Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers

Environmental conditions, such as photoperiod and temperature, can affect male fertility in plants. While this feature is heavily exploited in rice to generate male-sterile lines for hybrid breeding, the underlying molecular mechanisms remain largely unknown. In this study, we use a transcriptomics approach to identify key genes and regulatory networks affecting pollen maturation in rice anthers in response to different day lengths. A total of 11,726 differentially expressed genes (DEGs) were revealed, of which 177 were differentially expressed at six time points over a 24-h period. GO enrichment analysis revealed that genes at all time points were enriched in transport, carbohydrate, and lipid metabolic processes, and signaling pathways, particularly phytohormone signaling. In addition, co-expression network analysis revealed four modules strongly correlated with photoperiod. Within these four modules, 496 hub genes were identified with a high degree of connectivity to other photoperiod-sensitive DEGs, including two previously reported photoperiod- and temperature-sensitive genes affecting male fertility, Carbon Starved Anther and UDP-glucose pyrophosphorylase, respectively. This work provides a new understanding on photoperiod-sensitive pollen development in rice, and our gene expression data will provide a new, comprehensive resource to identify new environmentally sensitive genes regulating male fertility for use in crop improvement.

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Crop Improvement Through Temperature Resilience

Annual Review of Plant Biology ◽

10.1146/annurev-arplant-050718-100016 ◽

2019 ◽

Vol 70 (1) ◽

pp. 753-780 ◽

Cited By ~ 18

Author(s):

Jingyu Zhang ◽

Xin-Min Li ◽

Hong-Xuan Lin ◽

Kang Chong

Keyword(s):

Crop Production ◽

Molecular Mechanisms ◽

Crop Improvement ◽

Hybrid Breeding ◽

Plant Responses ◽

Temperature Sensitive ◽

Heat Stress Response ◽

Signal Perception ◽

Temperature Signal

Abnormal environmental temperature affects plant growth and threatens crop production. Understanding temperature signal sensing and the balance between defense and development in plants lays the foundation for improvement of temperature resilience. Here, we summarize the current understanding of cold signal perception/transduction as well as heat stress response. Dissection of plant responses to different levels of cold stresses (chilling and freezing) illustrates their common and distinct signaling pathways. Axillary bud differentiation in response to chilling is presented as an example of the trade-off between defense and development. Vernalization is a cold-dependent development adjustment mediated by O-GlcNAcylation and phosphorylation to sense long-term cold. Recent progress on major quantitative trait loci genes for heat tolerance has been summarized. Molecular mechanisms in utilizing temperature-sensitive sterility in super hybrid breeding in China are revealed. The way to improve crop temperature resilience using integrative knowledge of omics as well as systemic and synthetic biology, especially the molecular module program, is summarized.

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Increased expression of the MALE STERILITY1 transcription factor gene results in temperature-sensitive male sterility in barley

Journal of Experimental Botany ◽

10.1093/jxb/eraa382 ◽

2020 ◽

Vol 71 (20) ◽

pp. 6328-6339

Author(s):

José Fernández-Gómez ◽

Behzad Talle ◽

Zoe A Wilson

Keyword(s):

Transcription Factor ◽

Male Sterility ◽

Pollen Development ◽

Breeding Systems ◽

Hybrid Breeding ◽

Temperature Sensitive ◽

Hybrid Vigour ◽

Male Sterile ◽

The Impact

Abstract Understanding the control of fertility is critical for crop yield and breeding; this is particularly important for hybrid breeding to capitalize upon the resultant hybrid vigour. Different hybrid breeding systems have been adopted; however, these are challenging and crop specific. Mutants with environmentally reversible fertility offer valuable opportunities for hybrid breeding. The barley HvMS1 gene encodes a PHD-finger transcription factor that is expressed in the anther tapetum, which is essential for pollen development and causes complete male sterility when overexpressed in barley. This male sterility is due at least in part to indehiscent anthers resulting from incomplete tapetum degeneration, failure of anther opening, and sticky pollen under normal growth conditions (15 °C). However, dehiscence and fertility are restored when plants are grown at temperatures >20 °C, or when transferred to >20 °C during flowering prior to pollen mitosis I, with transfer at later stages unable to rescue fertility in vivo. As far as we are aware, this is the first report of thermosensitive male sterility in barley. This offers opportunities to understand the impact of temperature on pollen development and potential applications for environmentally switchable hybrid breeding systems; it also provides a ‘female’ male-sterile breeding tool that does not need emasculation to facilitate backcrossing.

