scholarly journals Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Xueyan Zhao ◽  
Cheng Wang ◽  
Yanping Wang ◽  
Haichao Lin ◽  
Huaizhong Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Adhesion ◽  
Candidate Genes ◽  
Meat Quality ◽  
Receptor Interaction ◽  
Drip Loss ◽  
Potential Candidate ◽  
Matrix Cell ◽  
Crucial Information ◽  
Go Terms

Abstract Background Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss. Results As a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss. Conclusions Our study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs.

scholarly journals An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs

2021 ◽  
Vol 12 ◽  
Author(s):  
Xianxian Liu ◽  
Junjie Zhang ◽  
Xinwei Xiong ◽  
Congying Chen ◽  
Yuyun Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Meat Quality ◽  
Integrative Analysis ◽  
Potential Candidate ◽  
Quality Traits ◽  
Eqtl Mapping ◽  
Meat Quality Traits ◽  
Genome Wide ◽  
A Genome

Understanding the genetic factors behind meat quality traits is of great significance to animal breeding and production. We previously conducted a genome-wide association study (GWAS) for meat quality traits in a White Duroc × Erhualian F2 pig population using Illumina porcine 60K SNP data. Here, we further investigate the functional candidate genes and their network modules associated with meat quality traits by integrating transcriptomics and GWAS information. Quantitative trait transcript (QTT) analysis, gene expression QTL (eQTL) mapping, and weighted gene co-expression network analysis (WGCNA) were performed using the digital gene expression (DGE) data from 493 F2 pig’s muscle and liver samples. Among the quantified 20,108 liver and 23,728 muscle transcripts, 535 liver and 1,014 muscle QTTs corresponding to 416 and 721 genes, respectively, were found to be significantly (p < 5 × 10−4) correlated with 22 meat quality traits measured on longissiums dorsi muscle (LM) or semimembranosus muscle (SM). Transcripts associated with muscle glycolytic potential (GP) and pH values were enriched for genes involved in metabolic process. There were 42 QTTs (for 32 genes) shared by liver and muscle tissues, of which 10 QTTs represent GP- and/or pH-related genes, such as JUNB, ATF3, and PPP1R3B. Furthermore, a genome-wide eQTL mapping revealed a total of 3,054 eQTLs for all annotated transcripts in muscle (p < 2.08 × 10−5), including 1,283 cis-eQTLs and 1771 trans-eQTLs. In addition, WGCNA identified five modules relevant to glycogen metabolism pathway and highlighted the connections between variations in meat quality traits and genes involved in energy process. Integrative analysis of GWAS loci, eQTL, and QTT demonstrated GALNT15/GALNTL2 and HTATIP2 as strong candidate genes for drip loss and pH drop from postmortem 45 min to 24 h, respectively. Our findings provide valuable insights into the genetic basis of meat quality traits and greatly expand the number of candidate genes that may be valuable for future functional analysis and genetic improvement of meat quality.

scholarly journals Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lili Du ◽  
Tianpeng Chang ◽  
Bingxing An ◽  
Mang Liang ◽  
Xinghai Duan ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Meat Quality ◽  
Relevant Literature ◽  
Transcriptome Profiling ◽  
Water Holding Capacity ◽  
Potential Candidate ◽  
Protein Protein Interaction ◽  
Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

scholarly journals Transcriptional epigenetic regulation of Fkbp1/Pax9 genes is associated with impaired sensitivity to platinum treatment in ovarian cancer

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Javier Andrés Soto ◽  
Carlos Rodríguez-Antolín ◽  
Olga Vera ◽  
Olga Pernía ◽  
Isabel Esteban-Rodríguez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Candidate Genes ◽  
Cell Lines ◽  
Clinical Data ◽  
Epigenetic Regulation ◽  
Chemotherapy Response ◽  
Potential Candidate ◽  
Platinum Sensitivity ◽  
Translational Level

