Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs

Alternative splicing (AS) is a common post-transcriptional regulatory mechanism that modulates gene expression to increase proteome diversity. Increasing evidence indicates that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate drought responses in soybean remains poorly understood. In this study, we performed a genome-wide analysis of AS events in soybean (Glycine max) roots grown under various drought conditions using the high-throughput RNA-sequencing method, identifying 385, 989, 1429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Among them, alternative 3′ splice sites and skipped exons were the major types of AS. Overall, 2120 genes that experienced significant AS regulation were identified from these drought-treated root samples. Gene Ontology term analysis indicated that the AS regulation of binding activity has vital roles in the drought response of soybean root. Notably, the genes encoding splicing regulatory factors in the spliceosome pathway and mRNA surveillance pathway were enriched according to the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. Splicing regulatory factor-related genes in soybean root also responded to drought stress and were alternatively spliced under drought conditions. Taken together, our data suggest that drought-responsive AS acts as a direct or indirect mode to regulate drought response of soybean roots. With further in-depth research of the function and mechanism of AS in the process of abiotic stress, these results will provide a new strategy for enhancing stress tolerance of plants.

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Molecular and Physiological Responses of Rice and Weedy Rice to Heat and Drought Stress

Agriculture ◽

10.3390/agriculture11010009 ◽

2020 ◽

Vol 11 (1) ◽

pp. 9

Author(s):

Leonard Bonilha Piveta ◽

Nilda Roma-Burgos ◽

José Alberto Noldin ◽

Vívian Ebeling Viana ◽

Claudia de Oliveira ◽

...

Keyword(s):

Genetic Diversity ◽

Heat Stress ◽

Drought Stress ◽

Intercellular Co2 Concentration ◽

Tiller Number ◽

Weedy Rice ◽

Photosynthetic Parameters ◽

World Population ◽

Rice Grain ◽

Rice Cultivars

Rice is the staple food for about half of the world population. Rice grain yield and quality are affected by climatic changes. Arguably, rice cultivars’ genetic diversity is diminished from decades of breeding using narrow germplasm, requiring introgressions from other Oryza species, weedy or wild. Weedy rice has high genetic diversity, which is an essential resource for rice crop improvement. Here, we analyzed the phenotypic, physiological, and molecular profiles of two rice cultivars (IRGA 424 and SCS119 Rubi) and five weedy rice (WR), from five different Brazilian regions, in response to heat and drought stress. Drought and heat stress affected the phenotype and photosynthetic parameters in different ways in rice and WR genotypes. A WR from Northern Brazil yielded better under heat stress than the non-stressed check. Drought stress upregulated HSF7A while heat stress upregulated HSF2a. HSP74.8, HSP80.2, and HSP24.1 were upregulated in both conditions. Based on all evaluated traits, we hypothesized that in drought conditions increasing HSFA7 expression is related to tiller number and that increase WUE (water use efficiency) and HSFA2a expression are associated with yield. In heat conditions, Gs (stomatal conductance) and E’s increases may be related to plant height; tiller number is inversely associated with HSPs expression, and chlorophyll content and Ci (intercellular CO2 concentration) may be related to yield. Based on morphology, physiology, and gene regulation in heat and drought stress, we can discriminate genotypes that perform well under these stress conditions and utilize such genotypes as a source of genetic diversity for rice breeding.

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Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana

International Journal of Molecular Sciences ◽

10.3390/ijms22105064 ◽

2021 ◽

Vol 22 (10) ◽

pp. 5064

Author(s):

Qinghua Chen ◽

Linghui Guo ◽

Yanwen Yuan ◽

Shuangling Hu ◽

Fei Guo ◽

...

Keyword(s):

Drought Stress ◽

Transmembrane Domain ◽

Tea Plant ◽

Microtubule Assembly ◽

Pcr Analysis ◽

Drought Response ◽

Stomatal Development ◽

Wild Type ◽

Over Expression ◽

Histone H3k4

Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.

