Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits
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PROVIDER: PRJNA511588 | ENA |
REPOSITORIES: ENA
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Project description:Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Using a genome-wide association study based on a fixed linear model, we identified 7,192 cis-eQTL corresponding to 2,098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6,400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9,815 significant ASE-SNPs in 2,253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3).This study provides valuable information on the genetics of gene expression in porcine skeletal muscle. The characterized cis-genes and ASE genes, combined with the correlations between gene expression level and meat quality traits will be useful to prioritize candidate genes in further studies.
2019-06-24 | GSE124315 | GEO
Project description: Not available
| S-EPMC7547458 | biostudies-literature
Project description: Not available
| S-EPMC3091721 | biostudies-literature
Project description:Improvement of feed efficiency would increase profitability of the poultry industries by decreasing the amount of feed required for production. Korat (KR) chicken is a new alternative meat-type chicken breed which its meat is recognized for its high protein, low fat and low purine content, whereas its low feed efficiency leads to high cost of production. Deeper understanding on how feed efficiency influences meat quality is poorly elucidated. To fulfill deeper understand molecular key that point the variation in feed efficiency and meat quality, the aim of this study was to investigate molecular pathways and genes involved in feed efficiency and meat quality in thigh of slow-growing KR chicken. A total of 75 males KR chicken were reared in individual cage until 10 weeks of age. Individual feed intake and body weight were collected weekly to calculate Feed Conversion Ratio (FCR) and Residual Feed Intake (RFI). Meat quality parameters were measured in thigh muscles such as ultimate pH (pHu), water-holding capacity (WHC), drip loss (DL), nucleotides content and several biomolecules (amide, …). Base on extreme values of FCR at 10 weeks of ages, 12 birds from the high FCR group (HFCR) and 9 birds from the low FCR group (LFCR) were selected for investigating their transcriptome using an 8×60K Agilent chicken microarray. In addition, a weighted gene coexpression network analysis was performed to detect the relationship between modules of co-expressed genes and feed efficiency, meat quality in thigh muscle. The result in this study indicated that selection on feed efficiency (FCR, RFI) would affect flavor precursor, lipid and protein content in thigh muscle. Based on WGCNA and functional enrichment analysis, results suggested that the key molecular pathways relate to FCR, RFI and meat quality (WHC, DL, IMP, AMP and inosine) in thigh muscle were the pathways of regulation of biological process, biological regulation and regulation of metabolic. Moreover, we revealed four genes there are assembly competence domain (ACD) gene, baculoviral IAP repeat containing 5 (BIRC5) gene, cytochrome c oxidase assembly factor 3 (COA3) gene and myosin light chain 9 (MYL9) gene that might be biomarker gene in feed efficiency and meat quality in thigh muscle. The hypothesis of the current study was alteration feed efficiency in slow-growing chicken will impact meat quality especially in term of texture and flavor.
2021-10-14 | GSE162848 | GEO
Project description:In this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific. We suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions.
2014-06-05 | GSE58239 | GEO
Project description:In this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific. We suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions. 4 samples - male and female, BxD and DxB adipose of pooled RNA (3 animals per pool) were analyzed with high coverage RNAseq data.
2014-06-05 | E-GEOD-58239 | biostudies-arrayexpress
Project description:Abstract:Genetical genomics has been suggested and proven to be a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfilment of its promise, especially for loci (QTL) of moderate effects. One strategy to overcome the issue is to use a targeted approach: to focus the experiment on one QTL of particular interest. It has two clear advantages: (i) It reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point to investigate downstream effects of the QTL. In the present study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 (12 from each homozygote genotypes at the QTL) were investigated. The targeted QTL was located on chromosome 1 and affected initial pH of meat. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in human. The gene expression study identified ten strong local signals (potentially cis-eQTL) which were markedly more significant compared to the rest of the genome. The differentially expressed genes all mapped to a region < 1 Mb, suggesting a remarkable reduction of the QTL interval compared to the linkage study. These results combined with analysis of downstream effect of the QTL (using gene network analysis) suggest that the QTL is controlling pH by governing oxidative stress. The eQTL results were reproducible with using as few as 4 arrays on pooled samples (with lower significance level). The results demonstrate that this cost effective approach is promising not only for characterization of a QTL also for studying its downstream effects. there are 24 samples from to different genotypes. Each group of genotype has 12 samples. The two groups are compared using a dye balanced design.
2014-05-02 | E-GEOD-47800 | biostudies-arrayexpress
Project description:Abstract:Genetical genomics has been suggested and proven to be a powerful approach to study the genotype-phenotype gap. However, the relatively low power of these experiments (usually related to the high cost) has hindered fulfilment of its promise, especially for loci (QTL) of moderate effects. One strategy to overcome the issue is to use a targeted approach: to focus the experiment on one QTL of particular interest. It has two clear advantages: (i) It reduces the problem to a simple comparison between different genotypic groups at the QTL and (ii) it is a good starting point to investigate downstream effects of the QTL. In the present study, from 698 F2 birds used for QTL mapping, gene expression profiles of 24 (12 from each homozygote genotypes at the QTL) were investigated. The targeted QTL was located on chromosome 1 and affected initial pH of meat. The biological mechanisms controlling this trait can be similar to those affecting malignant hyperthermia or muscle fatigue in human. The gene expression study identified ten strong local signals (potentially cis-eQTL) which were markedly more significant compared to the rest of the genome. The differentially expressed genes all mapped to a region < 1 Mb, suggesting a remarkable reduction of the QTL interval compared to the linkage study. These results combined with analysis of downstream effect of the QTL (using gene network analysis) suggest that the QTL is controlling pH by governing oxidative stress. The eQTL results were reproducible with using as few as 4 arrays on pooled samples (with lower significance level). The results demonstrate that this cost effective approach is promising not only for characterization of a QTL also for studying its downstream effects.
2014-05-02 | GSE47800 | GEO
Project description: Not available
| S-EPMC8016890 | biostudies-literature
Project description:The processing ability of chicken meat is highly related to its ultimate pH (pHu), which is mainly determined by the amount of glycogen in the muscle at death. The molecular mechanisms involved in variations of those traits for chicken remain to be fully described. For that purpose, two chicken lines were divergently selected on breast meat pHu, i.e. the pHu- and the pHu+ lines. In this study, Chicken Genome Arrays (60 K) were used to compare muscle gene expression profiles of chickens from both lines. The final goal of this experiment is to identify biomarkers of low and high-pHu chicken meat. This study was supported by INRA and the French Ministry of Agriculture through the RFI CASDAR #1309 OPTIVIANDE.
2017-02-01 | GSE89268 | GEO