Rich Region Research Articles

Interface engineering enabling thin lithium metal electrodes down to 0.78 μm for garnet-type solid-state batteries.

Controllable engineering of thin lithium (Li) metal is essential for increasing the energy density of solid-state batteries and clarifying the interfacial evolution mechanisms of a lithium metal negative electrode. However, fabricating a thin lithium electrode faces significant challenges due to the fragility and high viscosity of Li metal. Herein, through facile treatment of Ta-doped Li7La3Zr2O12 (LLZTO) with trifluoromethanesulfonic acid, its surface Li2CO3 species is converted into a lithiophilic layer with LiCF3SO3 and LiF components. It enables the thickness control of Li metal negative electrodes, ranging from 0.78 μm to 30 μm. Quasi-solid-state lithium-metal battery with an optimized 7.54 μm-thick lithium metal negative electrode, a commercial LiNi0.83Co0.11Mn0.06O2 positive electrode, and a negative/positive electrode capacity ratio of 1.1 shows a 500 cycles lifespan with a final discharge specific capacity of 99 mAh g-1 at 2.35 mA cm-2 and 25 °C. Through multi-scale characterizations of the thin lithium negative electrode, we clarify the multi-dimensional compositional evolution and failure mechanisms of lithium-deficient and -rich regions (0.78 μm and 7.54 μm), on its surface, inside it, or at the Li/LLZTO interface.

Fully human monoclonal antibody targeting the cysteine-rich substrate-interacting region of ADAM17 on cancer cells

ADAM17 sheds EGFR/erbB ligands and triggers oncogenic pathways that lead to the progression of solid tumors. We targeted the ADAM17 disintegrin and cysteine rich domain region (D+C) to generate a panel of single-chain antibody fragments (scFvs) that selectively bind to the D or C domains of ADAM17, but not of ADAM10 or ADAM19. From the panel, we selected one scFv, referred to as C12, based on its high binding affinity towards the target, and re-formatted it to a full IgG for further studies. High-resolution cryo-electron microscopy studies documented that the mAb binds to the ADAM17 C-domain that in ADAM proteases, notably ADAM10 and ADAM17, is known to impart substrate-specificity. The C12 mAb significantly inhibited EGFR phosphorylation in cancer cell lines by hindering the cleavage of EGFR ligands tethered to the cell surface. This inhibition provides a mechanism for potential anti-tumor effects, and indeed C12 diminished the viability of a variety of EGFR-expressing cancer cell lines. Cell-based ELISA studies revealed that C12 preferentially bound to activated ADAM17 present on tumor cells, as compared to the autoinhibited ADAM17 that is the predominant form on HEK293 and other non-tumor cells. C12 also exhibited tumor growth inhibition in an ovarian cancer xenograft mouse model. Consistent with its selective tumor cell binding in vitro, radioimmuno PET (positron emission tomography) imaging with 89Zr-DFO-C12 in mouse xenograft models confirmed tumoral accumulation of the C12 mAb.

ALMASOP. The Localized and Chemically Rich Features near the Bases of the Protostellar Jet in HOPS 87

HOPS 87 is a Class 0 protostellar core known to harbor an extremely young bipolar outflow and a hot corino. We report the discovery of localized, chemically rich regions near the bases of the two-lobe bipolar molecular outflow in HOPS 87 containing molecules such as H2CO, 13CS, H2S, OCS, and CH3OH, the simplest complex organic molecule (COM). The locations and kinematics suggest that these localized features are due to jet-driven shocks rather than being part of the hot-corino region encasing the protostar. The COM compositions of the molecular gas in these jet-localized regions are relatively simpler than those in the hot-corino zone. We speculate that this simplicity is due to either the liberation of ice with a less complex chemical history or the effects of shock chemistry. Our study highlights the dynamic interplay between the protostellar bipolar outflow, disk, inner-core environment, and the surrounding medium, contributing to our understanding of molecular complexity in solar-like young stellar objects.

