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

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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Comparative transcriptome analysis identifies jasmonic pathway genes related to anther dehiscence in Solanum melongena L.

10.21203/rs.3.rs-16718/v1 ◽

2020 ◽

Author(s):

Zhimin Wang ◽

Shaowei Zhang ◽

Chao Yuan ◽

Yi Niu ◽

Qinglin Tang ◽

...

Keyword(s):

Male Sterility ◽

Differentially Expressed Genes ◽

Protein Interaction ◽

Molecular Mechanisms ◽

Solanum Melongena ◽

Direct Interaction ◽

Differentially Expressed ◽

Anther Dehiscence ◽

Interaction Studies ◽

Pathway Analyses

Abstract Background: 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. Therefore, we performed RNA-seq analysis to investigate the molecular mechanisms of anther dehiscence in eggplant. Results: We used transcriptome sequencing and qRT-PCR assays to compare the anthers of normally developing (F142) and anther indehiscent (S12) eggplant. We identified 2670 differentially expressed genes between lines. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses identified 31 differentially expressed genes related to hormone biosynthesis. We therefore measured the contents of the phytohormones jasmonic acid (JA), IAA, GA3 and ABA in S12 and F142. There were no significant differences in IAA, GA3 or ABA levels between S12 and F142. However, 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, SmJAZ and SmJAR-like were significantly up-regulated and SmDAD1, SmLOX and SmCOI1 were down-regulated in S12 vs. F142. In DNA-protein interaction studies, SmLOX, SmAOC, SmOPR3, SmCOI1 and SmJAZ1 failed to be enriched on the chromatin of SmDAD1. Protein–protein interaction studies identified a direct interaction between SmDAD1 and SmLOX, but SmDAD1 failed to interact with SmAOC, SmOPR3, SmCOI1 and SmJAZ1. Conclusion: JA is an essential factor affecting anther dehiscence in eggplant. SmDAD1 interacts with SmLOX to alter JA levels, thereby regulating anther dehiscence. Our data represent a valuable resource for further exploring the regulatory mechanisms underlying anther dehiscence in eggplant.

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Comparative transcriptome analysis indicates that a core transcriptional network mediates isonuclear alloplasmic male sterility in wheat (Triticum aestivum L.)

BMC Plant Biology ◽

10.1186/s12870-019-2196-x ◽

2020 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Zihan Liu ◽

Sha Li ◽

Wei Li ◽

Qi Liu ◽

Lingli Zhang ◽

...

Keyword(s):

Male Sterility ◽

Candidate Genes ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Interaction Mechanism ◽

Outer Wall ◽

Comparative Transcriptome ◽

Male Sterile ◽

Comparative Transcriptome Analysis ◽

The Impact

Abstract Background Cytoplasmic male sterility (CMS) plays a crucial role in the utilization of heterosis and various types of CMS often have different abortion mechanisms. Therefore, it is important to understand the molecular mechanisms related to anther abortion in wheat, which remain unclear at present. Results In this study, five isonuclear alloplasmic male sterile lines (IAMSLs) and their maintainer were investigated. Cytological analysis indicated that the abortion type was identical in IAMSLs, typical and stainable abortion, and the key abortive period was in the binucleate stage. Most of the 1,281 core shared differentially expressed genes identified by transcriptome sequencing compared with the maintainer in the vital abortive stage were involved in the metabolism of sugars, oxidative phosphorylation, phenylpropane biosynthesis, and phosphatidylinositol signaling, and they were downregulated in the IAMSLs. Key candidate genes encoding chalcone--flavonone isomerase, pectinesterase, and UDP-glucose pyrophosphorylase were screened and identified. Moreover, further verification elucidated that due to the impact of downregulated genes in these pathways, the male sterile anthers were deficient in sugar and energy, with excessive accumulations of ROS, blocked sporopollenin synthesis, and abnormal tapetum degradation. Conclusions Through comparative transcriptome analysis, an intriguing core transcriptome-mediated male-sterility network was proposed and constructed for wheat and inferred that the downregulation of genes in important pathways may ultimately stunt the formation of the pollen outer wall in IAMSLs. These findings provide insights for predicting the functions of the candidate genes, and the comprehensive analysis of our results was helpful for studying the abortive interaction mechanism in CMS wheat.

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Transcriptomic and proteomic analyses of a new cytoplasmic male sterile line with a wild Gossypium bickii genetic background

BMC Genomics ◽

10.1186/s12864-020-07261-y ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Haiyan Zhao ◽

Jianshe Wang ◽

Yunfang Qu ◽

Renhai Peng ◽

Richard Odongo Magwanga ◽

...

