Identification of a candidate gene for bruchid resistance by combining fine mapping and transcriptome profiling in mung bean (Vigna radiata L.)

Abstract Bruchids or seed weevils are serious storage insect pests of mung bean and other pulses. Though bruchid-resistant mung bean germplasm accessions are screened out, the molecular mechanisms of bruchid resistance in mung bean are still unclear. In this study, a segregating population with 182 RILs plants was developed; delimit the controlling gene to a 111-kb physical interval, in which 11 genes were predicted. Vr04g00919 encoding the function of a polygalacturonase inhibitor, was the most likely candidate genes. Here, sequence analysis of the candidate gene coding regions revealed that it has six SNPs between the parental lines and three SNPs resulted in amino acid changes. Sequence alignment revealed that one of these three SNPs are located in a conserved leucine rich repeat (LRR) domain, which is essential for the function of the protein. Subcellular localization of the VrPGIP2-GFP fusion protein indicated that the candidate gene PGIP2 is located in the nucleus and cytosol. RNA-seq and quantitative real-time PCR (qRT-PCR) analysis indicated that many defense responses, cell wall synthesis, biotic and abiotic stresses, and hormone synthesis were greatly activated in the bruchid resistance plants. These findings contribute to the molecular marker assisted selection of bruchid resistance cultivars.

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Transcriptome Analysis of Ramie (Boehmeria niveaL. Gaud.) in Response to Ramie Moth (Cocytodes coeruleaGuenée) Infestation

BioMed Research International ◽

10.1155/2016/3702789 ◽

2016 ◽

Vol 2016 ◽

pp. 1-10 ◽

Cited By ~ 5

Author(s):

Liangbin Zeng ◽

Airong Shen ◽

Jia Chen ◽

Zhun Yan ◽

Touming Liu ◽

...

Keyword(s):

Protein Function ◽

Molecular Mechanisms ◽

Defense Mechanism ◽

Natural Fiber ◽

De Novo ◽

Average Length ◽

Expression Patterns ◽

Transcriptome Profiling ◽

Cdna Libraries ◽

Pcr Analysis

The ramie mothCocytodes coeruleaGuenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore,de novoassembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

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Transcriptome analysis reveals ethylene-mediated defense responses to Fusarium oxysporum f. sp. cucumerinum infection in Cucumis sativus

10.21203/rs.2.21765/v1 ◽

2020 ◽

Author(s):

Jingping Dong ◽

Yuean Wang ◽

Qianqian Xian ◽

Xuehao Chen ◽

Jun Xu

Keyword(s):

Fusarium Oxysporum ◽

Cucumis Sativus ◽

Fusarium Wilt ◽

Defense Mechanisms ◽

Molecular Mechanisms ◽

Severe Disease ◽

Defense Responses ◽

Differentially Expressed ◽

Pcr Analysis ◽

Positive Role

Abstract Background: Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is a severe disease affecting cucumber (Cucumis sativus L.) production worldwide, but the molecular mechanisms underlying Fusarium wilt resistance in cucumber remain unknown. To gain an improved understanding of the defense mechanisms elicited in response to Foc inoculation, RNA sequencing-based transcriptomic profiling of responses of the Fusarium wilt-resistant cucumber line ‘Rijiecheng’ at 0, 24, 48, 96, and 192 h after Foc inoculation was performed.Results: We identified 4116 genes that were differentially expressed between 0 h and other time points after inoculation. All ethylene-related and pathogenesis-related genes from among the differentially expressed genes were filtered out. Real-time PCR analysis showed that ethylene-related genes were induced in response to Foc infection. Importantly, after Foc infection and exogenous application of ethephon, a donor of ethylene, these genes were highly expressed. In response to exogenous ethephon treatment in conjunction with Foc inoculation, the infection resistance of cucumber seedlings was enhanced and endogenous ethylene biosynthesis increased dramatically. Conclusion: Collectively, ethylene signaling pathways play a positive role in regulating the defense response of cucumber to Foc infection. The results provide insight into the cucumber Fusarium wilt defense mechanisms and provide valuable information for breeding new cucumber cultivars with enhanced Fusarium wilt tolerance.