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Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism Underlying Salt and Alkali Stress Tolerance in Tobacco

International Journal of Molecular Sciences ◽

10.3390/ijms20102391 ◽

2019 ◽

Vol 20 (10) ◽

pp. 2391 ◽

Cited By ~ 3

Author(s):

Jiayang Xu ◽

Qiansi Chen ◽

Pingping Liu ◽

Wei Jia ◽

Zheng Chen ◽

...

Keyword(s):

Salinity Stress ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Crop Yields ◽

Antioxidant Activities ◽

Expression Patterns ◽

Differentially Expressed ◽

Alkali Stress ◽

Rna Seq ◽

Alkali Tolerance

Salinity is one of the most severe forms of abiotic stress and affects crop yields worldwide. Plants respond to salinity stress via a sophisticated mechanism at the physiological, transcriptional and metabolic levels. However, the molecular regulatory networks involved in salt and alkali tolerance have not yet been elucidated. We developed an RNA-seq technique to perform mRNA and small RNA (sRNA) sequencing of plants under salt (NaCl) and alkali (NaHCO3) stress in tobacco. Overall, 8064 differentially expressed genes (DEGs) and 33 differentially expressed microRNAs (DE miRNAs) were identified in response to salt and alkali stress. A total of 1578 overlapping DEGs, which exhibit the same expression patterns and are involved in ion channel, aquaporin (AQP) and antioxidant activities, were identified. Furthermore, genes involved in several biological processes, such as “photosynthesis” and “starch and sucrose metabolism,” were specifically enriched under NaHCO3 treatment. We also identified 15 and 22 miRNAs that were differentially expressed in response to NaCl and NaHCO3, respectively. Analysis of inverse correlations between miRNAs and target mRNAs revealed 26 mRNA-miRNA interactions under NaCl treatment and 139 mRNA-miRNA interactions under NaHCO3 treatment. This study provides new insights into the molecular mechanisms underlying the response of tobacco to salinity stress.

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MON-719 The Cellular and Molecular Landscape of Hypothalamic Patterning and Differentiation

Journal of the Endocrine Society ◽

10.1210/jendso/bvaa046.1237 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

Author(s):

Thomas Kim

Keyword(s):

Cell Fate ◽

Regulatory Networks ◽

Large Scale ◽

Molecular Mechanisms ◽

Brain Atlas ◽

Specific Gene ◽

Cell Fate Specification ◽

Human Hypothalamus ◽

Fate Specification ◽

Time Points

Abstract The hypothalamus is a central regulator of physiological homeostasis. During development, multiple transcription factors coordinate the patterning and specification of hypothalamic nuclei. However, the molecular mechanisms controlling hypothalamic patterning and cell fate specification are poorly understood. To identify genes that control these processes, we have used single-cell RNA sequencing (scRNA-Seq) to profile mouse hypothalamic gene expression across multiple developmental time points. We have further utilised scRNA-Seq to phenotype mutations in genes that play major roles in early hypothalamic patterning. To first understand hypothalamic development, hypothalami were collected at both embryonic (E10-E16, E18) and postnatal (PN4, PN8, PN14, PN45) time points. At early stages, when the bulk of hypothalamic patterning occurs (E11-E13), we observe a clear separation between mitotic progenitors and postmitotic neural precursor cells. We likewise observed clean segregation among cells expressing regional hypothalamic markers identified in previous large-scale analysis of hypothalamic development. This analysis reveals new region-specific markers and identifies candidate genes for selectively regulating patterning and cell fate specification in individual hypothalamic regions. With our rich dataset of developing mouse hypothalamus, we integrated our dataset with the Allen Brain Atlas in situ data, publicly available adult hypothalamic scRNA-Seq dataset to understand hierarchy of hypothalamic cell differentiation, as well as re-defining cell types of the hypothalamus. We next used scRNA-Seq to phenotype multiple mutant lines, including a line that has been extensively characterised as a proof of concept (Ctnnb1 overexpression), and lines that have not been characterised (Nkx2.1, Nkx2.2, Dlx1/2 deletion). We show that this approach can rapidly and comprehensively characterize mutants that have altered hypothalamic patterning, and in doing so, have identified multiple genes that simultaneously repress posterior hypothalamic identity while promoting prethalamic identity. This result supports a modified columnar model of organization for the diencephalon, where prethalamus and hypothalamus are situated in adjacent dorsal and ventral domains of the anterior diencephalon. These data serve as a resource for further studies of hypothalamic development and dysfunction, and able to delineate transcriptional regulatory networks of hypothalamic formation. Lastly, using our mouse hypothalamus as a guideline, we are comparing dataset of developing chicken, zebrafish and human hypothalamus, to identify evolutionarily conserved and divergent region-specific gene regulatory networks. We aim to use this knowledge and information of key molecular pathways of human hypothalamic development and produce human hypothalamus organoids.