Keyword(s):

Genetic Background ◽

Developmental Stages ◽

Interaction Network ◽

Differentially Expressed ◽

Future Research ◽

Glutathione S Transferase ◽

Male Sterile ◽

Genomic Databases ◽

Wild Cotton ◽

Pathway Analyses

Abstract Background Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conjoint transcriptomic and proteomic analysis was first performed between Yamian A and its maintainer Yamian B. Results We detected 550 differentially expressed transcript-derived fragments (TDFs) and at least 1013 proteins in anthers at various developmental stages. Forty-two TDFs and 11 differentially expressed proteins (DEPs) were annotated by analysis in the genomic databases of G. austral, G. arboreum and G. hirsutum. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed to better understand the functions of these TDFs and DEPs. Transcriptomic and proteomic results showed that UDP-glucuronosyl/UDP-glucosyltransferase, 60S ribosomal protein L13a-4-like, and glutathione S-transferase were upregulated; while heat shock protein Hsp20, ATPase, F0 complex, and subunit D were downregulated at the microspore abortion stage of Yamian A. In addition, several TDFs from the transcriptome and several DEPs from the proteome were detected and confirmed by quantitative real-time PCR as being expressed in the buds of seven different periods of development. We established the databases of differentially expressed genes and proteins between Yamian A and its maintainer Yamian B in the anthers at various developmental stages and constructed an interaction network based on the databases for a comprehensive understanding of the mechanism underlying CMS with a wild cotton genetic background. Conclusion We first analyzed the molecular mechanism of CMS Yamian A from the perspective of omics, thereby providing an experimental basis and theoretical foundation for future research attempting to analyze the abortion mechanism of new CMS with a wild Gossypium bickii background and to realize three-line matching.

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Comparative Transcriptome Analysis Reveals the Potential Mechanism of Abortion in Tobacco sua-Cytoplasmic Male Sterility

International Journal of Molecular Sciences ◽

10.3390/ijms21072445 ◽

2020 ◽

Vol 21 (7) ◽

pp. 2445

Author(s):

Zhiwen Liu ◽

Yanfang Liu ◽

Yuhe Sun ◽

Aiguo Yang ◽

Fengxia Li

Keyword(s):

Cytoplasmic Male Sterility ◽

Male Sterility ◽

Atp Synthesis ◽

Potential Mechanism ◽

Male Sterile ◽

Flower Buds ◽

Cms Line ◽

Cytological Characteristics ◽

Pathway Analyses ◽

Stress Pathway

sua-CMS (cytoplasmic male sterility) is the only male sterile system in tobacco breeding, but the mechanism of abortion is unclear. Cytological characteristics show that abortion in the sua-CMS line msZY occurs before the differentiation of sporogenous cells. In this study, a comparative transcriptomic analysis was conducted on flower buds at the abortion stage of msZY and its male fertile control ZY. A total of 462 differentially expressed genes were identified in msZY and ZY, which were enriched via protein processing in the endoplasmic reticulum (ER), oxidative phosphorylation, photosynthesis, and circadian rhythm-plant by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Most genes were downregulated in the ER stress pathway, heat-shock protein family, F1F0-ATPase encoding by the mitochondrial genome, and differentiation of stamens. Genes in the programmed cell death (PCD) pathway were upregulated in msZY. The transcriptome results were consistent with those of qRT-PCR. Ultrastructural and physiological analyses indicted active vacuole PCD and low ATP content in msZY young flower buds. We speculated that PCD and a deficiency in ATP synthesis are essential for the abortion of sua-CMS. This study reveals the potential mechanism of abortion of tobacco sua-CMS.

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Uncovering Potential Roles of Differentially Expressed Genes, Upstream Regulators, and Canonical Pathways in Endometriosis Using an In Silico Genomics Approach

Diagnostics ◽

10.3390/diagnostics10060416 ◽

2020 ◽

Vol 10 (6) ◽

pp. 416

Author(s):

Zeenat Mirza ◽

Umama A. Abdel-dayem

Keyword(s):

Gene Expression ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Meta Analysis ◽