An overview on the production, management and impact of microplastic contamination on marine species and marine environments: A review

The purpose of this paper is to review and evaluate published literature on the production, management and impact of microplastic contamination on marine species and marine environments. A systematic method was utilized to access research works of literature on “production, management and impact of microplastic contamination on marine species and marine environments”. A total of Sixty-two (62) research papers published between the years 1972 to 2022 was accumulated and used for this review. A subjective approach was used to select the topics: production, management and impact of microplastic contamination. In this paper, four (4) effects of microplastics on organisms and the environment was assessed. Additionally, the formation and classification of microplastics were evaluated. Subsequently, the paper delves into the production and the management of global plastic production as well as the sources of contamination. Further, this review assessed the quantity of microplastics in the gastrointestinal tract and edible muscles of various fish species. A mini checklist of sixty-one (61) fish species from thirty (30) families dwelling in nine (9) different marine habitats, all contaminated by microplastics was also presented in this review. Moreover, possible solutions to overcome the impact of microplastics on organisms and aquatic environments were also mentioned in this article. The published works of literature established that the global plastic production is constantly increasing with a growing world population thus leading to mismanagement of plastic resources and introducing them to the environment. Microplastics can cause serious complications in humans, marine organisms such as fishes, crustaceans, marine mammals and sea birds and even contribute to the degradation of mangrove forests and the coastal environment. This review highlights the fact that more extensive studies on the impact of microplastic contamination in organisms and the environment should be done in neotropical countries since there is a dearth and gaps of such information on research and published data in these biodiversity rich regions.

Learnable feature alignment with attention-based data augmentation for handling data issue in ancient documents

Recognizing ancient cursive handwritten characters presents unique challenges due to the diversity of writing styles and significant class imbalances, where some characters have disproportionately more samples than others. This imbalance leads to higher misclassification rates for minority classes compared to majority classes. To address these challenges, we propose a novel framework that integrates learnable channel and spatial attention modules to effectively align features between source and target domains for better representation. Our approach incorporates a learnable sequential feature alignment process that dynamically adjusts to the specific characteristics of the data, enhancing the transfer of knowledge across domains. Furthermore, we introduce an attention-based augmentation module to amplify the influence of tail classes. This module leverages class activation maps to identify and augment discriminative features, ensuring the model focuses on the most semantically rich regions, particularly for minority classes. As a result, it aligns the weight norms of minority classes with those of majority classes, effectively mitigating the limitations posed by imbalanced class distributions. This approach effectively mitigates the constraints posed by imbalanced character distributions in ancient handwritten documents. The proposed method increases the accuracy for the CCR, Hanja, Nancho, and Kuzushiji datasets.

Temporal Range Dynamics of the Lataste's Viper (Vipera latastei Boscá, 1878) in Doñana (Spain): Insights into Anthropogenically Driven Factors.

Doñana (southern Spain), a region of notable biodiversity richness, is highly threatened by ongoing landscape transformation and climate change. We investigated the local effect of these anthropogenic factors on the temporal range dynamics of Lataste's viper (Vipera latastei), an Iberian endemic Mediterranean reptile that has apparently become rare over the years in Doñana. Using ecological niche-based models, based on climatic and remote sensing variables, we analyzed historical (1959-1999) and contemporary (2000-2022) records of the species to assess range shifts and identify environmental factors that may influence them. Our results show that V. latastei is mostly restricted to the coastal region of Doñana and that one temperature variable is the most important factor explaining this distribution pattern in both periods. Additional climatic and vegetation variables play a role in its historical distribution, but they become less important in contemporary times, suggesting a niche simplification over time. We found 30.5% of reduction in the species suitable area from historical to contemporary conditions, a reduction that would be even greater (83.37%) in the absence of niche shift. These findings underscore the species' heightened vulnerability to ongoing environmental changes and highlight the urgent need for targeted conservation strategies.

