Promotion of apoplastic oxidative burst by artificially selected GhCBSX3A enhances Verticillium dahliae resistance in upland cotton.

Verticillium wilt (VW) is a devasting disease affecting various plants, including upland cotton, a crucial fiber crop. Despite its impact, the genetic basis underlying cotton's susceptibility or defense against VW remains unclear. Here, we conducted a genome-wide association study on VW phenotyping in upland cotton and identified a locus on A13 that is significantly associated with VW resistance. We then identified a cystathionine ß-synthase domain gene at A13 locus, GhCBSX3A, which was induced by Verticillium dahliae. Functional analysis, including expression silencing in cotton and overexpression in Arabidopsis thaliana, confirmed that GhCBSX3A is a causal gene at the A13 locus, enhancing SAR-RBOHs-mediated apoplastic oxidative burst. We found allelic variation on the TATA-box of GhCBSX3A promoter attenuated its expression in upland cotton, thereby weakening VW resistance. Interestingly, we discovered that altered artificial selection of GhCBSX3A_R (an elite allele for VW) under different VW pressures during domestication and other improved processes allows specific human needs to be met. Our findings underscore the importance of GhCBSX3A in response to VW, and we propose a model for defense-associated genes being selected depending on the pathogen's pressure. The identified locus and gene serve as promising targets for VW resistance enhancement in cotton through genetic engineering.

The microRNA miR-202 prevents precocious spermatogonial differentiation and meiotic initiation during mouse spermatogenesis.

Spermatogonial differentiation and meiotic initiation during spermatogenesis are tightly regulated by a number of genes, including those encoding enzymes for miRNA biogenesis. However, whether and how single miRNAs regulate these processes remain unclear. Here, we report that miR-202, a member of the let-7 family, prevents precocious spermatogonial differentiation and meiotic initiation in spermatogenesis by regulating the timely expression of many genes, including those for key regulators such as STRA8 and DMRT6. In miR-202 knockout (KO) mice, the undifferentiated spermatogonial pool is reduced, accompanied by age-dependent decline of fertility. In KO mice, SYCP3, STRA8 and DMRT6 are expressed earlier than in wild-type littermates, and Dmrt6 mRNA is a direct target of miR-202-5p. Moreover, the precocious spermatogonial differentiation and meiotic initiation were also observed in KO spermatogonial stem cells when cultured and induced in vitro, and could be partially rescued by the knockdown of Dmrt6. Therefore, we have not only shown that miR-202 is a regulator of meiotic initiation but also identified a previously unknown module in the underlying regulatory network.

MicroRNA-202 safeguards meiotic progression by preventing premature SEPARASE-mediated REC8 cleavage.

MicroRNAs (miRNAs) are believed to play important roles in mammalian spermatogenesis but the in vivo functions of single miRNAs in this highly complex developmental process remain unclear. Here, we report that miR-202, a member of the let-7 family, plays an important role in spermatogenesis by phenotypic evaluation of miR-202 knockout (KO) mice. Loss of miR-202 results in spermatocyte apoptosis and perturbation of the zygonema-to-pachynema transition. Multiple processes during meiosis prophase I including synapsis and crossover formation are disrupted, and inter-sister chromatid synapses are detected. Moreover, we demonstrate that Separase mRNA is a miR-202 direct target and provides evidence that miR-202 upregulates REC8 by repressing Separase expression. Therefore, we have identified miR-202 as a new regulating noncoding gene that acts on the established SEPARASE-REC8 axis in meiosis.

Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement.