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Introduksi Konstruk Over-Ekspresi Kandidat Gen OsWRKY76 melalui Agrobacterium tumefaciens pada Tanaman Padi Nipponbare

Jurnal AgroBiogen ◽

10.21082/jbio.v7n1.2011.p19-27 ◽

2011 ◽

Vol 7 (1) ◽

pp. 19

Author(s):

Aniversari Apriana ◽

Atmitri Sisharmini ◽

Wening Enggarini ◽

Sudarsono Sudarsono ◽

Nurul Khumaida ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Candidate Gene ◽

Wide Spectrum ◽

Defense Responses ◽

Chromosome 9 ◽

Pcr Analysis ◽

Plant Defense Responses ◽

Embryogenic Calli ◽

Over Expression ◽

Expression Construct

Delivering of Over-Expression Construct OsWRKY76 Candidate Gene in Rice cv. Nipponbare through Agrobacterium tumefaciens. Aniversari Apriana, Atmitri Sisharmini, Wening Enggarini, Sudarsono, Nurul. Khumaida, and Kurniawan R. Trijatmiko. Plant genetic improvement can be done through classical breeding or genetic engineering. WRKY is a transcription factor involved in regulating plant defense responses. OsWRKY76 gene is located in a narrow segment of chromosome 9 which is identified previously to be related to wide spectrum resistance in rice. A sequence of OsWRKY76 (+1.200 bp) has available in the gene bank and it makes possible to isolate, clone, and construct the gene into over-expression vector. The aim of this research was to assemble an overexpression construct of OsWRKY76 candidate gene and introduce it into rice through Agrobacterium-mediated transformation. A construct of pCAMBIA- 1301::35S::OsWRKY76 has been successfully assembled and transformed into embryogenic calli of rice cv. Nipponbare using A. tumefaciens strain Agl-1 and EHA 105. A number of 126 independent lines has been produced, in which Agl-1 showed 3.8 times more efficient than EHA 105. PCR analysis of randomly selected 25 independent lines showed that all of them positively contained hptII gene, a selectable marker used in the over-expression construct of the OsWRKY76 candidate gene. Based on the result, it could be concluded that the over-expression construct of OsWRKY76 candidate gene have been successfully introduced into the tissue of Nipponbare.

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iTRAQ-Based Proteomic Analysis of Ogura-CMS Cabbage and Its Maintainer Line

International Journal of Molecular Sciences ◽

10.3390/ijms19103180 ◽

2018 ◽

Vol 19 (10) ◽

pp. 3180 ◽

Cited By ~ 2

Author(s):

Fengqing Han ◽

Xiaoli Zhang ◽

Limei Yang ◽

Mu Zhuang ◽

Yangyong Zhang ◽

...

Keyword(s):

Oxidative Phosphorylation ◽

Male Sterility ◽

Molecular Mechanisms ◽

Transcriptome Profiling ◽

Pcr Analysis ◽

Hybrid Seed Production ◽

Protein Species ◽

Absolute Quantitation ◽

Maintainer Line ◽

Cms Line

Ogura cytoplasmic male sterility (CMS) contributes considerably to hybrid seed production in Brassica crops. To detect the key protein species and pathways involved in Ogura-CMS, we analysed the proteome of the cabbage Ogura-CMS line CMS01-20 and its corresponding maintainer line F01-20 using the isobaric tags for the relative and absolute quantitation (iTRAQ) approach. In total, 162 differential abundance protein species (DAPs) were identified between the two lines, of which 92 were down-accumulated and 70 were up-accumulated in CMS01-20. For energy metabolism in the mitochondrion, eight DAPs involved in oxidative phosphorylation were down-accumulated in CMS01-20, whereas in the tricarboxylic acid (TCA) cycle, five DAPs were up-accumulated, which may compensate for the decreased respiration capacity and may be associated with the elevated O2 consumption rate in Ogura-CMS plants. Other key protein species and pathways involved in pollen wall assembly and programmed cell death (PCD) were also identified as being male-sterility related. Transcriptome profiling revealed 3247 differentially expressed genes between the CMS line and the fertile line. In a conjoint analysis of the proteome and transcriptome data, 30 and 9 protein species/genes showed the same and opposite accumulation patterns, respectively. Nine noteworthy genes involved in sporopollenin synthesis, callose wall degeneration, and oxidative phosphorylation were presumably associated with the processes leading to male sterility, and their expression levels were validated by qRT-PCR analysis. This study will improve our understanding of the protein species involved in pollen development and the molecular mechanisms underlying Ogura-CMS.

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Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

Agronomy ◽

10.3390/agronomy11071328 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1328

Author(s):

Noushin Jahan ◽

Yang Lv ◽

Mengqiu Song ◽

Yu Zhang ◽

Liangguang Shang ◽

...

