%CI= 23.0-47.0%; I2 =97.5%), and the total scores (TS) of TAS-20 was 59.90 (95% CI=56.34-63.47; I2 =100.0%). Subgroup analysis revealed significant variation in TAS-20 scores across different geographical regions. Specifically, the total TAS-20 score in Chinese stroke patients (62.95, 95%CI=58.75-67.14; I2=100%) was higher compared to non-Chinese stroke patients (52.58, 95%CI=49.12-56.04; I2 = 99.0%). CONCLUSIONS: The prevalence of alexithymia is high among stroke patients, with TAS-20 scores surpassing those observed in patients with certain other medical conditions. This underscores the importance of addressing alexithymia in stroke patients promptly through assessment and intervention to mitigate negative emotional consequences and enhance overall quality of life. Future research could explore the influence of demographic factors such as age and sex on alexithymia in stroke patients, enabling a more comprehensive understanding of alexithymia.

MOF-Derived Mn2 O3 Nanocage with Oxygen Vacancies as Efficient Cathode Catalysts for Li-O2 Batteries.

Designing efficient and cost-effective electrocatalysts is the primary imperative for addressing the pivotal concerns confronting lithium-oxygen batteries (LOBs). The microstructure of the catalyst is one of the key factors that influence the catalytic performance. This study proceeds to the advantage of metal-organic frameworks (MOFs) derivatives by annealing manganese 1,2,3-triazolate (MET-2) at different temperatures to optimize Mn2 O3 crystals for special microstructures. It is found that at 350 °C annealing temperature, the derived Mn2 O3 nanocage maintains the structure of MOF, the inherited high porosity and large specific surface area provide more channels for Li+ and O2 diffusion, beside the oxygen vacancies on the surface of Mn2 O3 nanocages enhance the electrocatalytic activity. With the synergy of unique structure and rich oxygen vacancies, the Mn2 O3 nanocage exhibits ultrahigh discharge capacity (21 070.6 mAh g-1 at 500 mA g-1 ) and excellent cycling stability (180 cycles at the limited capacity of 600 mAh g-1 with a current of 500 mA g-1 ). This study demonstrates that the Mn2 O3 nanocage structure containing oxygen vacancies can significantly enhance catalytic performance for LOBs, which provide a simple method for structurally designed transition metal oxide electrocatalysts.

Biochar nanosphere-functionalized carbon fibers for in-tube solid-phase microextraction of polycyclic aromatic hydrocarbons in environmental water followed by liquid chromatography and diode array detection.

In order to improve the extraction ability of carbon fibers (CFs) for microextraction of polycyclic aromatic hydrocarbons (PAHs), biochar nanospheres derived from glucose were in-situ grown onto the surface of CFs via hydrothermal synthesis. The surface morphology and elemental composition of biochar nanospheres-CFs were investigated by scanning electron microscopy and X-ray photoelectron spectroscopy. Thereafter, the biochar nanosphere-CFs were pulled into the polyetheretherketone tube for solid-phase microextraction, and the tube was combined with high-performance liquid chromatography-diode array detector to online detect PAHs. With the help of π-stacking, hydrophobic, and hydrophilic effect of biochar nanospheres, the extraction efficiency of CFs was greatly enhanced (enrichment factor increased by 293% compared with  the original). The conditions affecting the analytical performance (sampling volume, sampling rate, methanol content, and desorption time) were investigated. Under the optimal conditions, an online analytical method for microextraction and determination of several PAHs was developed, and satisfactory results were achieved. The limits of detection were 0.003-0.010 ng mL-1 owing to high enrichment effect (2973-3600), linearity ranged from  0.010-15.0 ng mL-1, and relative standard deviations were 0.4%-1.6% (intra-day) and 2.4%-4.4% (inter-day), respectively. The method was applied to analyze environmental water samples (rain water, snow water, and river water), and spiked recoveries within 80.0%-119% were obtained.

Comparative Transcriptome Profiling of CMS-D2 and CMS-D8 Systems Characterizes Fertility Restoration Genes Network in Upland Cotton.