BACKGROUND: Upland cotton wild/landraces represent a valuable resource for disease resistance alleles. Genetic differentiation between genotypes, as well as variation in Verticillium wilt (VW) resistance, has been poorly characterized for upland cotton accessions on the domestication spectrum (from wild/landraces to elite lines). RESULTS: To illustrate the effects of modern breeding on VW resistance in upland cotton, 37 wild/landraces were resequenced and phenotyped for VW resistance. Genomic patterns of differentiation were identified between wild/landraces and improved upland cotton, and a significant decline in VW resistance was observed in association with improvement. Four genotypes representing different degrees of improvement were used in a full-length transcriptome analysis to study the genetic basis of VW resistance. ROS signaling was highly conserved at the transcriptional level, likely providing the basis for VW resistance in upland cotton. ASN biosynthesis and HSP90-mediated resistance moderated the response to VW in wild/landraces, and loss of induction activity of these genes resulted in VW susceptibility. The observed genomic differentiation contributed to the loss of induction of some important VW resistance genes such as HSP90.4 and PR16. CONCLUSIONS: Besides providing new insights into the evolution of upland cotton VW resistance, this study also identifies important resistance pathways and genes for both fundamental research and cotton breeding.

Recent progression and future perspectives in cotton genomic breeding.

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.

Scalar thermal radiation using the adding-doubling method.

The scalar radiative transfer equation in the presence of thermal radiation source is solved in detail, using the adding-doubling method; Planck functions within any given layer are assumed to possess constant, linear, or exponential parameterizations with optical thickness. The radiance profile in any zenith direction is calculated directly in terms of matrix inversions. The inputs to the model are the inherent optical properties (layer total single-scattering albedos, scattering phase functions, and optical thickness) along with temperature and altitude profiles, and the top of the atmosphere and ground surface boundary conditions. The algorithm is implemented in a state-of-the-art MATLAB program, with the cosmic microwave background as the source at the upper boundary and a Lambertian surface reflection at the lower boundary. The simulations are validated against the VLIDORT discrete ordinate radiative transfer model. Results are compared in detail for cases with linear and exponential Planck function parameterizations.

Capability and convergence of linearized invariant-imbedding T-matrix and physical-geometric optics methods for light scattering.

The linearized invariant-imbedding T-matrix method (LIITM) and linearized physical-geometric optics method (LPGOM) were applied on regular hexagonal prisms from small to large sizes to obtain the scattering properties and their partial derivatives. T-matrices and their derivatives from the LIITM are presented and discussed in the expansion order, where the minor diagonal elements are dominant. The simulation results of single-scattering properties and their corresponding linearization from both methods are compared. The mutual agreements can be treated as further verification of both linearized methods. Using extinction efficiency as the criterion, the LPGOM are convergent at the LIITM for the particle size parameter larger than 130 with a relative difference of less than 1%, with errors of about 3% and 5% for particle sizes of 50 and 30, respectively. The capability and convergence of the LIITM and LPGOM are discussed in detail based on linearized properties.

Integration of eQTL Analysis and GWAS Highlights Regulation Networks in Cotton under Stress Condition.

The genus Gossypium is one of the most economically important crops in the world. Here, we used RNA-seq to quantify gene expression in a collection of G. arboreum seedlings and performed eGWAS on 28,382 expressed genes. We identified a total of 30,089 eQTLs in 10,485 genes, of which >90% were trans-regulate target genes. Using luciferase assays, we confirmed that different cis-eQTL haplotypes could affect promoter activity. We found ~6600 genes associated with ~1300 eQTL hotspots. Moreover, hotspot 309 regulates the expression of 325 genes with roles in stem length, fresh weight, seed germination rate, and genes related to cell wall biosynthesis and salt stress. Transcriptome-wide association study (TWAS) identified 19 candidate genes associated with the cotton growth and salt stress response. The variation in gene expression across the population played an essential role in population differentiation. Only a small number of the differentially expressed genes between South China, the Yangtze River region, and the Yellow River region sites were located in different chromosomal regions. The eQTLs found across the duplicated gene pairs showed conservative cis- or trans- regulation and that the expression levels of gene pairs were correlated. This study provides new insights into the evolution of gene expression regulation in cotton, and identifies eQTLs in stress-related genes for use in breeding improved cotton varieties.