Impact of stacking faults on the luminescence of a zincblende InGaN/GaN single quantum well

Abstract In this paper, we investigate the optical properties of a zincblende InGaN single quantum well structure containing stacking faults. Cathodoluminescence studies revealed the presence of sharp emission features adjacent to stacking faults, identified as quantum wires via their spatial anisotropy. Scanning transmission electron microscopy provided evidence of indium rich regions adjacent to stacking faults which intersect the quantum well along the [110] and [1-10] directions, whilst atom probe tomography revealed that the indium rich regions have an elongated structure, creating a quantum wire. This work sheds light on the intricate relationship between stacking faults and quantum wires in zincblende InGaN single quantum well structures, offering insights into the underlying mechanisms governing their optical behaviour.

CCTV image‐based classification of blocked trash screens

AbstractThis study introduces image‐based classification techniques to identify whether trash screens in urban rivers are blocked. The study obtained 755 images from a CCTV camera surveying a trash screen located on an urban river at Tongwynlais in Cardiff. Manual quality control reduced the dataset to 577 images, labelled as either blocked (80%) or unblocked (20%). The performance of a logistic regression for classification of images was investigated using three different subsets of the labelled images: (1) the original dataset, (2) a balanced but under‐sampled dataset with equal number of blocked and unblocked images, and (3) an augmented dataset with an equal number of blocked and unblocked images using Gaussian noise augmentation to increase the number of unblocked images. Results show that our data‐augmentation method enhanced model accuracy by 8%, successfully classifying images as blocked or unblocked with an accuracy of 88%; by overcoming the bias in the dataset these results also highlight potential solutions to overcome the challenges of operating this methodology across a network of cameras. This enables authorities in both data rich and data scarce regions the ability to take advantage of machine learning to open up the next generation of a distributed, data‐driven flood warning systems, protecting people, infrastructure and the environment.

Manipulation of defect state emission in Zn chalcogenide quantum dots and their effects on chlorophyll spectral response

Water soluble Zn based quantum dots (QDs) are of interest due to their biocompatibility and less toxic features. They have been frequently used in studies related to biotechnology, especially in agriculture studies. However, to control the optical properties of Zn based QDs has still been a challenge. In this work, the defect state emission of ZnSe QDs was successfully controlled through two different routes; 1) By creating a sulfur rich outer region around the Se rich core 2) By changing the capping agent. Gradient alloyed ZnSeS QDs with Se rich core and S rich outer region were successfully synthesized with two different capping agents; N-Acetyl-L-Cysteine (NAC) and 3-Mercaptopropionic Acid (3-MPA). The contribution of emission originated from surface-defects almost disappeared in NAC capped ZnSeS QDs, with causing a significant increase in photoluminescence quantum yield. The interaction between Zn based QDs with chlorophyll molecules was also investigated. The absorption capacity of chlorophylls significantly enhanced upon interaction with 3-MPA capped ZnSeS QDs. Also, the spectral response of chlorophylls could be modulated through interaction with 3-MPA capped ZnSeS QDs, which could be manipulated by using ZnSeS QDs with different chemical composition. Our results indicated that ZnSeS QDs have potential to be used in agriculture, which could act as a modulator of light-harvesting capacity of chlorophylls. The ability to modulate chlorophyll spectral responses through QD interaction opens new possibilities for optimizing light utilization in photosynthetic organisms, thereby contributing to enhanced crop yields and more efficient use of light energy in natural and artificial ecosystems.

Buffer-gas cooling of hydrogen cyanide quantified by cavity-ringdown spectroscopy

We describe an instrument that uses continuous-wave (CW) cavity-ringdown spectroscopy to measure the translational and rotational temperature of buffer-gas cooled molecules and demonstrate its use on hydrogen cyanide. This instrument can access the near-infrared region around 1.5 μm—a rich spectral region that features the rotationally resolved first overtone of the C-H stretch for many astrophysically relevant molecules. Molecules are probed directly inside the buffer-gas cell, further enabling quantitative measurements of the effectiveness of this cooling technique.