Resolving the genetic basis of fertility restoration for cytoplasmic male sterility (CMS) can improve the efficiency of three-line hybrid breeding. However, the genetic determinants of male fertility restoration in cotton are still largely unknown. This study comprehensively compared the full-length transcripts of CMS-D2 and CMS-D8 systems to identify potential genes linked with fertility restorer genes Rf1 or Rf2. Target comparative analysis revealed a higher percentage of differential genes in each restorer line as compared to their corresponding sterile and maintainer lines. An array of genes with specific expression in the restorer line of CMS-D2 had functional annotations related to floral development and pathway enrichments in various secondary metabolites, while specifically expressed genes in the CMS-D8 restorer line showed functional annotations related to anther development and pathway enrichment in the biosynthesis of secondary metabolites. Further analysis identified potentially key genes located in the target region of fertility restorer genes Rf1 or Rf2. In particular, Ghir_D05G032450 can be the candidate gene related to restorer gene Rf1, and Ghir_D05G035690 can be the candidate gene associated with restorer gene Rf2. Further gene expression validation with qRT-PCR confirmed the accuracy of our results. Our findings provide useful insights into decoding the potential regulatory network that retrieves pollen fertility in cotton and will help to further reveal the differences in the genetic basis of fertility restoration for two CMS systems.

Development of mitochondrial simple sequence repeat markers to simultaneously distinguish cytoplasmic male sterile sources in cotton.

Deleterious effects on anther development and main economy traits caused by sterile genes or cytoplasms are one of the important genetic characteristics of cytoplasmic male sterility (CMS) systems in cotton, which severely hinder the large-scale application of "three-line" hybrids in production. Therefore, distinct characterization of each cytoplasmic type is mandatory to improve the breeding efficiency of cotton hybrids. In this study, four isonuclear-alloplasmic cotton male sterile lines with G. hirsutum (CMS-(AD)1), G. barbadense (CMS-(AD)2), G. harknessii (CMS-D2), and G. trilobum (CMS-D8) cytoplasms were first created by multiple backcrosses with common genotype Shikang126. Then, 64 pairs of mitochondrial simple sequence repeat (mtSSR) markers were designed to explore the mitochondrial DNA diversities among four isonuclear-alloplasmic cotton male sterile lines, and a total of nine pairs of polymorphic mtSSR molecular markers were successfully developed. Polymorphism analysis indicated that mtSSR59 marker correlated to the atp1 gene could effectively divide the CMS-D2, CMS-(AD)1, and CMS-(AD)2 in one category while the CMS-D8 in another category. Further cytological observation and determination of ATP contents also confirmed the accurate classification of CMS-D2 and CMS-D8 lines. Moreover, the mtSSR59 marker was successfully applied in the marker-assisted selection (MAS) for breeding new male sterile lines and precise differentiation or purity identification of different CMS-based "three-line" and conventional cotton hybrids. This study provides new technical measures for classifying various cytoplasmic sterile lines, and our results will significantly improve the efficiency of there-line hybrid breeding in cotton.

Titania hybridized melamine-formaldehyde aerogel for online in-tube solid-phase microextraction of polycyclic aromatic hydrocarbons prior to HPLC-DAD.

In order to improve the selectivity and stability of melamine-formaldehyde (MF) aerogel, it was composited with TiO2 aerogel. A TiO2-MF hybrid aerogel was in situ prepared on the surface of carbon fibers for in-tube solid-phase microextraction (SPME). The extraction performance of TiO2-MF aerogel was regulated by changing the ratio of TiO2 sol and MF sol during the material preparation. Coupled with high-performance liquid chromatography-diode array detection (HPLC-DAD), the extraction tube filled by TiO2-MF aerogel-coated carbon fibers was evaluated with several types of environmental pollutants including polycyclic aromatic hydrocarbons (PAHs), estrogens, and ultraviolet filters. Because of favourable extraction performance of PAHs they were selected as model analytes, and some important influence factors were optimized for satisfactory sensitivity. The detection limits were in the range 0.05-0.10 µg L-1, owing to high enrichment factors (653-1007). The online in-tube SPME-HPLC-DAD method was verified for the determination of trace PAHs in environmental water samples, and acceptable recovery (70-118%) was achieved. The analytical methods also displayed some advantages in comparison with other reports. Moreover, the extraction tube exhibited satisfactory chemical stability.

