Global profiling of alternative splicing landscape responsive to salt stress in wheat (Triticum aestivum L.)

Guo, Weiwei; Yu, Kuohai; Han, Li; Li, Ximei; Wang, Hong; Liu, Yiguo; Zhang, Yumei

doi:10.1007/s10725-020-00623-2

Cited by 12 publications

(5 citation statements)

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“…The resulting genetic modifications alter transcript abundance and gene expression and eventually produce variant proteins ( Liu Z. et al, 2018 ). During plant growth and development, AS plays key roles in different biological processes and most importantly, in response to biotic and abiotic stress ( Guo et al, 2020 ). It is becoming increasingly evident that AS is not a by-product of stress but a regulatory part of the larger stress response ( Kannan et al, 2018 ).…”

Section: Impact Of Polyploidy and Alternative Splicing On Heat Stressmentioning

confidence: 99%

“…In a recent study, analysis of differential AS landscape among A, B, and D wheat subgenomes under salt treatment found that homologous genes displayed differential AS responses under salt stress and more AS events were identified in the salt-sensitive cultivar than in the salt-tolerant one. Interestingly, specific AS events were found induced at different time points of salt stress ( Guo et al, 2020 ). When multiple stresses were assessed, combined heat and drought stresses (HD) induced specific AS events compared with those induced by individual stresses.…”

Section: Impact Of Polyploidy and Alternative Splicing On Heat Stressmentioning

confidence: 99%

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Genetic and Physiological Responses to Heat Stress in Brassica napus

et al. 2022

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Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.

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Section: Impact Of Polyploidy and Alternative Splicing On Heat Stressmentioning

confidence: 99%

Section: Impact Of Polyploidy and Alternative Splicing On Heat Stressmentioning

confidence: 99%

Genetic and Physiological Responses to Heat Stress in Brassica napus

et al. 2022

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“…have also been generated and analyzed 11 – 14 , but there is little information on AS within different tissues and in response to environmental stressors and signaling molecules. Moreover, despite an abundance of studies investigating individual stress responses or specific AS events 15 – 17 , the current literature notably lacks comprehensive examinations of AS events that are common across multiple stress conditions in the pepper.…”

Section: Background and Summarymentioning

confidence: 99%

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

Kim,

Lee,

Yeom

et al. 2024

Sci Data

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Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.

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“…For instance, comparative proteomics of salt stress in the leaves and roots of soybean seedlings indicated that salt-responsive proteins were correlated with protein synthesis, amino acid metabolism, carbohydrate metabolism, and oxidative homeostasis [37][38][39]. In Arabidopsis [34], cotton [40], and wheat [41], it was demonstrated that AS events were responsive to salt stress. Although some roles of AS in response to abiotic stress have been revealed, exactly how AS contributes to plant development, stress responses, and adaptation to changing environments, among other aspects, need to be further explored.…”

Section: Introductionmentioning

confidence: 99%

Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress

Han,

Niu,

Gao

et al. 2024

IJMS

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Salt stress profoundly affects plant growth, prompting intricate molecular responses, such as alternative splicing (AS), for environmental adaptation. However, the response of AS events to salt stress in Opisthopappus (Opisthopappus taihangensis and Opisthopappus longilobus) remains unclear, which is a Taihang Mountain cliff-dwelling species. Using RNA-seq data, differentially expressed genes (DEGs) were identified under time and concentration gradients of salt stress. Two types of AS, skipped exon (SE) and mutually exclusive exons (MXE), were found. Differentially alternative splicing (DAS) genes in both species were significantly enriched in “protein phosphorylation”, “starch and sucrose metabolism”, and “plant hormone signal transduction” pathways. Meanwhile, distinct GO terms and KEGG pathways of DAS occurred between two species. Only a small subset of DAS genes overlapped with DEGs under salt stress. Although both species likely adopted protein phosphorylation to enhance salt stress tolerance, they exhibited distinct responses. The results indicated that the salt stress mechanisms of both Opisthopappus species exhibited similarities and differences in response to salt stress, which suggested that adaptive divergence might have occurred between them. This study initially provides a comprehensive description of salt responsive AS events in Opisthopappus and conveys some insights into the molecular mechanisms behind species tolerance on the Taihang Mountains.

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Global profiling of alternative splicing landscape responsive to salt stress in wheat (Triticum aestivum L.)

Cited by 12 publications

References 50 publications

Genetic and Physiological Responses to Heat Stress in Brassica napus

Genetic and Physiological Responses to Heat Stress in Brassica napus

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

Responsive Alternative Splicing Events of Opisthopappus Species against Salt Stress

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