Mithila Women in the Past and Present: A Journey of Resilience and Transformation

This paper explores the multifaceted journey of Mithila women, tracing their evolution from historical to contemporary times. Situated in the culturally rich region of Mithila, spanning parts of Northern India and Nepal, these women have been the custodians of a profound heritage characterized by resilience and adaptability. The paper delves into their roles within traditional societal frameworks, where they have long been pivotal in maintaining cultural practices such as the renowned Madhubani art. Through examining historical texts, cultural studies, and contemporary research, this study highlights Mithila women's enduring strength and agency. Despite rigid patriarchal structures and socio-economic challenges, Mithila women have continually carved out spaces for self-expression and empowerment. The paper investigates the transformative impact of education, economic participation, and political involvement on their lives. It emphasises how access to education has not only enhanced their capacities but also contributed to the socio economic development of their communities. The rise of Mithila women in local governance and their increasing role in Panchayati Raj institutions signify a shift towards greater political empowerment and social change. Ultimately, this paper aims to contribute to the broader discourse on gender and development by offering insights into the unique experiences of Mithila women. It underscores their journey of resilience and transformation as a testament to their enduring spirit and as a critical aspect of the region's socio-cultural fabric. The study calls for sustained efforts to address the challenges faced by Mithila women and to support their ongoing journey towards equality and empowerment.

The microstructure and mechanical property of W-TiC/Ti composites via chemical-mechanical milling method

Carbide dispersion strengthened W(CDS-W) has attracted much attention as a plasma-facing material (PFM). However, the carbide tends to segregate at W grain boundaries and has poor interface properties with W due to the large difference in the bond structure. In this work, nanometer Ti was added to improve the performance of the W/TiC interface, and nanoscaled W-TiC-x%Ti (x=0.1,0.5 and 1.0) composites were prepared by chemical-mechanical milling and ordinary sintering method. The effects of Ti on powder morphology, phase composition, microstructure and mechanical properties were systematically investigated using XRD, SEM, EDS, TEM and HADDF technologies. Simultaneously, the existence form and distribution of Ti elements, and W/TiC interface characteristics of powders and composites were analyzed. Moreover, the microstructure evolution and strengthening mechanism were preliminarily discussed. Results show that the W-TiC/Ti powder has an obvious core-shell multilayer structure with a particle size range of 50-120 nm. The addition of Ti exists in the forms of TiC, Ti, and TiO2, and has no effect on the morphology and phase composition. Besides, the phase transformation and solution-precipitation of the Ti-added occurs during the sintering process. Part of Ti precipitates on the W/TiC surface to form Ti rich region, which significantly promotes the dispersion of TiC and improves the W/TiC interface, as well as prevents the growth of W grains, and the average grain size is 2.90 μm. Moreover, the orientation relationship of [013]( 00)TiCFCC||[ 13]( 0)WBCC exists at the W/TiC interface, especially the coherent phase interface is formed. The tensile strength and microhardness at room temperature are 520 MPa and 850 HV0.2, respectively, which is attributed to the synergistic effect of fine-grained strengthening, dispersion strengthening and interface strengthening. This work can provide a new strategy and direction for preparing high-performance CDS-W materials.

HuR (ELAVL1) regulates the CCHFV minigenome and HAZV replication by associating with viral genomic RNA.

Crimean-Congo Hemorrhagic Fever virus (CCHFV) is a tick-borne pathogen that causes severe acute fever disease in humans and requires a biosafety level 4 laboratory for handling. Hazara virus (HAZV), belonging to the same virus genus as CCHFV, does not exhibit pathogenesis in humans. To investigate host RNA-binding proteins (RBPs) that regulate CCHFV replication, we generated a series of mutant RAW264.7 cells by CRISPR/Cas9 system and these cells were infected with HAZV. The viral titers in the supernatant of these cells was investigated, and HuR (ELAVL1) was identified. HuR KO RAW264.7 cells reduced HAZV replication. HuR is an RBP that enhances mRNA stability by binding to adenyl-uridine (AU)-rich regions in their 3' non-coding region (NCR). HuR regulates innate immune response by binding to host mRNAs of signaling molecules. The expression of cytokine genes such as Ifnb, Il6, and Tnf was reduced in HuR KO cells after HAZV infection. Although HuR supports the innate immune response during HAZV infection, we found that innate immune activation by HAZV infection did not affect its replication. We then investigated whether HuR regulates HAZV genome RNA stability. HAZV RNA genome was precipitated with an anti-HuR antibody, and HAZV genome RNA stability was lowered in HuR KO cells. We found that HuR associated with HAZV RNA and stabilized it to enhance HAZV replication. Furthermore, HuR-deficiency reduced CCHFV minigenome replication. CCHFV is a negative-strand RNA virus and positive-strand RNA is produced during replication. HuR was associated with positive-strand RNA rather than negative-strand RNA, and AU-rich region in 3'-NCR of S segment was responsible for immunoprecipitation with anti-HuR antibody and minigenome replication. Additionally, HuR inhibitor treatment reduced CCHFV minigenome replication. Our results indicate that HuR aids replication of the CCHFV minigenome by associating with the AU-rich region in the 3'-NCR.