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A survey of computational methods in transcriptome-wide alternative splicing analysis

BioMolecular Concepts ◽

10.1515/bmc-2014-0040 ◽

2015 ◽

Vol 6 (1) ◽

pp. 59-66 ◽

Cited By ~ 10

Author(s):

Jianbo Wang ◽

Zhenqing Ye ◽

Tim H.-M. Huang ◽

Huidong Shi ◽

Victor Jin

Keyword(s):

Alternative Splicing ◽

Experimental Validation ◽

Gene Diversity ◽

Exon Skipping ◽

Differential Splicing ◽

Sequencing Data ◽

Future Directions ◽

Specific Analysis ◽

Software Implementations ◽

Expected Outcomes

AbstractAlternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

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Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa)

Functional Plant Biology ◽

10.1071/fp12015 ◽

2012 ◽

Vol 39 (5) ◽

pp. 402 ◽

Cited By ~ 28

Author(s):

Veeresh R. P. Gowda ◽

Amelia Henry ◽

Vincent Vadez ◽

H. E. Shashidhar ◽

Rachid Serraj

Keyword(s):

Oryza Sativa ◽

Drought Stress ◽

Root Growth ◽

Water Uptake ◽

Root Length Density ◽

Oryza Sativa L ◽

Root Water Uptake ◽

Snp Markers ◽

Drought Response ◽

Genotypic Differences

In addition to characterising root architecture, evaluating root water uptake ability is important for understanding drought response. A series of three lysimeter studies were conducted using the OryzaSNP panel, which consists of 20 diverse rice (Oryza sativa L.) genotypes. Large genotypic differences in drought response were observed in this genotype panel in terms of plant growth and water uptake. Total water uptake and daily water uptake rates in the drought-stress treatment were correlated with root length density, especially at depths below 30 cm. Patterns of water uptake among genotypes remained consistent throughout the stress treatments: genotypes that initially extracted more water were the same genotypes that extracted more water at the end of the study. These results suggest that response to drought by deep root growth, rather than a conservative soil water pattern, seems to be important for lowland rice. Genotypes in the O. sativa type aus group showed some of the greatest water uptake and root growth values. Since the OryzaSNP panel has been genotyped in detail with SNP markers, we expect that these results will be useful for understanding the genetics of rice root growth and function for water uptake in response to drought.

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Single-cell Differential Splicing Analysis Reveals High Heterogeneity of Liver Tumor-infiltrating T Cells

10.21203/rs.3.rs-123121/v1 ◽

2020 ◽

Author(s):

Shang Liu ◽

Biaofeng Zhou ◽

Liang Wu ◽

Yan Sun ◽

Jie Chen ◽

...

Keyword(s):

T Cells ◽

Alternative Splicing ◽

T Cell ◽

Single Cell ◽

Regulatory Factor ◽

Differential Splicing ◽

Cell Level ◽

Comprehensive Investigation ◽

Cancer Initiation ◽

Cell Groups

Abstract Recent advances in single-cell RNA sequencing (scRNA-seq) have improved our understanding of the association between tumor-infiltrating lymphocyte (TILs) heterogeneity and cancer initiation and progression. However, studies investigating alternative splicing (AS) as an important regulatory factor of heterogeneity remain limited. Here, we developed a new computational tool, DESJ-detection, which accurately detects differentially expressed splicing junctions (DESJs) between cell groups at the single-cell level. We analyzed 5,063 T cells of hepatocellular carcinoma (HCC) and identified 1,176 DESJs across 11 T cell subtypes. Interestingly, DESJs were enriched in UTRs, and have putative effects on heterogeneity. Cell subtypes with a similar function closely clustered together at the AS level. Meanwhile, we identified two novel cell states, pre-exhaustion and pre-activation with the isoform markers CD103-201 and ARHGAP15-205. In summary, we present a comprehensive investigation of alternative splicing differences, which provided novel insights into T cell heterogeneity and can be applied to other full-length scRNA-seq datasets.