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Uncovering of Key Pathways and miRNAs for Intracranial Aneurysm Based on Weighted Gene Co-Expression Network Analysis

European Neurology ◽

10.1159/000521390 ◽

2022 ◽

pp. 1-12

Author(s):

Zhengfei Ma ◽

Ping Zhong ◽

Peidong Yue ◽

Zhongwu Sun

Keyword(s):

Network Analysis ◽

Intracranial Aneurysm ◽

Differentially Expressed Genes ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Area Under The Curve ◽

Enrichment Analysis ◽

Functional Enrichment ◽

Differentially Expressed

Background: Intracranial aneurysm (IA) is a serious cerebrovascular disease. The identification of key regulatory genes can provide research directions for early diagnosis and treatment of IA. Methods: Initially, the miRNA and mRNA data were downloaded from the Gene Expression Omnibus database. Subsequently, the limma package in R was used to screen for differentially expressed genes. In order to investigate the function of the differentially expressed genes, a functional enrichment analysis was performed. Moreover, weighted gene co-expression network analysis (WGCNA) was performed to identify the hub module and hub miRNAs. The correlations between miRNAs and mRNAs were assessed by constructing miRNA-mRNA regulatory networks. In addition, in vitro validation was performed. Finally, diagnostic analysis and electronic expression verification were performed on the GSE122897 dataset. Results: In the present study, 955 differentially expressed mRNAs (DEmRNAs, 480 with increased and 475 with decreased expression) and 46 differentially expressed miRNAs (DEmiRNAs, 36 with increased and 10 with decreased expression) were identified. WGCNA demonstrated that the yellow module was the hub module. Moreover, 16 hub miRNAs were identified. A total of 1,124 negatively regulated miRNA-mRNA relationship pairs were identified. Functional analysis demonstrated that DEmRNAs in the targeted network were enriched in vascular smooth muscle contraction and focal adhesion pathways. In addition, the area under the curve of 16 hub miRNAs was >0.8. It is implied that 16 hub miRNAs may be used as potential diagnostic biomarkers of IA. Conclusion: Hub miRNAs and key signaling pathways were identified by bioinformatics analysis. This evidence lays the foundation for understanding the underlying molecular mechanisms of IA and provided potential therapeutic targets for the treatment of this disease.

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Comprehensive analysis of coding and non-coding RNA transcriptomes related to hypoxic adaptation in Tibetan chickens

Journal of Animal Science and Biotechnology ◽

10.1186/s40104-021-00582-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ying Zhang ◽

Woyu Su ◽

Bo Zhang ◽

Yao Ling ◽

Woo Kyun Kim ◽

...

Keyword(s):

Energy Metabolism ◽

High Altitude ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Tibet Plateau ◽