Abstract Background In an effort to contribute to overcoming the platinum resistance exhibited by most solid tumors, we performed an array of epigenetic approaches, integrating next-generation methodologies and public clinical data to identify new potential epi-biomarkers in ovarian cancer, which is considered the most devastating of gynecological malignancies. Methods We cross-analyzed data from methylome assessments and restoration of gene expression through microarray expression in a panel of four paired cisplatin-sensitive/cisplatin-resistant ovarian cancer cell lines, along with publicly available clinical data from selected individuals representing the state of chemoresistance. We validated the methylation state and expression levels of candidate genes in each cellular phenotype through Sanger sequencing and reverse transcription polymerase chain reaction, respectively. We tested the biological role of selected targets using an ectopic expression plasmid assay in the sensitive/resistant tumor cell lines, assessing the cell viability in the transfected groups. Epigenetic features were also assessed in 189 primary samples obtained from ovarian tumors and controls. Results We identified PAX9 and FKBP1B as potential candidate genes, which exhibited epigenetic patterns of expression regulation in the experimental approach. Re-establishment of FKBP1B expression in the resistant OVCAR3 phenotype in which this gene is hypermethylated and inhibited allowed it to achieve a degree of platinum sensitivity similar to the sensitive phenotype. The evaluation of these genes at a translational level revealed that PAX9 hypermethylation leads to a poorer prognosis in terms of overall survival. We also set a precedent for establishing a common epigenetic signature in which the validation of a single candidate, MEST, proved the accuracy of our computational pipelines. Conclusions Epigenetic regulation of PAX9 and FKBP1B genes shows that methylation in non-promoter areas has the potential to control gene expression and thus biological consequences, such as the loss of platinum sensitivity. At the translational level, PAX9 behaves as a predictor of chemotherapy response to platinum in patients with ovarian cancer. This study revealed the importance of the transcript-specific study of each gene under potential epigenetic regulation, which would favor the identification of new markers capable of predicting each patient’s progression and therapeutic response.

scholarly journals Transcriptomic profile of leg muscle during early growth and development in Haiyang yellow chicken

2021 ◽  
Vol 64 (2) ◽  
pp. 405-416
Author(s):  
Xuemei Yin ◽  
Yulin Wu ◽  
Shanshan Zhang ◽  
Tao Zhang ◽  
Genxi Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Developmental Stages ◽  
Insulin Signalling ◽  
Muscle Growth ◽  
Pairwise Comparison ◽  
Early Growth ◽  
Receptor Interaction ◽  
Potential Candidate ◽  
Chicken Muscle

Abstract. Skeletal muscle growth and development from embryo to adult consists of a series of carefully regulated changes in gene expression. This study aimed to identify candidate genes involved in chicken growth and development and to investigate the potential regulatory mechanisms of early growth in Haiyang yellow chicken. RNA sequencing was used to compare the transcriptomes of chicken muscle tissues at four developmental stages. In total, 6150 differentially expressed genes (DEGs) (|fold change| ≥ 2; false discovery rate (FDR) ≤ 0.05) were detected by pairwise comparison in female chickens. Functional analysis showed that the DEGs were mainly involved in the processes of muscle growth and development and cell differentiation. Many of the DEGs, such as MSTN, MYOD1, MYF6, MYF5, and IGF1, were related to chicken growth and development. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DEGs were significantly enriched in four pathways related to growth and development: extracellular matrix (ECM)–receptor interaction, focal adhesion, tight junction, and insulin signalling pathways. A total of 42 DEGs assigned to these pathways are potential candidate genes for inducing the differences in growth among the four development stages, such as MYH1A, EGF, MYLK2, MYLK4, and LAMB3. This study identified a range of genes and several pathways that may be involved in regulating early growth.

scholarly journals Reference genes for qRT-PCR normalisation in different tissues, developmental stages, and stress conditions of Hypericum perforatum

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7133 ◽  
Author(s):  
Wen Zhou ◽  
Shiqiang Wang ◽  
Lei Yang ◽  
Yan Sun ◽  
Qian Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Reference Genes ◽  
Hypericum Perforatum ◽  
Developmental Stages ◽  
Pcr Analysis ◽  
Potential Candidate ◽  
Qrt Pcr ◽  
Expression Studies ◽  
Different Tissues