Keyword(s):

Salt Stress ◽

Molecular Mechanisms ◽

Oryza Sativa L ◽

Transcriptome Profiling ◽

Bhlh Transcription Factor ◽

F1 Hybrid ◽

Salt Stress Response ◽

Productivity Losses ◽

Expression Of Genes ◽

Trait Locus

Salinity is a major abiotic stressor that leads to productivity losses in rice (Oryza sativa L.). In this study, transcriptome profiling and heterosis-related genes were analyzed by ribonucleic acid sequencing (RNA-Seq) in seedlings of a mega rice hybrid, Liang-You-Pei-Jiu (LYP9), and its two parents 93–11 and Pei-ai64s (PA64s), under control and two different salinity levels, where we found 8292, 8037, and 631 salt-induced differentially expressed genes (DEGs), respectively. Heterosis-related DEGs were obtained higher after 14 days of salt treatment than after 7 days. There were 631 and 4237 salt-induced DEGs related to heterosis under 7-day and 14-day salt stresses, respectively. Gene functional classification showed the expression of genes involved in photosynthesis activity after 7-day stress treatment, and in metabolic and catabolic activity after 14 days. In addition, we correlated the concurrence of an expression of DEGs for the bHLH transcription factor and a shoot length/salinity-related quantitative trait locus qSL7 that we fine-mapped previously, providing a confirmed case of heterosis-related genes. This experiment reveals the transcriptomic divergence of the rice F1 hybrid and its parental lines under control and salt stress state, and enlightens about the significant molecular mechanisms developed over time in response to salt stress.

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Endurance Training Regulates Expression of Some Angiogenesis-Related Genes in Cardiac Tissue of Experimentally Induced Diabetic Rats

Biomolecules ◽

10.3390/biom11040498 ◽

2021 ◽

Vol 11 (4) ◽

pp. 498

Author(s):

Mojdeh Khajehlandi ◽

Lotfali Bolboli ◽

Marefat Siahkuhian ◽

Mohammad Rami ◽

Mohammadreza Tabandeh ◽

...

Keyword(s):

Gene Expression ◽

Endurance Training ◽

Molecular Mechanisms ◽

Cardiac Tissue ◽

Critical Role ◽

Diabetic Rats ◽

Moderate Intensity ◽

Pcr Analysis ◽

Cardiac Tissues ◽

The Impact

Exercise can ameliorate cardiovascular dysfunctions in the diabetes condition, but its precise molecular mechanisms have not been entirely understood. The aim of the present study was to determine the impact of endurance training on expression of angiogenesis-related genes in cardiac tissue of diabetic rats. Thirty adults male Wistar rats were randomly divided into three groups (N = 10) including diabetic training (DT), sedentary diabetes (SD), and sedentary healthy (SH), in which diabetes was induced by a single dose of streptozotocin (50 mg/kg). Endurance training (ET) with moderate-intensity was performed on a motorized treadmill for six weeks. Training duration and treadmill speed were increased during five weeks, but they were kept constant at the final week, and slope was zero at all stages. Real-time polymerase chain reaction (RT-PCR) analysis was used to measure the expression of myocyte enhancer factor-2C (MEF2C), histone deacetylase-4 (HDAC4) and Calmodulin-dependent protein kinase II (CaMKII) in cardiac tissues of the rats. Our results demonstrated that six weeks of ET increased gene expression of MEF2C significantly (p < 0.05), and caused a significant reduction in HDAC4 and CaMKII gene expression in the DT rats compared to the SD rats (p < 0.05). We concluded that moderate-intensity ET could play a critical role in ameliorating cardiovascular dysfunction in a diabetes condition by regulating the expression of some angiogenesis-related genes in cardiac tissues.

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Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms22052683 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2683

Author(s):

Princess D. Rodriguez ◽

Hana Paculova ◽

Sophie Kogut ◽

Jessica Heath ◽

Hilde Schjerven ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

B Cell ◽

Molecular Mechanisms ◽

Lymphoblastic Leukemia ◽

Transcriptome Profiling ◽

Rna Seq ◽

Protein Coding ◽

Non Coding Rna ◽

Technological Developments ◽

Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

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Characterization of an A-type cyclin-dependent kinase gene from Dendrobium candidum

Biologia ◽

10.2478/s11756-012-0016-y ◽

2012 ◽

Vol 67 (2) ◽

Cited By ~ 1

Author(s):