A Paradoxical Tumor Antigen Specific Response in the Liver.

Functional tumor-specific CD8+ T cells are essential for an effective anti-tumor immune response and the efficacy of immune checkpoint inhibitor therapy. In comparison to other organ sites, we found higher numbers of tumor-specific CD8+ T cells in primary, metastatic liver tumors in murine tumor models. Despite their abundance, CD8+ T cells in the liver displayed an exhausted phenotype. Depletion of CD8+ T cells showed that liver tumor-reactive CD8+ T failed to control liver tumors but was effective against subcutaneous tumors. Similarly, analysis of single-cell RNA sequencing data from patients showed a higher frequency of exhausted tumor-reactive CD8+ T cells in liver metastasis compared to paired primary colon cancer. High-dimensional, multi-omic analysis combining proteomic CODEX and scRNA-seq data revealed enriched interaction of SPP1+ macrophages and CD8+ tumor-reactive T cells in profibrotic, alpha-SMA rich regions in the liver. Liver tumors grew less in Spp1-/- mice and the tumor-specific CD8+ T cells were less exhausted. Differential pseudotime trajectory inference analysis revealed extrahepatic signaling promoting an intermediate cell (IC) population in the liver, characterized by co-expression of VISG4, CSF1R, CD163, TGF-βR, IL-6R, SPP1. scRNA-seq of a third data set of premetastatic adenocarcinoma showed that enrichment of this population may predict liver metastasis. Our data suggests a mechanism by which extrahepatic tumors facilitate the formation of liver metastasis by promoting an IC population inhibiting tumor-reactive CD8+ T cell function.

Structural Insights into the Role of the Proline Rich Region in Tau Function.

Tau is a microtubule–associated protein that plays an important role in modulating axonal microtubules in neurons. Intracellular tau aggregates are found in a broad class of disorders, including Alzheimer&#8242s disease, termed tauopathies. Tau is an intrinsically disordered protein, and its structural disorder appears to be critical to its microtubule-related functions. Tubulin binding sites are found in tau&#8242s proline-rich region (PRR), microtubule binding repeats (MTBR: R1–R4), and pseudo–repeat, R′. While many post-translational modifications have been identified on tau, phosphorylation sites, which both regulate tubulin dimer and microtubule interactions and are correlated with disease, cluster with high frequency within the PRR. Here, we use fluorescence correlation spectroscopy and structural mass spectrometry techniques to characterize the impact of phosphomimic mutations in the PRR on tubulin dimer binding and probe the structure of the PRR–tubulin dimer complex. We find that phosphomimics cumulatively diminish tubulin dimer binding and slow microtubule polymerization. Additionally, we map two ~15 residue regions of the PRR as primary tubulin dimer binding sites and propose a model in which PRR enhances lateral interactions between tubulin dimers, complementing the longitudinal interactions observed for MTBR. Together these measurements provide insight into the previously overlooked relevance of tau&#8242s PRR in functional interactions with tubulin.

