Background
Salt stress is one of the main abiotic stresses that limits rice production worldwide. Rice salt tolerance at the bud burst stage directly affects the seedling survival rate and the final ...yield in the direct seeding cultivation model. However, the reports on quantitative trait locus (QTL) mapping and map-based cloning for salt tolerance at the bud burst stage are limited.
Results
Here, an F
2:3
population derived from a cross between IR36 (salt-sensitive) and Weiguo (salt-tolerant) was used to identify salt-tolerant QTL interval at the bud burst stage using a whole-genome sequencing-based QTL-seq containing 40 extreme salt-tolerant and 40 extreme salt-sensitive individuals. A major QTL,
qRSL7
, related to relative shoot length (RSL) was detected on chromosome 7 using ΔSNP index algorithms and Euclidean Distance (ED) algorithms. According to single nucleotide polymorphisms (SNPs) between the parents, 25 Kompetitive allele-specific PCR (KASP) markers were developed near
qRSL7
, and regional QTL mapping was performed using 199 individuals from the F
2:3
population. We then confirmed and narrowed down
qRSL7
to a 222 kb genome interval. Additionally, RNA sequencing (RNA-seq) was performed for IR36 and Weiguo at 36 h after salt stress and control condition at the bud burst stage, and 5 differentially expressed genes (DEGs) were detected in the candidate region. The qRT-PCR results showed the same expression patterns as the RNA-seq data. Furthermore, sequence analysis revealed a 1 bp Indel difference in
Os07g0569700
(
OsSAP16
) between IR36 and Weiguo.
OsSAP16
encodes a stress-associated protein whose expression is increased under drought stress.
Conclusion
These results indicate that
OsSAP16
was the candidate gene of
qRSL7
. The results is useful for gene cloning of
qRSL7
and for improving the salt tolerance of rice varieties by marker assisted selection (MAS).
Background
Salinity-alkalinity stress is one of the major factors limiting rice production. Damage caused by alkaline salt stress is more severe than that caused by neutral salt stress. Alkali ...tolerance at the bud stage in rice directly affects seedling survival and final yield when using the direct seeding cultivation model. However, genetic resources (QTLs and genes) for rice breeders to improve alkali tolerance are limited. In this study, we combined linkage mapping and a genome-wide association study (GWAS) to analyze the genetic structure of this trait in
japonica
rice at the bud stage.
Results
A population of 184 recombinant inbred lines (RILs) was utilized to map quantitative trait loci (QTLs) for the root length under control condition (RL), alkaline stress (ARL) and relative root length (RRL) at the bud stage. A major QTL related to alkali tolerance at the rice bud stage,
qAT11
, was detected on chromosome 11. Interestingly, a GWAS identified a lead SNP (Chr_21,999,659) in
qAT11
that was significantly associated with alkaline tolerance. After filtering by linkage disequilibrium (LD), haplotype analysis, quantitative real-time PCR, we obtained three candidate genes (
LOC_Os11g37300
,
LOC_Os11g37320
and
LOC_Os11g37390
). In addition, we performed phenotype verification on the CRISPR/Cas9 mutant of
LOC_Os11g37390
.
Conclusion
Based on these results,
LOC_Os11g37300
,
LOC_Os11g37320
and
LOC_Os11g37390
were the candidate genes contributing to alkaline tolerance in
japonica
rice. This study provides resources for breeding aimed at improving rice responses to alkalinity stress.
The paper discusses the responses of eutectic silicon and eutectic cells in Al–10Si alloy upon inoculation with an Al–10Si–2Fe master alloy. The further inoculation hardly destroys the modification ...effect of Sr but significantly refines the eutectic cells in Sr-modified samples, while in unmodified samples, it stimulates the occurrences of polyhedral silicon particles and divorced eutectic. Thermal analysis, scanning electron microscopy, (high-resolution) transmission electron microscopy and scanning and transmission electron microscopy have been used to elucidate the underlying mechanism. A cluster-assisted nucleation mechanism responsible for the enhanced nucleation of silicon phase upon inoculation is proposed. Icosahedral (AlFeSi) clusters are speculated to evolve from the added Al–10Si–2Fe master alloy in Al–10Si melt, around which aggregations of silicon atoms form. Through a series of structural evolutions, these clusters transform into precursors of a silicon crystal. The subsequent formation of silicon particles is achieved by the agglomerations and attachments of these precursors and individual silicon atoms. This hypothesis is further consolidated by the increased characteristic temperatures of eutectic and the anomalous appearance of a high density of nanoscale particles, as well as the abnormal disappearance of Sr-induced twins in further inoculated silicon particles. The increased characteristic temperatures are strong indications of the enhanced nucleation of the silicon phase. The high density of nanoscale particles with an indeterminate crystal structure are the survivors of these precursors. In an Sr-modified and further inoculated sample, the formation of Sr-induced twins is consequently inhibited due to the participation of these precursors during the growth of silicon particles. Furthermore, based on the proposed nucleation mechanism, the dependence of eutectic cell size on Sr level is elucidated in detail.
Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes ...containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.
•miR-98 is significantly reduced in both clinical LSCC specimens and cell lines.•miR-98 directly targets HMGA2 in mediating EMT.•HMGA2 mRNA level is negatively correlated with miR-98 level in LSCC ...tissues.•HMGA2 overexpression transforms LSCC cells to acquire stem cell-like features.•HMGA2 directly regulates POSTN expression to affect EMT in LSCC.
It has been widely considered that reversing epithelial-to-mesenchymal transition (EMT) is a potential access to restrain cancer progression and therapeutic resistance. Here, we aim to uncover the novel mechanisms by which we can reverse EMT and inhibit metastasis in laryngeal squamous cell carcinoma (LSCC). We show that miR-98 is significantly reduced in both LSCC specimens and cell lines. Over-expression of miR-98 inhibits the EMT-related gene expression and metastasis and invasive behavior in LSCC in vitro, as well as reduces lung metastasis in mouse model. In the mechanistically study, miR-98 directly targets HMGA2 in mediating EMT. HMGA2 knock down by si-RNA method declines several EMT-related genes expression and LSCC migration and invasion. In parallel, overexpression of HMGA2 transforms LSCC cells to acquire stem cell-like features. Furthermore, we reveal that HMGA2-mediated EMT is closely linked with the expression of POSTN that inhibits EMT, as a tumor suppressor, by gene profiling analyses. POSTN is transcriptionally repressed by HMGA2. In clinic, the HMGA2 mRNA level is negatively correlated with the miR-98 level in LSCC patient cohort. In conclusion, our study confers a powerful signal: miR-98-HMGA-POSTN in LSCC, which is able to reverse EMT and inhibit metastasis, underlining the therapeutic potential of this signal.
Rice (Oryza sativa L.) is one of the most widely grown food crops, and its yield and quality are particularly important for a warm-saturated diet. Cold stress restricts rice growth, development, and ...yield; however, the specific mechanism of cold tolerance in rice remains unknown.
The analysis of leaf physiological and photosynthetic characteristics showed that the two rice varieties were significantly affected by cold stress, but the cold-tolerant variety KY131 had more stable physiological characteristics, maintaining relatively good photosynthetic capacity. To better explore the transcriptional regulation mechanism and biological basis of rice response to cold stress, a comprehensive analysis of the rice transcriptome and lipidome under low temperature and control temperature conditions was carried out. The transcriptomic analysis revealed that lipid metabolism, including membrane lipid and fatty acid metabolism, may be an important factor in rice cold tolerance, and 397 lipid metabolism related genes have been identified. Lipidomics data confirmed the importance of membrane lipid remodeling and fatty acid unsaturation for rice adaptation to cold stress. This indicates that the changes in the fluidity and integrity of the photosynthetic membrane under cold stress lead to the reduction of photosynthetic capacity, which could be relieved by increased levels of monogalactosyldiacylglycerol that mainly caused by markedly increased expression of levels of 1,2-diacylglycerol 3-beta-galactosyltransferase (MGD). The upregulation of phosphatidate phosphatase (PAP2) inhibited the excessive accumulation of phosphatidate (PA) to produce more phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylglycerol (PG), thereby preventing of membrane phase transition under cold stress. In addition, fatty acid β-oxidation is worth further study in rice cold tolerance. Finally, we constructed a metabolic model for the regulatory mechanism of cold tolerance in rice, in which the advanced lipid metabolism system plays a central role.
Lipidome analysis showed that membrane lipid composition and unsaturation were significantly affected, especially phospholipids and galactolipids. Our study provides new information to further understand the response of rice to cold stress.
Abstract
The role of 5-methylcytosine (m5C) in tumor initiation and progression has been increasingly recognized. However, the precise association between the regulation of m5C and the progression, ...metastasis, and prognosis of head and neck squamous cell carcinoma (HNSCC) has not yet been fully explored. Data from 545 HNSCC patients obtained from The Cancer Genome Atlas (TCGA) database were analyzed. Unsupervised cluster analysis was conducted using the expression levels of m5C regulatory genes. Additionally, gene set variation analysis (GSVA), single-sample gene set enrichment analysis (ssGSEA), and Cox regression analysis were utilized. Quantitative reverse transcription polymerase chain reaction (RT-qPCR), colony formation assay, transwell experiments and western blots were performed in the HNSCC cell line UM-SCC-17B to assess the expression and functional role of one of the novel signatures, CNFN. Significant expression differences were found in m5C regulatory genes between tumor and normal tissues in HNSCC. Two distinct m5C modification patterns, characterized by substantial prognostic differences, were identified. Cluster-2, which exhibited a strong association with epithelial-mesenchymal transition (EMT), was found to be associated with a poorer prognosis. Based on the m5C clusters and EMT status, differentially expressed genes (DEGs) were identified. Using DEGs, an 8-gene signature (CAMK2N1, WNT7A, F2RL1, AREG, DEFB1, CNFN, TGFBI, and CAV1) was established to develop a prognostic model. The performance of this signature was validated in both the training and external validation datasets, demonstrating its promising efficacy. Furthermore, additional investigations using RT-qPCR on clinical specimens and experimental assays in cell lines provided compelling evidence suggesting that CNFN, one of the genes in the signature, could play a role in HNSCC progression and metastasis through the EMT pathway. This study highlighted the role of m5C in HNSCC progression and metastasis. The relationship between m5C and EMT has been elucidated for the first time. A robust prognostic model was developed for accurately predicting HNSCC patients’ survival outcomes. Potential molecular mechanisms underlying these associations have been illuminated through this research.