Sulfonic acid-functionalized covalent organic frameworks as the coating for stir bar sorptive extraction of fluoroquinolones in milk samples.

Sulfonic acid-functionalized covalent organic frameworks (COF-SO3) as a coating of stir bar sorptive extraction (SBSE) for capturing three fluoroquinolones from milk have been developed. The COF-SO3 material was characterized by X-ray diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, and infrared spectroscopy. Milk without any typical treatments like protein precipitation and defatting was only diluted five times with water for test. Combined with high-performance liquid chromatography (HPLC), a SBSE-HPLC method was established for detecting fluoroquinolones in milk samples. The corresponding wide linear ranges (4.00-500.0 µg L-1), low detection limits (1.20-2.62 µg L-1), good test repeatability (RSD < 5.2%), and acceptable enrichment factors (56.2-61.5) were implemented for three fluoroquinolones. The analytical method was applied to determine trace targets and provided satisfactory results. Furthermore, the research displayed satisfied reproducibility for bar-to-bar (RSD < 6.5%) and batch-to-batch (RSD < 8.6%) tests.

Single-molecule real-time transcript sequencing of developing cotton anthers facilitates genome annotation and fertility restoration candidate gene discovery.

Heterosis refers to the superior phenotypes observed in hybrids. Cytoplasmic male sterility (CMS) system plays an important role in cotton heterosis utilization. However, the global gene expression patterns of CMS-D2 and its interaction with the restorer gene Rf1 remain unclear. Here, the full-length transcript sequencing was performed in anthers of the CMS-D2 restorer line using PacBio single-molecule real-time sequencing technology. Combining PacBio SMRT long-read isoforms and Illumina RNA-seq data, 107,066 isoforms from 44,338 loci were obtained, including 10,086 novel isoforms of novel genes and 66,419 new isoforms of known genes. Totally 56,572 alternative splicing (AS) events, 1146 lncRNAs, 61 fusion transcripts and 10,466 genes exhibited alternative polyadenylation (APA), and 60,995 novel isoforms with predicted open reading frames (ORFs) were further identified. Furthermore, the specifically expressed genes in restorer line were selected and confirmed by qRT-PCR. These findings provide a basis for upland cotton genome annotation and transcriptome research, and will help to reveal the molecular mechanism of interaction between Rf1 and CMS-D2 cytoplasm.

Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton.

BACKGROUND: Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. METHODS: The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. RESULTS: The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. CONCLUSIONS: This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.

Comparative analysis of sRNAs, degradome and transcriptomics in sweet sorghum reveals the regulatory roles of miRNAs in Cd accumulation and tolerance.

MAIN CONCLUSION: Key miRNAs including sbi-miR169p/q, sbi-miR171g/j, sbi-miR172a/c/d, sbi-miR172e, sbi-miR319a/b, sbi-miR396a/b, miR408, sbi-miR5384, sbi-miR5565e and nov_23 were identified to function in the regulation of Cd accumulation and tolerance. As an energy plant, sweet sorghum shows great potential in the phytoremediation of Cd-contaminated soils. However, few studies have focused on the regulatory roles of miRNAs and their targets under Cd stress. In this study, comparative analysis of sRNAs, degradome and transcriptomics was conducted in high-Cd accumulation (H18) and low-Cd accumulation (L69) genotypes of sweet sorghum. A total of 38 conserved and 23 novel miRNAs with differential expressions were identified under Cd stress or between H18 and L69, and 114 target genes of 41 miRNAs were validated. Furthermore, 25 miRNA-mRNA pairs exhibited negatively correlated expression profiles and sbi-miR172e together with its target might participate in the distinct Cd tolerance between H18 and L69 as well as sbi-miR172a/c/d. Additionally, two groups of them: miR169p/q-nov_23 and miR408 were focused through the co-expression analysis, which might be involved in Cd uptake and tolerance by regulating their targets associated with transmembrane transportation, cytoskeleton activity, cell wall construction and ROS (reactive oxygen species) homeostasis. Further experiments exhibited that cell wall components of H18 and L69 were different when exposed to cadmium, which might be regulated by miR169p/q, miR171g/j, miR319a/b, miR396a/b, miR5384 and miR5565e through their targets. Through this study, we aim to reveal the potential miRNAs involved in sweet sorghum in response to Cd stress and provide references for developing high-Cd accumulation or high Cd-resistant germplasm of sweet sorghum that can be used in phytoremediation.