Analytical Jacobians of single scattering optical properties using the invariant imbedding T-matrix method.

Integrated and differential optical properties of a single particle, such as the scattering, absorption, and extinction cross sections, single scattering albedo, asymmetry factor, and scattering phase matrix, are derived from electromagnetic scattering theory. This process depends on microphysical inputs which include particle shape, refractive index, aspect ratio, and size parameter. In this work, we use the invariant imbedding T-matrix method (IITM) to derive analytic expressions for Jacobians of these optical properties with respect to the input parameters. These IITM-derived Jacobians for spheroids, cylinders, and hexagonal prisms are validated by comparison with results calculated with the extended boundary condition method (EBCM) and further validated using finite-difference estimates. We examine the dependencies of these Jacobians as functions of the input microphysical parameters, focusing again on spheroids, cylinders, and hexagonal prisms.

A cross-disease, pleiotropy-driven approach for therapeutic target prioritization and evaluation.

Cross-disease genome-wide association studies (GWASs) unveil pleiotropic loci, mostly situated within the non-coding genome, each of which exerts pleiotropic effects across multiple diseases. However, the challenge "W-H-W" (namely, whether, how, and in which specific diseases pleiotropy can inform clinical therapeutics) calls for effective and integrative approaches and tools. We here introduce a pleiotropy-driven approach specifically designed for therapeutic target prioritization and evaluation from cross-disease GWAS summary data, with its validity demonstrated through applications to two systems of disorders (neuropsychiatric and inflammatory). We illustrate its improved performance in recovering clinical proof-of-concept therapeutic targets. Importantly, it identifies specific diseases where pleiotropy informs clinical therapeutics. Furthermore, we illustrate its versatility in accomplishing advanced tasks, including pathway crosstalk identification and downstream crosstalk-based analyses. To conclude, our integrated solution helps bridge the gap between pleiotropy studies and therapeutics discovery.

Prospective observational study on biomarkers of response in pancreatic ductal adenocarcinoma.

Adjuvant chemotherapy benefits patients with resected pancreatic ductal adenocarcinoma (PDAC), but the compromised physical state of post-operative patients can hinder compliance. Biomarkers that identify candidates for prompt adjuvant therapy are needed. In this prospective observational study, 1,171 patients with PDAC who underwent pancreatectomy were enrolled and extensively followed-up. Proteomic profiling of 191 patient samples unveiled clinically relevant functional protein modules. A proteomics-level prognostic risk model was established for PDAC, with its utility further validated using a publicly available external cohort. More importantly, through an interaction effect regression analysis leveraging both clinical and proteomic datasets, we discovered two biomarkers (NDUFB8 and CEMIP2), indicative of the overall sensitivity of patients with PDAC to adjuvant chemotherapy. The biomarkers were validated through immunohistochemistry on an internal cohort of 386 patients. Rigorous validation extended to two external multicentic cohorts-a French multicentric cohort (230 patients) and a cohort from two grade-A tertiary hospitals in China (466 patients)-enhancing the robustness and generalizability of our findings. Moreover, experimental validation through functional assays was conducted on PDAC cell lines and patient-derived organoids. In summary, our cohort-scale integration of clinical and proteomic data demonstrates the potential of proteomics-guided prognosis and biomarker-aided adjuvant chemotherapy for PDAC.

Optimization of strains for fermentation of kiwifruit juice and effects of mono- and mixed culture fermentation on its sensory and aroma profiles.