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The Vegetation Drought Response Index (VegDRI): A New Integrated Approach for Monitoring Drought Stress in Vegetation

GIScience & Remote Sensing ◽

10.2747/1548-1603.45.1.16 ◽

2008 ◽

Vol 45 (1) ◽

pp. 16-46 ◽

Cited By ~ 236

Author(s):

Jesslyn F. Brown ◽

Brian D. Wardlow ◽

Tsegaye Tadesse ◽

Michael J. Hayes ◽

Bradley C. Reed

Keyword(s):

Drought Stress ◽

Integrated Approach ◽

Drought Response ◽

Response Index

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Infection with an asymptomatic virus in rice results in a delayed drought response

Functional Plant Biology ◽

10.1071/fp19241 ◽

2020 ◽

Vol 47 (3) ◽

pp. 239 ◽

Cited By ~ 1

Author(s):

Jaymee R. Encabo ◽

Reena Jesusa A. Macalalad-Cabral ◽

Jerlie Mhay K. Matres ◽

Sapphire Charlene Thea P. Coronejo ◽

Gilda B. Jonson ◽

...

Keyword(s):

Drought Stress ◽

Abiotic Stresses ◽

Water Status ◽

Drought Response ◽

Plant Responses ◽

Leaf Rolling ◽

Rice Tungro Spherical Virus ◽

Biotic And Abiotic Stresses ◽

Rice Plants ◽

Increased Susceptibility

Infection of viruses in plants often modifies plant responses to biotic and abiotic stresses. In the present study we examined the effects of Rice tungro spherical virus (RTSV) infection on drought response in rice. RTSV infection delayed the onset of leaf rolling by 1–2 days. During the delay in drought response, plants infected with RTSV showed higher stomatal conductance and less negative leaf water potential under drought than those of uninfected plants, indicating that RTSV-infected leaves were more hydrated. Other growth and physiological traits of plants under drought were not altered by infection with RTSV. An expression analysis of genes for drought response-related transcription factors showed that the expression of OsNAC6 and OsDREB2a was less activated by drought in RTSV-infected plants than in uninfected plants, further suggesting improved water status of the plants due to RTSV infection. RTSV accumulated more in plants under drought than in well-watered plants, indicating the increased susceptibility of rice plants to RTSV infection by drought. Collectively, these results indicated that infection with RTSV can transiently mitigate the influence of drought stress on rice plants by increasing leaf hydration, while drought increased the susceptibility of rice plants to RTSV.

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Assessment of yield based selection under managed field stress condition for breeding for rice yield improvement under drought

Biologia ◽

10.2478/s11756-013-0194-2 ◽

2013 ◽

Vol 68 (4) ◽

Cited By ~ 1

Author(s):

Abhinav Jain ◽

Padma Balaravi ◽

Vinay Shenoy

Keyword(s):

Drought Stress ◽

Stress Condition ◽

Rice Yield ◽

Direct Selection ◽

Rice Cultivars ◽

The Past ◽

Drought Tolerant ◽

Selection For ◽

Target Environment ◽

Very High

AbstractThe progress in development and dissemination of drought tolerant lines has been slow as compared to the increasing drought prevalence in the rice growing regions. Significant amount of work has been done in the past on drought resistance traits in rice crop, still the benefit of improved drought tolerant rice cultivars reaching the farmer’s field is not very high and ways to expedite the development of drought tolerant and productive rice cultivars needs to be addressed. In this article, an assessment of easily practicable approach of managed stress screening and prospect of direct selection for yield under drought stress is discussed. Also the large effect yield QTLs identified for grain yield under drought stress field conditions is being reviewed for successful introgression into elite genetic background for developing drought tolerant cultivars with improved yield for the drought prone target environment.

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