Hypericum perforatum L. is a widely known medicinal herb used mostly as a remedy for depression because it contains high levels of naphthodianthrones, phloroglucinols, alkaloids, and some other secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is essential for the interpretation of qRT-PCR data. In this study, we investigated the expression of 14 candidate genes, including nine housekeeping genes (HKGs) (ACT2, ACT3, ACT7, CYP1, EF1-α, GAPDH, TUB-α, TUB-β, and UBC2) and five potential candidate genes (GSA, PKS1, PP2A, RPL13, and SAND). Three programs—GeNorm, NormFinder, and BestKeeper—were applied to evaluate the gene expression stability across four different plant tissues, four developmental stages and a set of abiotic stress and hormonal treatments. Integrating all of the algorithms and evaluations revealed that ACT2 and TUB-β were the most stable combination in different developmental stages samples and all of the experimental samples. ACT2, TUB-β, and EF1-α were identified as the three most applicable reference genes in different tissues and stress-treated samples. The majority of the conventional HKGs performed better than the potential reference genes. The obtained results will aid in improving the credibility of the standardization and quantification of transcription levels in future expression studies on H. perforatum.

scholarly journals Transcriptome Analysis Reveals a Gene Expression Pattern Associated with Fuzz Fiber Initiation Induced by High Temperature in Gossypium barbadense

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1066
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Temperature ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gossypium Barbadense ◽  
Fiber Development ◽  
Potential Candidate ◽  
Fiber Initiation

Gossypium barbadense is an important source of natural textile fibers, as is Gossypium hirsutum. Cotton fiber development is often affected by various environmental factors, such as abnormal temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation. In this study, we reveal that high temperatures (HT) accelerate fiber development, improve fiber quality, and induced fuzz initiation of a thermo-sensitive G. barbadense variety L7009. It was proved that fuzz initiation was inhibited by low temperature (LT), and 4 dpa was the stage most susceptible to temperature stress during the fuzz initiation period. A total of 43,826 differentially expressed genes (DEGs) were identified through comparative transcriptome analysis. Of these, 9667 were involved in fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were potentially involved in fuzz initiation induced by high temperature. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in the asparagine biosynthetic process, cell wall biosynthesis, and stress response. The expression trends of sixteen genes randomly selected from the RNA-seq data were almost consistent with the results of qRT-PCR. Our study revealed several potential candidate genes and pathways related to fuzz initiation induced by high temperature. This provides a new view of temperature-induced tissue and organ development in Gossypium barbadense.

High-Throughput Screening of Alternative Micro-Metastasis-Specific Gene Predictors of Circulating Osteosarcoma Cells

2021 ◽  
Author(s):  
Pattaralawan Sittiju ◽  
Parunya Chaiyawat ◽  
Dumnoensun Pruksakorn ◽  
Jeerawan Klangjorhor ◽  
Weerinrada Wongrin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
High Throughput Screening ◽  
Characteristic Curve ◽  
Diagnostic Model ◽  
Specific Gene ◽  
Molecular Technique ◽  
Potential Candidate ◽  
Discriminative Ability ◽  
Qrt Pcr

Abstract Background Current techniques to identify circulating-tumor cells (CTCs) in osteosarcoma (OS), which are an indication of a poor prognosis in cases of intermediate levels of metastasis, are complicated and time-consuming. This study investigated the efficacy of quantitative reverse transcription PCR (qRT-PCR), a molecular technique that is available in most laboratories, for detection of CTCs in buffy coat samples of OS patients and healthy donors. Methods Previously published reports on data-reviewing and retrieval of data by calculation of differential gene expression from the Gene Expression Omnibus (GEO) database repository were reviewed identify candidate genes. Following analysis of the expression of the candidate genes identified a diagnostic model for detection of specific gene expression was derived using binary logistic regression with a multivariable fractional polynomial (MFP) algorithm. Results A model incorporating VIM, ezrin, COL1A2, and PLS3 exhibited an outstanding discriminative ability as determined by the receiver operating characteristic curve (AUC = 0.9896, 95%CI 0.9695, 1.000). At the probability cut-off value 0.2943, the sensitivity and the specificity of the model for detection of OS were 100% (95%CI 94.8, 100.0) and 96.49% (95%CI 87.9, 99.6), respectively. Conclusion The qRT-PCR can identify the existence of OS circulating cells by detection of potential candidate genes (VIM, Ezrin, COL1A2 and PLS3). Thus, these genes are worthy to be considered diagnostic biomarkers and alternative micro-metastasis predictors for OS.

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