Rapid detection of Impatiens necrotic spot virus from thrips vectors using reverse transcription-recombinase polymerase amplification

The plant virus, Impatiens necrotic spot virus (INSV), is an economically important pathogen of vegetables, fruits, and ornamental crops. INSV is vectored by the western flower thrips, Frankliniella occidentalis, a small insect pest that is globally distributed. In recent years, INSV outbreaks have reached epidemic levels in the Salinas Valley of California—an agriculturally rich region where most of the lettuce (Lactuca sativa) is produced in the United States. Due to the obligate nature in which virus transmission occurs, new tools that could rapidly detect INSV from thrips vectors would enhance our ability to predict where virus outbreaks may occur. Here, we report on the development of a reverse transcription-recombinase polymerase amplification (RT-RPA) assay that can detect INSV from individual thrips. The assay uses crude extraction methods, is performed at a single temperature of 42 °C, can be completed in 25 min, and provides sensitivity levels that are comparable to other available detection methods. When the assay was used on field populations of thrips, INSV was successfully identified and quantified from individual larvae and adults. The work provides a new cost-effective surveillance tool that can rapidly detect INSV from its insect vector and from plants.

G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonism.

G-quadruplexes (G4s) are non-canonical nucleic acid structures that form in guanine (G)-rich genomic regions. X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease in which a SINE-VNTR-Alu (SVA) retrotransposon, characterised by amplification of a G-rich repeat, is inserted into the coding sequence of TAF1, a key partner of RNA polymerase II. XDP SVA alters TAF1 expression, but the cause of this outcome in XDP remains unknown. To assess whether G4s form in XDP SVA and affect TAF1 expression, we first characterised bioinformatically predicted XDP SVA G4s in vitro. We next showed that highly stable G4s can form and stop polymerase amplification at the SVA region from patient-derived fibroblasts and neural progenitor cells. Using chromatin immunoprecipitazion (ChIP)with an anti-G4 antibody coupled tosequencing orquantitativePCR, we showed that XDP SVA G4s are folded even when embedded in a chromatin context in patient-derived cells. Using the G4 ligands BRACO-19 and quarfloxin and total RNA-sequencinganalysis, we showed that stabilisation of the XDP SVA G4s reduces TAF1 transcripts downstream and around the SVA, and increases upstream transcripts, while destabilisation using the G4 unfolderPhpCincreases TAF1 transcripts. Our data indicate that G4 formation in the XDP SVA is a major cause of aberrant TAF1 expression, opening the way for the development of strategies to unfold G4s and potentially target the disease.

Evaluating AlphaFold for Clinical Pharmacology and Pharmacogenetics: A Case-Study of Huntingtin Variants Linked to Huntington's Disease.

To evaluate the artificial intelligence (AI)-guided AlphaFold algorithm for studying the binding interactions of human huntingtin and the aggregation of huntingtin peptides. Variants of huntingtin protein implicated in Huntington's disease were used as a model system to evaluate AlphaFold. Variants of huntingtin and huntingtin peptides with polyglutamine tracts (PQT) containing 21, 31, 51, or 78 glutamines were studied. The 3-dimensional structures of huntingtin variants and their interactions with huntingtin-associated protein-40 (HAP40) were obtained. Aggregation experiments were conducted with peptide sequences corresponding to variants of PQT, amino terminal sequence (NTS) plus PQT, NTS plus PQT plus proline rich region (PRR), and the 300 amino acid sequence from the NTS through HEAT3 of huntingtin. Oligomerization experiments with 1, 3, 6, or 12 peptide sequences were used to assess the quaternary structures of aggregates. The PQT and PQT plus NTS peptides formed a helical secondary structure that formed a central core in the quaternary structure of the aggregates The PRR formed an extended type II polyproline helix that did not participate in central core the aggregates. The distance between the amino and carboxyl termini of disease-linked 31Q, 51Q, and 78Q variants of full-length huntingtin was prominently decreased compared to the 21Q huntingtin. The interaction of HAP40 with the 78Q variant increased the distance between the amino and carboxyl termini. AlphaFold identified key tertiary structure changes in human huntingtin that have been independently corroborated in experimental models. The results highlight the utility of AlphaFold for hypothesis generation in pharmaceutical research.