In this study, a quality evaluation model of fermented kiwifruit juice (KJ) based on strain growth characteristics, sensory quality and functional characteristics was established by PCA, and the effects of mono- and mixed culture fermentation on the sensory and aroma profiles of KJ were comparatively studied. Experiments determined that L. brevis (LB) was the optimal strain for monoculture fermentation, and L. plantarum (LP2):LB = 1:2 was the optimum ratio for mixed fermentation. The results showed that lactic acid bacteria (LAB) fermentation significantly reduced the pH, soluble solid content and lightness, and improved its functional characteristics and viscosity. Mixed culture fermentation was superior to monoculture fermentation in terms of colony counts, sensory quality and viscosity. In general, after LAB fermentation, the concentrations of esters, ketones, alcohols and terpenoids in KJ increased significantly, while the concentrations of aldehydes decreased significantly. The production of esters and terpenoids was more strongly promoted by monoculture fermentation, while mixed culture fermentation promoted the production of more ketones and alcohols. 2,5-octanedione and 1-octen-3-ol could be the characteristic aroma compounds of mixed fermented KJ.

High-quality genome assembly of Verticillium dahliae VD991 allows for screening and validation of pathogenic genes.

Verticillium dahliae (V. dahliae) is a notorious soil-borne pathogen causing Verticillium wilt in more than 400 dicotyledonous plants, including a wide range of economically important crops, such as cotton, tomato, lettuce, potato, and romaine lettuce, which can result in extensive economic losses. In the last decade, several studies have been conducted on the physiological and molecular mechanisms of plant resistance to V. dahliae. However, the lack of a complete genome sequence with a high-quality assembly and complete genomic annotations for V. dahliae has limited these studies. In this study, we produced a full genomic assembly for V. dahliae VD991 using Nanopore sequencing technology, consisting of 35.77 Mb across eight pseudochromosomes and with a GC content of 53.41%. Analysis of the genome completeness assessment (BUSCO alignment: 98.62%; Illumina reads alignment: 99.17%) indicated that our efforts resulted in a nearly complete and high-quality genomic assembly. We selected 25 species closely related to V. dahliae for evolutionary analysis, confirming the evolutionary relationship between V. dahliae and related species, and the identification of a possible whole genome duplication event in V. dahliae. The interaction between cotton and V. dahliae was investigated by transcriptome sequencing resulting in the identification of many genes and pathways associated with cotton disease resistance and V. dahliae pathogenesis. These results will provide new insights into the pathogenic mechanisms of V. dahliae and contribute to the cultivation of cotton varieties resistant to Verticillium wilt.

Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton.

BACKGROUND: Verticillium wilt is one of the most devasting diseases for many plants, leading to global economic loss. Cotton is known to be vulnerable to its fungal pathogen, Verticillium dahliae, yet the related genetic mechanism remains unknown. RESULTS: By genome-wide association studies of 419 accessions of the upland cotton, Gossypium hirsutum, we identify ten loci that are associated with resistance against Verticillium wilt. Among these loci, SHZDI1/SHZDP2/AYDP1 from chromosome A10 is located on a fragment introgressed from Gossypium arboreum. We characterize a large cluster of Toll/interleukin 1 (TIR) nucleotide-binding leucine-rich repeat receptors in this fragment. We then identify a dual-TIR domain gene from this cluster, GhRVD1, which triggers an effector-independent cell death and is induced by Verticillium dahliae. We confirm that GhRVD1 is one of the causal gene for SHZDI1. Allelic variation in the TIR domain attenuates GhRVD1-mediated resistance against Verticillium dahliae. Homodimerization between TIR1-TIR2 mediates rapid immune response, while disruption of its αD- and αE-helices interface eliminates the autoactivity and self-association of TIR1-TIR2. We further demonstrate that GhTIRP1 inhibits the autoactivity and self-association of TIR1-TIR2 by competing for binding to them, thereby preventing the resistance to Verticillium dahliae. CONCLUSIONS: We propose the first working model for TIRP1 involved self-association and autoactivity of dual-TIR domain proteins that confer compromised pathogen resistance of dual-TIR domain proteins in plants. The findings reveal a novel mechanism on Verticillium dahliae resistance and provide genetic basis for breeding in future.

Oil candidate genes in seeds of cotton (Gossypium hirsutum L.) and functional validation of GhPXN1.