Cell Cycle Checkpoint ◽

Reproductive Age ◽

Differentially Expressed ◽

Checkpoint Control ◽

Canonical Pathways

Endometriosis is characterized by ectopic endometrial tissue implantation, mostly within the peritoneum, and affects women in their reproductive age. Studies have been done to clarify its etiology, but the precise molecular mechanisms and pathophysiology remain unclear. We downloaded genome-wide mRNA expression and clinicopathological data of endometriosis patients and controls from NCBI’s Gene Expression Omnibus, after a systematic search of multiple independent studies comprising 156 endometriosis patients and 118 controls to identify causative genes, risk factors, and potential diagnostic/therapeutic biomarkers. Comprehensive gene expression meta-analysis, pathway analysis, and gene ontology analysis was done using a bioinformatics-based approach. We identified 1590 unique differentially expressed genes (129 upregulated and 1461 downregulated) mapped by IPA as biologically relevant. The top upregulated genes were FOS, EGR1, ZFP36, JUNB, APOD, CST1, GPX3, and PER1, and the top downregulated ones were DIO2, CPM, OLFM4, PALLD, BAG5, TOP2A, PKP4, CDC20B, and SNTN. The most perturbed canonical pathways were mitotic roles of Polo-like kinase, role of Checkpoint kinase proteins in cell cycle checkpoint control, and ATM signaling. Protein–protein interaction analysis showed a strong network association among FOS, EGR1, ZFP36, and JUNB. These findings provide a thorough understanding of the molecular mechanism of endometriosis, identified biomarkers, and represent a step towards the future development of novel diagnostic and therapeutic options.

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Identification and Interaction Analysis of Significant Genes and MicroRNAs in Pterygium

BioMed Research International ◽

10.1155/2019/2767512 ◽

2019 ◽

Vol 2019 ◽

pp. 1-12 ◽

Cited By ~ 2

Author(s):

Siying He ◽

Hui Sun ◽

Yifang Huang ◽

Shiqi Dong ◽

Chen Qiao ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Interaction Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Gene Expression Omnibus ◽

Functional Enrichment ◽

Differentially Expressed ◽

Differentially Expressed Mirnas

Purpose. MiRNAs have been widely analyzed in the occurrence and development of many diseases, including pterygium. This study aimed to identify the key genes and miRNAs in pterygium and to explore the underlying molecular mechanisms. Methods. MiRNA expression was initially extracted and pooled by published literature. Microarray data about differentially expressed genes was downloaded from Gene Expression Omnibus (GEO) database and analyzed with the R programming language. Functional and pathway enrichment analyses were performed using the database for Annotation, Visualization and Integrated Discovery (DAVID). The protein-protein interaction network was constructed with the STRING database. The associations between chemicals, differentially expressed miRNAs, and differentially expressed genes were predicted using the online resource. All the networks were constructed using Cytoscape. Results. We found that 35 miRNAs and 301 genes were significantly differentially expressed. Functional enrichment analysis showed that upregulated genes were significantly enriched in extracellular matrix (ECM) organization, while downregulated genes were mainly involved in cell death and apoptotic process. Finally, we concluded the chemical-gene affected network, miRNA-mRNA interacted networks, and significant pathway network. Conclusion. We identified lists of differentially expressed miRNAs and genes and their possible interaction in pterygium. The networks indicated that ECM breakdown and EMT might be two major pathophysiological mechanisms and showed the potential significance of PI3K-Akt signalling pathway. MiR-29b-3p and collagen family (COL4A1 and COL3A1) might be new treatment target in pterygium.

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Comparative Transcriptome Analysis of the Anthers from the Cytoplasmic Male-Sterile Pepper Line HZ1A and Its Maintainer Line HZ1B

Horticulturae ◽

10.3390/horticulturae7120580 ◽

2021 ◽

Vol 7 (12) ◽

pp. 580

Author(s):

Zhixing Nie ◽

Jianying Chen ◽

Yunpeng Song ◽

Hongfei Fu ◽

Hong Wang ◽

...

Keyword(s):

Male Sterility ◽

Molecular Mechanisms ◽

Male Sterile ◽

Maintainer Line ◽

Breeding Programs ◽

Kegg Pathways ◽

Kegg Analysis ◽

Cms Line ◽

Phenylpropanoid Biosynthesis ◽

Go Terms

Cytoplasmic male-sterility (CMS) is important for the utilization of crop heterosis and study of the molecular mechanisms involved in CMS could improve breeding programs. In the present study, anthers of the pepper CMS line HZ1A and its maintainer line HZ1B were collected from stages S1, S2, and S3 for transcriptome sequencing. A total of 47.95 million clean reads were obtained, and the reads were assembled into 31,603 unigenes. We obtained 42 (27 up-regulated and 15 down-regulated), 691 (346 up-regulated and 345 down-regulated), and 709 (281 up-regulated and 428 down-regulated) differentially expressed genes (DEGs) in stages S1, S2, and S3, respectively. Through Gene Ontology (GO) analysis, the DEGs were found to be composed of 46 functional groups. Two GO terms involved in photosynthesis, photosynthesis (GO:0015986) and photosystem I (GO:0009522), may be related to CMS. Through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, oxidative phosphorylation (ko00190) and phenylpropanoid biosynthesis (ko00940) were significantly enriched in the S1 and S2 stages, respectively. Through the analysis of 104 lipid metabolism-related DEGs, four significantly enriched KEGG pathways may help to regulate male sterility during anther development. The mitochondrial genes orf470 and atp6 were identified as candidate genes of male sterility for the CMS line HZ1A. Overall, the results will provide insights into the molecular mechanisms of pepper CMS.