Main conclusion
We projected meta-QTL (MQTL) for drought, salinity, cold state, and high metal ion tolerance in rice using a meta-analysis based on high-density consensus maps. In addition, a ...genome-wide association analysis was used to validate the results of the meta-analysis, and four new chromosome intervals for mining abiotic stress candidate genes were obtained.
Drought, severe cold, high salinity, and high metallic ion concentrations severely restrict rice production. Consequently, the breeding of abiotic stress-tolerant variety is being paid increasingly more attention. This study aimed to identify meta-quantitative trait loci (MQTL) for abiotic stress tolerance in rice, as well as the molecular markers and potential candidate genes of the MQTL regions. We summarized 2785 rice QTL and conducted a meta-analysis of 159 studies. We found 82 drought tolerance (DT), 70 cold tolerance (CT), 70 salt tolerance (ST), and 51 heavy metal ion tolerance (IT) meta-QTL, as well as 20 DT, 11 CT, 22 ST, and 5 IT candidate genes in the MQTL interval. Thirty-one multiple-tolerance related MQTL regions, which were highly enriched, were also detected, and 13 candidate genes related to multiple-tolerance were obtained. In addition, the correlation between DT, CT, and ST was significant in the rice genome. Four candidate genes and four MM-QTL regions were detected simultaneously by GWAS and meta-analysis. The four candidate genes showed distinct genetic differentiation and substantial genetic distance between
indica
and
japonica
rice, and the four MM-QTL are potential intervals for mining abiotic stress-related candidate genes. The candidate genes identified in this study will not only be useful for marker-assisted selection and pyramiding but will also accelerate the fine mapping and cloning of the candidate genes associated with abiotic stress-tolerance mechanisms in rice.
Cold stress caused by low temperatures is an important factor restricting rice production. Identification of cold-tolerance genes that can stably express in cold environments is crucial for molecular ...rice breeding. In this study, we employed high-throughput quantitative trait locus sequencing (QTL-seq) analyses in a 460-individual F.sub.2:3 mapping population to identify major QTL genomic regions governing cold tolerance at the seedling stage in rice. A novel major QTL (qCTS6) controlling the survival rate (SR) under low-temperature conditions of 9degreesC/10 days was mapped on the 2.60-Mb interval on chromosome 6. Twenty-seven single-nucleotide polymorphism (SNP) markers were designed for the qCST6 region based on re-sequencing data, and local QTL mapping was conducted using traditional linkage analysis. Eventually, we mapped qCTS6 to a 96.6-kb region containing 13 annotated genes, of which seven predicted genes contained 13 non-synonymous SNP loci. Quantitative reverse transcription PCR analysis revealed that only Os06g0719500, an OsbZIP54 transcription factor, was strongly induced by cold stress. Haplotype analysis confirmed that +376 bp (T>A) in the OsbZIP54 coding region played a key role in regulating cold tolerance in rice. We identified OsbZIP54 as a novel regulatory gene associated with rice cold-responsive traits, with its Dongfu-104 allele showing specific cold-induction expression serving as an important molecular variation for rice improvement. This result is expected to further exploration of the genetic mechanism of rice cold tolerance at the seedling stage and improve cold tolerance in rice varieties by marker-assisted selection.
Transcranial alternating current stimulation (tACS) applies a sinusoidal oscillating current to modulate intrinsic oscillatory activity. Relevant studies of tACS have indicated that tACS can increase ...spontaneous brain activity in the occipital area. However, few studies have compared the effects of tACS with different current intensities on spontaneous brain activity in the occipital region. In this study, 10-Hz tACS was delivered to the occipital region at different current intensities (i.e., 1 and 2 mA). We investigated the effect of the tACS on both eyes-open and eyes-closed resting-state electroencephalography (EEG). A total of 20 subjects and fifteen subjects were recruited to participate in the 1-mA tACS experiment and the 2-mA tACS experiment, respectively. Ten subjects participated in both experiments. The experimental results demonstrated that both 1-mA tACS and 2-mA tACS could increase occipital resting-state EEG activities. For the eyes-open condition, alpha activity elicited by 2-mA tACS increased significantly greater than that elicited by 1-mA tACS, while 1-mA tACS could produce greater alpha activity compared to 2 mA for the eyes-closed condition. These results suggested that the optimal current intensity might be different for the eyes-open and eyes-closed resting-state conditions, laying a foundation for the subsequent study of occipital tACS on task-state EEG activities.
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