BACKGROUND: Cottonseed oil is a promising edible plant oil with abundant unsaturated fatty acids. However, few studies have been conducted to explore the characteristics of cottonseed oil. The molecular mechanism of cottonseed oil accumulation remains unclear. RESULTS: In the present study, we conducted comparative transcriptome and weighted gene co-expression network (WGCNA) analysis for two G. hirsutum materials with significant difference in cottonseed oil content. Results showed that, between the high oil genotype 6053 (H6053) and the low oil genotype 2052 (L2052), a total of 412, 507, 1,121, 1,953, and 2,019 differentially expressed genes (DEGs) were detected at 10, 15, 20, 25, and 30 DPA, respectively. Remarkably, a large number of the down-regulated DEGs were enriched in the phenylalanine metabolic processes. Investigation into the dynamic changes of expression profiling of genes associated with both phenylalanine metabolism and oil biosynthesis has shed light on a significant competitive relationship in substrate allocation during cottonseed development. Additionally, the WGCNA analysis of all DEGs identified eight distinct modules, one of which includes GhPXN1, a gene closely associated with oil accumulation. Through phylogenetic analysis, we hypothesized that GhPXN1 in G. hirsutum might have been introgressed from G. arboreum. Overexpression of the GhPXN1 gene in tobacco leaf suggested a significant reduction in oil content compared to the empty-vector transformants. Furthermore, ten other crucial oil candidate genes identified in this study were also validated using quantitative real-time PCR (qRT-PCR). CONCLUSIONS: Overall, this study enhances our comprehension of the molecular mechanisms underlying cottonseed oil accumulation.

Identification and characterization of BEND2 as a key regulator of meiosis during mouse spermatogenesis.

The chromatin state, which undergoes global changes during spermatogenesis, is critical to meiotic initiation and progression. However, the key regulators involved and the underlying molecular mechanisms remain to be uncovered. Here, we report that mouse BEND2 is specifically expressed in spermatogenic cells around meiotic initiation and that it plays an essential role in meiotic progression. Bend2 gene knockout in male mice arrested meiosis at the transition from zygonema to pachynema, disrupted synapsis and DNA double-strand break repair, and induced nonhomologous chromosomal pairing. BEND2 interacted with chromatin-associated proteins that are components of certain transcription-repressor complexes. BEND2-binding sites were identified in diverse chromatin states and enriched in simple sequence repeats. BEND2 inhibited the expression of genes involved in meiotic initiation and regulated chromatin accessibility and the modification of H3K4me3. Therefore, our study identified BEND2 as a previously unknown key regulator of meiosis, gene expression, and chromatin state during mouse spermatogenesis.

Highly oriented MAPbI3 crystals for efficient hole-conductor-free printable mesoscopic perovskite solar cells.

Highly crystalline perovskite films with large grains and few grain boundaries are conducive for efficient and stable perovskite solar cells. Current methods for preparing perovskite films are mostly based on a fast crystallization process, with rapid nucleation and insufficient growth. In this study, MAPbI3 perovskite with inhibited nucleation and promoted growth in the TiO2/ZrO2/carbon triple mesoscopic scaffold was crystallized by modulating the precursor and the crystallization process. N-methylformamide showed high solubility for both methylammonium iodide and PbI2 and hampered the formation of large colloids in the MAPbI3 precursor solution. Furthermore, methylammonium chloride was added to reduce large colloids, which are a possible source of nucleation sites. During the crystallization of MAPbI3, the solvent was removed at a slow controlled speed, to avoid rapid nucleation and provide sufficient time for crystal growth. As a result, highly oriented MAPbI3 crystals with suppressed non-radiative recombination and promoted charge transport were obtained in the triple mesoscopic layer with disordered pores. The corresponding hole-conductor-free, printable mesoscopic perovskite solar cells exhibited a highest power conversion efficiency of 18.82%. The device also exhibited promising long-term operational stability of 1000 h under continuous illumination at maximum power point at 55 ± 5 °C and damp-heat stability of 1340 h aging at 85 °C as well as 85% relative humidity.