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Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

10.21203/rs.2.9609/v3 ◽

2020 ◽

Author(s):

Takuma Sakamoto ◽

Maaya Nishiko ◽

Hidemasa Bono ◽

Takeru Nakazato ◽

Jin Yoshimura ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Molecular Interaction ◽

Functional Annotation ◽

Molecular Mechanisms ◽

Fatty Acid Biosynthesis ◽

Interaction Analysis ◽

Differentially Expressed ◽

Control Group ◽

Copidosoma Floridanum ◽

Human Genes

Abstract Background: Polyembryony is defined as the formation of several embryos from a single egg. This phenomenon can occur in humans, armadillo, and some endoparasitoid insects. However, the mechanism underlying polyembryogenesis in animals remains to be elucidated. The polyembryonic parasitoid wasp Copidosoma floridanum oviposits its egg into an egg of the host insect; eventually, over 2,000 individuals will arise from one egg. Previously, we reported that polyembryogenesis is enhanced when the juvenile hormone (JH) added to the culture medium in the embryo culture. Hence, in the present study, we performed RNA sequencing (RNA-Seq) analysis to investigate the molecular mechanisms controlling polyembryogenesis of C. floridanum . Functional annotation of genes is not fully available for C.floridanum ; however, whole genome assembly has been archived. Hence, we constructed a pipeline for gene functional annotation in C. floridanum and performed molecular network analysis. We analyzed differentially expressed genes between control and JH-treated molura after 48 h of culture, then used the tblastx program to assign whole C. floridanum transcripts to human gene. Results: We obtained 11,117 transcripts in the JH treatment group and identified 217 differentially expressed genes compared with the control group. As a result, 76% of C. floridanum transcripts were assigned to human genes. Gene enrichment analysis revealed genes associated with platelet degranulation, fatty acid biosynthesis, cell morphogenesis in the differentiation and integrin signaling pathways were fluctuated following JH treatment. Furthermore, Cytoscape analysis revealed a molecular interaction that was possibly associated with polyembryogenesis . Conclusions: We have constructed a pipeline for gene functional annotation of C. floridanum , and identified transcripts with high similarity to human genes during early embryo developmental. Additionally, this study reveals new molecular interactions associated with polyembryogenesis; these interactions could indicate the molecular mechanisms underlying polyembryony. Our results highlight the potential utility of molecular interaction analysis in human twins.

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Anther and pollen development in male-sterile intermediate wheatgrass plants derived from wheat × wheatgrass hybrids

Canadian Journal of Botany ◽

10.1139/b79-078 ◽

1979 ◽

Vol 57 (6) ◽

pp. 602-618 ◽

Cited By ~ 14

Author(s):

B. A. Young ◽

J. Schulz-Schaeffer ◽

T. W. Carroll

Keyword(s):

Male Sterility ◽

Anther Development ◽

Anther Dehiscence ◽

Male Sterile ◽

Pollen Abortion ◽

Backcross Generation ◽

Intermediate Wheatgrass ◽

The Third ◽

Meiotic Irregularities ◽

High Degree

Several different expressions of male sterility were observed in the plants sampled for the study of pollen and anther development in the third substitution backcross generation to intermediate wheatgrass. These included (1) pollen abortion following engorgement with starch, (2) abortion of microspores with exine abnormalities (found most often in plants with a high degree of meiotic irregularities), (3) abortion of microspores with normal exines, (4) release at anther dehiscence of normal-appearing late vacuolate microspores, (5) enlargement of one of the parietal layers of the anther, and (6) tapetal abnormalities, including orbicular wall malformations. Anthers from plants which were male sterile or partially male sterile and meiotically irregular were shorter than anthers from fertile or partially male-sterile, meiotically regular plants.Definite statements about specific causes of the male sterility could not be made. Meiotic irregularities may be involved in some of the male sterility, and exine malformations appeared to be directly related to sterile microspores. Tapetal disturbances were observed infrequently. Probably the consequences of several factors were observed in the backcross material.

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