Recent advances in micro- and nanomaterial-based adsorbents for pipette-tip solid-phase extraction.

There are a lot of review papers of sample pretreatment, but the comprehensive review on pipette-tip solid-phase extraction (PT-SPE) is lacking. This review (133 references) is mainly devoted to the development of different types of micro- and nanosorbent-based PT-SPE, including silica materials, carbon materials, organic polymers, molecularly imprinted polymers, and metal-organic frameworks. Each section mainly introduces and discusses the preparation methods, advantages and limitations of adsorbents, and their applications to environmental, biological, and food samples. This review also demonstrates the advantages of PT-SPE like convenience, speed, less organic solvent, and low cost. Finally, the future application and development trend of PT-SPE are prospected.

Poly(ionic liquid)-hybridized silica aerogel for solid-phase microextraction of polycyclic aromatic hydrocarbons prior to gas chromatography-flame ionization detection.

Using poly(ionic liquid) (PIL) and tetraethyl orthosilicate (TEOS) as the co-precursors, PIL-hybridized silica aerogel was prepared via sol-gel method for solid-phase microextraction (SPME). The ratio between PIL and TEOS was regulated to achieve the best extraction effect. The aerogel was coated onto the surface of stainless steel wire to get SPME fiber. Coupled to gas chromatography-flame ionization detector (GC-FID), the fiber was separately evaluated by the determination of alkanes, polycyclic aromatic hydrocarbons (PAHs), as well as BTEX (benzene, toluene, ethylbenzene, and xylenes) in immersion mode. The extraction performance of PAHs was attributed to π stacking and hydrophobic effect. After optimization of main extraction and desorption conditions, the SPME-GC-FID method was established towards eight PAHs, and it provided low detection limits (0.005 µg L-1, 0.010 µg L-1) and wide linear ranges (0.016-20.00 µg L-1, 0.033-20.00 µg L-1) with good linear coefficients (0.9991-0.9998). The method was applied to detect trace PAHs in real water samples, with relative recoveries of 86.2-119.2%. Furthermore, PIL-hybridized silica aerogel exhibits some superiorities like higher sensitivity, shorter extraction time, and better repeatability over other extraction coatings. The present work not only extends the range of aerogel materials but also promoted their further applications in sample preparation. Graphical abstract.

Comparative transcriptome analysis of inbred lines and contrasting hybrids reveals overdominance mediate early biomass vigor in hybrid cotton.

BACKGROUND: Heterosis breeding is the most useful method for yield increase around the globe. Heterosis is an intriguing process to develop superior offspring to either parent in the desired character. The biomass vigor produced during seedling emergence stage has a direct influence on yield heterosis in plants. Unfortunately, the genetic basis of early biomass vigor in cotton is poorly understood. RESULTS: Three stable performing F1 hybrids varying in yield heterosis named as high, medium and low hybrids with their inbred parents were used in this study. Phenotypically, these hybrids established noticeable biomass heterosis during the early stage of seedling growth in the field. Transcriptome analysis of root and leaf revealed that hybrids showed many differentially expressed genes (DEGs) relative to their parents, while the comparison of inbred parents showed limited number of DEGs indicating similarity in their genetic constitution. Further analysis indicated expression patterns of most DEGs were overdominant in both tissues of hybrids. According to GO results, functions of overdominance genes in leaf were enriched for chloroplast, membrane, and protein binding, whereas functions of overdominance genes in root were enriched for plasma membrane, extracellular region, and responses to stress. We found several genes of circadian rhythm pathway related to LATE ELONGATED HYPOCOTYL (LHY) showed downregulated overdominant expressions in both tissues of hybrids. In addition to circadian rhythm, several leaf genes related to Aux/IAA regulation, and many root genes involved in peroxidase activity also showed overdominant expressions in hybrids. Twelve genes involved in circadian rhythm plant were selected to perform qRT-PCR analysis to confirm the accuracy of RNA-seq results. CONCLUSIONS: Through genome-wide comparative transcriptome analysis, we strongly predict that overdominance at gene expression level plays a pivotal role in early biomass vigor of hybrids. The combinational contribution of circadian rhythm and other metabolic process may control vigorous growth in hybrids. Our result provides an important foundation for dissecting molecular mechanisms of biomass vigor in hybrid cotton.

Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton.

BACKGROUND: Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. RESULTS: In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. CONCLUSIONS: Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

Single-base resolution methylome of cotton cytoplasmic male sterility system reveals epigenomic changes in response to high-temperature stress during anther development.

Anther development in flowering plants is highly sensitive to high-temperature (HT) stress. Understanding the potential epigenetic mechanism of anther infertility induced by HT stress in cotton (Gossypium hirsutum L.) is crucial for the effective use of genetic resources to guide plant breeding. Using the whole-genome bisulfite sequencing, we map cytosine methylation at single-base resolution across the whole genome of cotton anthers, and changes in the methylome of the cytoplasmic male sterility system associated with HT stress were analysed in two cotton lines with contrasting HT stress tolerance. The cotton anther genome was found to display approximately 31.6%, 68.7%, 61.8%, and 21.8% methylation across all sequenced C sites and in the CG, CHG, and CHH sequence contexts, respectively. In an integrated global methylome and transcriptome analysis, only promoter-unmethylated genes showed higher expression levels than promoter-methylated genes, whereas gene body methylation presented an obvious positive correlation with gene expression. The methylation profiles of transposable elements in cotton anthers were characterized, and more differentially methylated transposable elements were demethylated under HT stress. HT-induced promoter methylation changes led to the up-regulation of the mitochondrial respiratory chain enzyme-associated genes GhNDUS7, GhCOX6A, GhCX5B2, and GhATPBM, ultimately promoting a series of redox processes to form ATP for normal anther development under HT stress. In vitro application of the common DNA methylation inhibitor 5-azacytidine and accelerator methyl trifluoromethanesulfonate demonstrated that DNA demethylation promoted anther development, while increased methylation only partially inhibited anther development under HT stress.

Development and utilization of an InDel marker linked to the fertility restorer genes of CMS-D8 and CMS-D2 in cotton.

The cytoplasmic male sterility (CMS) system is a useful tool for commercial hybrid cotton seed production. Two main CMS systems, CMS-D8 and CMS-D2, have been recognized with Rf2 and Rf1 as the restorer genes, respectively. The development of molecular markers tightly linked with restorer genes can facilitate the breeding of restorer lines. In this study, the InDel-1892 marker was developed to distinguish Rf2 and Rf1 simultaneously. Sequence alignment implied that CMS-D8-Rf2 has a 32 bp insertion and that CMS-D2-Rf1 has a 186 bp insertion at the InDel-1892 locus. The codominant marker was co-segregated with Rf1 and Rf2. Hence, this marker can be used for tracing Rf1 and Rf2 simultaneously and identifying the allele status at the restorer gene locus. The results of this study will facilitate efficient marker-assisted selection for restorer lines and hybrids of CMS systems.

Triazine-based organic polymers@SiO2 nanospheres for sensitive solid-phase microextraction of polycyclic aromatic hydrocarbons.

Triazine-based organic polymers@SiO2 nanospheres were prepared and applied as an extraction coating onto stainless steel wires and the wires were filled into polyetheretherketone tube for in-tube solid-phase microextraction. Taking polycyclic aromatic hydrocarbons as targets, main factors affecting extraction performance of the tube were investigated through coupling to high performance liquid chromatography. Under the optimum conditions, an online analytical method for polycyclic aromatic hydrocarbons was established with large linear ranges (0.010-20 µg/L), low limits of detection (0.003-0.010 µg/L), high enrichment factors (533-2954), and good repeatability (relative standard deviations <1.7% for intraday test, <5.0% for interday test). The analysis method was successfully applied to the detection of trace targets in real water samples and the relative recoveries ranged from 82.9 to 119.9%, which demonstrated the applicability of extraction tube in sample preparation.