Analysis of the Aroma Chemical Composition of Commonly Planted Kiwifruit Cultivars in China.

The aroma chemical composition of commonly planted kiwifruit cultivars in China was analyzed. The combination of 2-octanone with 3-octanone was the most suitable dual internal standard for quantitative analysis in GC-MS. A total of 172 aroma components in 23 kiwifruit cultivars were detected, and ethyl butanoate, (E)-2-hexen-1-ol, and (E)-2-hexenal could be considered the core aroma components in kiwifruit, but still need further confirmation using Sensomics. E-nose could effectively distinguish different cultivars of kiwifruit. Clustering based on GC-MS and E-nose results tends to be consistent and demonstrate a certain degree of similarity. Kiwifruit cultivars with different flesh colors cannot be effectively distinguished by their aroma chemical compositions. Different species of kiwifruit can be distinguished to some extent by their aroma chemical compositions, but the effect was not satisfactory. These results could prove valuable in the breeding, planting, and marketing of kiwifruits.

Thermosonication Combined with Natural Antimicrobial Nisin: A Potential Technique Ensuring Microbiological Safety and Improving the Quality Parameters of Orange Juice.

Currently, thermal pasteurisation (TP) remains the most widely applied technique for commercial orange juice preservation; however, a high temperature causes adverse effects on the quality attributes of orange juice. In order to explore a novel non-thermal sterilization method for orange juice, the impacts of thermosonication combined with nisin (TSN) and TP treatments on the quality attributes including microbial and enzyme inactivation and the physicochemical, nutritional, functional, and sensory qualities of orange juice were studied. Both TP and TSN treatments achieved desirable bactericidal and enzyme inactivation effects, and nisin had a significant synergistic lethal effect on aerobic bacteria in orange juice (p < 0.05). Additionally, TSN treatment significantly improved the color attributes of orange juice and well maintained its physicochemical properties and sensory quality. More importantly, TSN treatment significantly increased the total polyphenols content (TPC) and total carotenoids (TC) by 10.03% and 20.10%, increased the ORAC and DPPH by 51.10% and 10.58%, and the contents of total flavonoids and ascorbic acid were largely retained. Correlation analysis of antioxidant activity showed that the ORAC and scavenging ability of DPPH radicals of orange juice are mainly attributed to TC and TPC. These findings indicate that TSN shows great potential application value, which could guarantee the microbiological safety and improve the quality attributes of orange juice.

Comparative Analysis of Physicochemical Characteristics, Nutritional and Functional Components and Antioxidant Capacity of Fifteen Kiwifruit (Actinidia) Cultivars-Comparative Analysis of Fifteen Kiwifruit (Actinidia) Cultivars.

Physicochemical characteristics, nutritional and functional components, and the antioxidant capacity of 15 kinds of domestic and imported kiwifruit in China were studied. Kiwifruit was classified according to flesh color or species, and the differences were analyzed and compared. Results demonstrated Ruiyu had the highest sugar-acid ratio, and Hongshi No.2 was an excellent cultivar with strong antioxidant capacity. TPC (total polyphenol content) and AAC (ascorbic acid content) showed a significant positive correlation. TPC was the greatest antioxidant contributor in the DPPH and FRAP assays. The sugar-acid ratio and TFC (total flavonoids content) in red-fleshed kiwifruit were significantly higher than those in yellow-fleshed and green-fleshed ones. The composition of free amino acids had a tendency to distinguish A. deliciosa and A. chinensis, but this needs further verification. In addition, the contents of mineral elements, folic acid and L-5-methyltetrahydrofolate were also analyzed. Generally, kiwifruit contains comprehensive nutrients and has strong antioxidant capacity. Cultivar is one of the main factors affecting nutritional and functional properties and antioxidant capacity.