Hypoxic Adaptation ◽

Native Breed ◽

Non Coding Rnas

Abstract Background Tibetan chickens, a unique native breed in the Qinghai-Tibet Plateau of China, possess a suite of adaptive features that enable them to tolerate the high-altitude hypoxic environment. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play roles in the hypoxic adaptation of high-altitude animals, although their exact involvement remains unclear. Results This study aimed to elucidate the global landscape of mRNAs, lncRNAs, and miRNAs using transcriptome sequencing to construct a regulatory network of competing endogenous RNAs (ceRNAs) and thus provide insights into the hypoxic adaptation of Tibetan chicken embryos. In total, 354 differentially expressed genes (DE genes), 389 differentially expressed lncRNAs (DE lncRNAs), and 73 differentially expressed miRNAs (DE miRNAs) were identified between Tibetan chickens (TC) and control Chahua chickens (CH). GO and KEGG enrichment analysis revealed that several important DE miRNAs and their target DE lncRNAs and DE genes are involved in angiogenesis (including blood vessel development and blood circulation) and energy metabolism (including glucose, carbohydrate, and lipid metabolism). The ceRNA network was then constructed with the predicted DE gene-DE miRNA-DE lncRNA interactions, which further revealed the regulatory roles of these differentially expressed RNAs during hypoxic adaptation of Tibetan chickens. Conclusions Analysis of transcriptomic data revealed several key candidate ceRNAs that may play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and energy metabolism. These results provide insights into the molecular mechanisms of hypoxic adaptation regulatory networks from the perspective of coding and non-coding RNAs.

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Multi-omics Analysis Reveals Whether and how Naphthylacetic Acid Affects the Quality of Rehmannia Glutinosa

10.21203/rs.3.rs-109124/v1 ◽

2020 ◽

Author(s):

Jianjun LI ◽

Luying SHAO ◽

Jialin ZHU ◽

Jingxiao MA ◽

Yanqing ZHOU ◽

...

Keyword(s):

Small Rna ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Rehmannia Glutinosa ◽

Degradome Sequencing ◽

Differentially Expressed Mirnas ◽

Naphthylacetic Acid

Abstract Background: Rehmannia glutinosa (R.glutinosa) is an important medicinal plant. The tuberous root of R.glutinosa is often used as herbal medicine. Naphthylacetic acid (NAA) as expansin can improve its yield, but knowledge about gene regulation and metabolome in its root is limited.Results: Full-length transcriptome, next generation transcriptome(NGS), small RNA and degradome sequencing and metabolomics were used to elucidate whether and how NAA affected its quality.30 differential expression metabolites (DEMs) (11 upregulated, 19downregulated) were identified, but catalpol and Rehmannioside D as quality standards were unchanged in its tuberous roots under control and NAA conditions (CKs and NTs); Their NGS identified 1,113 differentially expressed transcripts (DETs) (596 upregulated, 517downregulated) verified by RT-qPCR; Small RNA sequencing identified 78miRNAs (11known, 67 novel), of which 3 were differentially expressed miRNAs (1upregulated, 2downregulated). Among them, 274 differentially expressed miRNAs target transcripts (DEMTs) were predicted found and then validated by degradome sequencing; DETs and DEMTs were mainly related to metabolism. 4 miRNA-mRNA interaction pairs that regulates 4 metabolites (2 negatively correlated, 2 positively correlated) were identified; DETs, DEMs, differentially expressed miRNAs and DEMTs involved in phenylpropanoid biosynthesis regulated metabolites.Conclusions: The identification of DETs, DEMs, differentially expressed miRNAs and DEMTs could help to elucidate the regulatory networks and molecular mechanisms important for NAA-improving root quality of R.glutinosa.

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Screening and Interaction Analysis Identify Genes Related to Anther Dehiscence in Solanum melongena L.

Frontiers in Plant Science ◽

10.3389/fpls.2021.648193 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhimin Wang ◽

Chao Yuan ◽

Shaowei Zhang ◽

Shibing Tian ◽

Qinglin Tang ◽

...

Keyword(s):

Male Sterility ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Solanum Melongena ◽

Direct Interaction ◽

Differentially Expressed ◽

Anther Dehiscence ◽

Male Sterile ◽

Reverse Transcription Pcr ◽

Pathway Analyses

Anther indehiscence is an important form of functional male sterility that can facilitate the production of hybrid seeds. However, the molecular mechanisms of anther indehiscence-based male sterility in eggplant (Solanum melongena L.) have not been thoroughly explored. We performed transcriptome sequencing and real-time quantitative reverse transcription-PCR (qRT-PCR) assays to compare the fertile line (F142) and male sterile line (S12) eggplant. We identified 2,670 differentially expressed genes (DEGs) between lines. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified 31 DEGs related to hormone biosynthesis. We, therefore, measured phytohormone contents, such as jasmonic acid (JA), auxin (IAA), gibberellin (GA), and abscisic acid (ABA) in S12 and F142. There were differences in IAA, GA3, and ABA levels between S12 and F142, while JA levels were significantly lower in S12 than in F142. Five key genes in the JA signaling pathway were differentially expressed in S12 vs. F142. Of these, SmJAZ1 and SmJAR1 were significantly upregulated and SmDAD1, SmLOX, and SmCOI1 were downregulated in S12 vs. F142. Protein–protein interaction studies identified a direct interaction between SmDAD1 and SmLOX, while SmDAD1 failed to interact with SmJAR1, SmCOI1, and SmJAZ1. The data represent a valuable resource for further exploration of regulatory mechanisms underlying anther dehiscence in eggplant.