Gang Zhang ◽

Chao Song ◽

Ming-Ming Zhao ◽

Biao Li ◽

Shun-Xing Guo

Keyword(s):

Molecular Mechanisms ◽

Three Dimensional ◽

Postembryonic Development ◽

Kinase Domain ◽

Dimensional Structure ◽

Pcr Analysis ◽

Kinase Gene ◽

Multiple Sequence ◽

Dendrobium Candidum ◽

Rapid Amplification

AbstractCyclin-dependent kinases (CDKs) play an essential role in cell cycle regulation during the embryonic and postembryonic development of organisms. To better understand the molecular mechanisms of CDKs involved in embryogenesis regulation in the endangered medicinal plant Dendrobium candidum Wall. ex Lindl., a 1229-bp full-length cDNA of an A-type CDK gene, Denca;CDKA;1, was identified using 3′ rapid amplification of cDNA end (RACE) PCR. Denca;CDKA;1 was predicted to encode a 294 amino acid residue-long protein of 33.76 kDa with an isoelectric point of 7.72. The deduced Denca;CDKA;1 protein contained a conserved serine/threonine-protein kinase domain (S-TKc) and a canonical cyclinbinding “PSTAIRE” motif. Multiple sequence alignment indicated that members of CDKA family from various plants exhibited a high degree of sequence identity ranging from 82% to 93%. A neighbor-joining phylogenetic tree showed that Denca;CDKA;1 was clustered into the plant group and was distant from the animal and fungal groups. The modeled three-dimensional structure of Denca;CDKA;1 exhibited the similar functional structure of a fold consisting of β-sheets and α-helices joined by discontinuous random coils forming two relatively independent lobes. Quantitative real-time PCR analysis revealed that Denca;CDKA;1 transcripts were the most abundant in protocorm-like bodies with 4.76 fold, followed by that in roots (4.19 fold), seeds (2.57 fold), and stems (1.57 fold). This study characterized the novel Denca;CDKA;1 gene from D. candidum for the first time and the results will be useful for further functional determination of the gene.

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Discovery and Characterization of Differentially Expressed Soybean MiRNAs and Their Targets During Soybean Mosaic Virus Infection Unveils Novel Insight Into Soybean-SMV Interaction

10.21203/rs.3.rs-775142/v1 ◽

2021 ◽

Author(s):

Bowen Li ◽

Adhimoolam Karthikeyan ◽

Liqun Wang ◽

Jinlong Yin ◽

Tongtong Jin ◽

...

Keyword(s):

Virus Infection ◽

Mosaic Virus ◽

Target Genes ◽

Soybean Mosaic Virus ◽

Expression Patterns ◽

Defense Responses ◽

Pcr Analysis ◽

Functional Annotations ◽

Additional Information ◽

Insight Into

Abstract Background: Soybean mosaic virus (SMV) is the most devastating pathogen of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) and play important roles in regulating defense responses against pathogens. However, miRNA's response to SMV in soybean is not as well documented. Result: In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1× Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi, and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs responded during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. Eventually, the expression patterns of several miRNAs validated by quantitative real-time PCR analysis are consistent with sequencing results. Conclusion: We have identified a large number of miRNAs and their target genes and also functional annotations. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

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Elicitor Recognition and Signal Transduction in Plant Defense Gene Activation

Zeitschrift für Naturforschung C ◽

10.1515/znc-1990-0601 ◽

1990 ◽

Vol 45 (6) ◽

pp. 569-575 ◽

Cited By ~ 56

Author(s):

Dierk Scheel ◽

Jane E. Parker

Keyword(s):

Signal Transduction ◽

Plant Defense ◽

Transcriptional Activation ◽

Molecular Mechanisms ◽

Plant Protection ◽

Plant Cells ◽

Defense Responses ◽

Plant Defense Responses ◽

Defense Genes ◽

Plant Defense Genes

Abstract Plants defend themselves against pathogen attack by activating a whole set of defense responses, most of them relying on transcriptional activation of plant defense genes. The same responses are induced by treatment of plant cells with elicitors released from the pathogen or from the plant surface. Several plant/elicitor combinations have been used successfully as experimental systems to investigate the molecular basis of plant defense responses. Receptor-like structures on the plasma membrane of plant cells appear to bind the elicitors. Thereby, intracellular signal transduction chains are initiated which finally result in the activation of plant defense genes. A better understanding of the molecular mechanisms of early processes in plant defense responses, as provided by these studies, may in the long term help to develop environmentally safe plant protection methods for agriculture.

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