Towards Low NOx Emissions Performance of A 65KW Recuperated Gas Turbine Operated on 100% Hydrogen

Abstract This work supports the development of a low NOx emission 65 kW natural gas turbine capable of operating on 100% hydrogen. This gas turbine has been demonstrated to operate from cold start to full load on up to 30% hydrogen mixed into natural gas with single digit ppm NOx emissions. To reach operation on 100% hydrogen, injectors specifically designed to 1) avoid challenges with flashback and 2) be field retrofittable were developed and tested. Successful operation of the engine from cold start to full load on 100% hydrogen was demonstrated. To support the development, a chemical reactor network (CRN) is used in conjunction with experimental injector mixing characterization. A strategy to account for variation in mixing performance was developed and utilized with the CRN to connect NOx emissions to the injector mixing performance. Measured fuel concentration profiles and the CRN model was used to infer the effects of mixing on NOx emission. The results illustrate how NOx emissions are directly influenced by local fuel rich regions found at the injector outlet. The CRN model can thus be used to screen injector designs and infer NOx performance and will be used to guide the development of injectors for hydrogen that can attain desired fuel distributions, concentrations, and velocities. The results affirm the direction needed to attain improved mixing and to operate at overall leaner conditions made possible by the stabilizing features inherent to hydrogen.

IDENTIFICATION CANDIDATE SSR, SNPs AND GENES ASSOCIATED SALT TOLERANCE IN ASIATIC COTTON (GOSSYPIUM ARBOREUM)

Soil is a vital resource for feeding the growing global population. Increased salt tolerance of perennial species used for fodder or fuel production is an important and natural method for controlling the spread of secondary salinity. This study was carried out to identify marker-trait association analysis using 7 traits and one comprehensive index of salt tolerance (CIST) and SSR and SNP markers for 215 accessions of Asiatic cotton (G. arboretum). The traits related to salt tolerance like germination rate (GR), fresh weight (FW), stem length (SL), water content (WC), chlorophyll content (ChlC), electric conduct (EC) and methylene dioxyamphetamine (MDA), of 215 cotton accessions were screened out using 150mM NaCl concentration after 7 days of seed growth. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions (top 5%) with high salinity tolerance were selected for breeding. Group 1 contained 12 accessions that were sensitive to high salt treatment (<0.6), group 2 contained 26 accessions that were moderate tolerant to salt treatment (0.6～1.5), group 3 includes 153 accession that were tolerant (1.5～2.5), and group 4 had 24 accessions that were highly tolerant to salt treatment (>2.5). The natural population of 215 accessions of G. arboretum was first classified into 3 main groups by phylogenic analysis, in which Group 2 (G2) and Group 3 (G3) represented the Yellow River and Yangtze River accessions respectively, while Group 1 (G1) contained mixed cotton accessions which belongs to different cotton growing areas in China. The grouped accessions results were largely congruent with the breeding history and ecological region, which indicates the extensive genetic diversity of G. arboretum accessions both in phenotype and genotype. The relative value (R) of the traits was used for marker-trait association analysis. Twenty-two strong SSR marker-trait associations were obtained with strict significant P value i.e. P< 0.01 and four makers including NAU1023, NAU1099, JESPR222, and NAU2783 were significantly related to salt tolerance. The marker NAU2783 was highest associated (P= 1.98E-12) with REC, and with the highest phenotype variation of 20.87%. Some markers are significantly associated with more than two traits. MUSS020 was significantly (P<0.01) related with RFW, and RMDA, NAU1375 was associated with RFW and RSL, while NAU3468 was significantly associated with RFW, RGR, and RWC. By applying the threshold of –log10 P≥4.0, the 2062 SNP markers covered all 13 chromosomes and 100 SNP markers locations that were unknown. Among these 2062 marker‐trait associations, 61 markers were associated with RGR, 187 markers were associated with RFW, 255 markers were associated with RSL, 370 markers were associated with RWC, 190 markers were associated with RChlC, 583 markers were associated with REC, 335 markers were associated with RMDA and 81 markers were associated with CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of −log10P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. The classification information derived from these studies may be used to facilitate the development of salt tolerant cotton accessions that could give economic yield in salinity prone areas. The strong marker-trait association results might provide insights for marker-assistant selecting salt-tolerant varieties and will be useful for future cotton breeding programs.