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Integration of Transcriptional and Post-transcriptional Analysis Revealed the Early Response Mechanism of Sugarcane to Cold Stress

Frontiers in Genetics ◽

10.3389/fgene.2020.581993 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xing Huang ◽

Yongsheng Liang ◽

Baoqing Zhang ◽

Xiupeng Song ◽

Yangrui Li ◽

...

Keyword(s):

Cold Stress ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Transcriptional Regulatory Network ◽

Mirna Gene ◽

Signal Transduction Pathway ◽

Early Response ◽

Differentially Expressed ◽

Transcriptional Analysis ◽

Late Embryogenesis Abundant Protein

Cold stress causes major losses to sugarcane production, yet the precise molecular mechanisms that cause losses due to cold stress are not well-understood. To survey miRNAs and genes involved in cold tolerance, RNA-seq, miRNA-seq, and integration analyses were performed on Saccharum spontaneum. Results showed that a total of 118,015 genes and 6,034 of these differentially expressed genes (DEGs) were screened. Protein–protein interaction (PPI) analyses revealed that ABA signaling via protein phosphatase 2Cs was the most important signal transduction pathway and late embryogenesis abundant protein was the hub protein associated with adaptation to cold stress. Furthermore, a total of 856 miRNAs were identified in this study and 109 of them were differentially expressed in sugarcane responding to cold stress. Most importantly, the miRNA–gene regulatory networks suggested the complex post-transcriptional regulation in sugarcane under cold stress, including 10 miRNAs−42 genes, 16 miRNAs−70 genes, and three miRNAs−18 genes in CT vs. LT0.5, CT vs. LT1, and CT0.5 vs. LT1, respectively. Specifically, key regulators from 16 genes encoding laccase were targeted by novel-Chr4C_47059 and Novel-Chr4A_40498, while five LRR-RLK genes were targeted by Novel-Chr6B_65233 and Novel-Chr5D_60023, 19 PPR repeat proteins by Novel-Chr5C_57213 and Novel-Chr5D_58065. Our findings suggested that these miRNAs and cell wall-related genes played vital regulatory roles in the responses of sugarcane to cold stress. Overall, the results of this study provide insights into the transcriptional and post-transcriptional regulatory network underlying the responses of sugarcane to cold stress.

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Identifcation of Pathways and Genes Associated With Meniscus Degeneration Using Bioinformatics Analyses

10.21203/rs.3.rs-145945/v1 ◽

2021 ◽

Author(s):

Hui Huang ◽

Jiaxuan Zheng ◽

Haiquan Tian ◽

Yehan Fang ◽

Wei Wang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Regulatory Networks ◽

Molecular Mechanisms ◽

Trp Channels ◽

Cruciate Ligament ◽

Differentially Expressed ◽

Bioinformatics Analyses ◽

Chip Technology ◽

Meniscus Tissue ◽

Meniscus Degeneration

Abstract There are few studies on the genetic changes of meniscus degeneration. We used anterior cruciate ligament resection of Wuzhishan pig to prepare a meniscus degeneration model, and applied gene chip technology to detect differentially expressed genes in degenerative meniscus tissue. Then we applied GO analysis, Pathway analysis, Core gene network analysis and Relevant miRNAs analysis to discover relevant regulatory networks of meniscus degeneration. As a result, we detected 893 differentially expressed genes, mainly involving hormone, apoptosis, inflammation and other mechanisms, and obtained MUC13, Inflammatory mediator regulation of TRP channels, MDFI, mir-335-5p and so on that may play a key role. In summary, we have established a reliable animal model of meniscus degeneration and found that meniscus degeneration involves several possible molecular mechanisms, which will provide molecular targets for further research of the disease in the future.

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