Phenotypic and genotypic relationships between meat quality characteristics and expression of target genes associated with broiler meat quality defects
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PROVIDER: PRJNA419898 | ENA |
REPOSITORIES: ENA
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Project description:The objective of this project was to employ customized Agilent 8x60 chicken whole genome microarray to identify differentially expressed genes associated with white striping (WS) and wooden breast (WB) defects in breast meat collected from commercial broilers with different slaughter age. Following harvest of chicken breasts (n = 184), the breast samples were classified as based on their appearance into non-defect, WS or WB. The defective samples were further grouped based on defect severity (WS = mild, moderate, severe; WB = moderate, severe). A total numbers of 40 samples were selected to represent various degree of the defects. Total RNA from deep-frozen skeletal muscle was isolated, integrity check (RIN > 7.0) and subjected for one-colored microarray hybridization according to Agilent’s instruction. The array was designed (design ID: AMADID G4102A084792) based on the National Center for Biotechnology Information (NCBI) Gallus gallus Annotation Release 103 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Gallus_gallus/103/). Differential gene expression (p-value < 0.05) was confirmed using qPCR and droplet digital PCR. Biological pathways associated with WS and WB were identified.
2018-05-01 | GSE107362 | GEO
Project description:This study investigates the impact of stress on muscle physiology and meat quality in broiler chickens by comparing protein expression profiles between organic and conventional farming systems using label-free quantitative (LFQ) proteomics. Muscle samples were analyzed via nanoLC-ESI-MS/MS coupled with comprehensive bioinformatics to identify differences in protein abundance associated with rearing conditions.A total of 7,221 proteins were identified, with 1,645 proteins upregulated and 1,612 downregulated in organic chickens compared to conventional ones. Functional analyses including Gene Ontology (GO) and STRING network analyses revealed that proteins upregulated in organic chickens were predominantly involved in oxygen transport, oxygen binding, and muscle structural organization, indicating enhanced oxygen metabolism and muscle development consistent with improved animal welfare. Conversely, proteins related to ribosomal function and RNA binding were enriched in conventional chickens, suggesting stress-related alterations in protein synthesis. KEGG pathway analysis showed significant enrichment of carbon metabolism, amino acid biosynthesis, nitrogen metabolism, and the tricarboxylic acid (TCA) cycle pathways in organic chickens, while glycolysis, gluconeogenesis, and ribosomal pathways were downregulated. Key differentially expressed proteins identified as potential biomarkers distinguishing organic from conventional meat include downregulated PGM1, AMPD1, LDHA, ENO3, and PKLR, and upregulated COL1A1, COL1A2, TTN, TPM2, CA3, MB, HSPB1, ACO2, ACAA2, and TF. These proteins are involved in muscle structure and energy metabolism and may serve as indicators of meat quality linked to stress and welfare conditions. Overall, this proteomic analysis provides novel insights into how stress modulates the muscle proteome in broiler chickens and supports the adoption of welfare-focused organic poultry production practices to improve meat quality.
2025-12-29 | PXD066589 | Pride
Project description:This study, conducted as part of the mEATquality European Union project, used a large intervention experiment to examine the main effects and interactions of extensification factors in higher-welfare, non-organic systems with relatively low chicken stocking density. The study focused on how chicken genetics and on-farm enrichments (as two extensification factors) influence broiler performance, intrinsic meat quality and the molecular mechanisms underlying these traits with the aim of supporting improved production strategies.
2026-05-29 | PXD066390 | Pride
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.
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2022-07-08 | GSE207449 | GEO
Project description:Our analysis revealed the unique and common lncRNA-miRNA-mRNA networks of two kinds of adipocytes. Several lncRNAs that regulate goat meat quality were identified, such as XR_001918647.1, XR_001917728.1, XR_001297263.2 and LNC_004191. Our study utilized RNA-seq analysis to predict the functions of lncRNA on goat meat quality. Furthermore, our findings of lncRNA-miRNA-mRNA network, may contribute to a better understanding of the molecular mechanisms underlying in goat meat quality and provide a theoretical basis for further goat molecular breeding.
2021-12-25 | GSE186988 | GEO
Project description:Residual feed intake (RFI) as a measure of feed efficiency (FE) is an index that can help producers reduce costs by enabling the selection of more efficient and profitable cattle. However, the meat quality of these animals may be negatively impacted due to the lower subcutaneous fat deposition commonly observed in more efficient (low RFI) cattle. Traits such as tenderness, color, and juiciness may be affected by the reduced fat deposition, influencing consumers' purchasing decisions. Although low RFI cattle exhibit better FE in feedlot systems, few studies have described the molecular mechanisms regulating meat quality traits in these animals. Therefore, the objective of this project is to compare low RFI (efficient) and high RFI (inefficient) cattle finished in feedlots and to evaluate their meat quality in both physicochemical and molecular contexts. Comparing efficient and inefficient feedlot-finished cattle in terms of meat quality traits and identifying associations with the proteome of muscle tissue may contribute to a better understanding of the metabolic pathways that influence economically important characteristics in these animals.
2025-04-15 | MSV000097636 | MassIVE
Project description:To investigate the impact of adding succinate to the diet on the production performance, meat quality, muscle fiber characteristics, and transcriptome of the longissimus dorsi muscle in Tan sheep, 36 Tan sheep were selected and fed with different levels of succinate (0%, 0.5%, 1.0%, 2.0%) for a 60-day trial period. Overall, compared to the control group, the addition of succinate to the diet improved the production performance, slaughter performance, and meat quality of Tan sheep. It significantly increased dry matter intake, carcass weight, eye muscle area, and the GR value while significantly reducing the shear force and cooking loss of the longissimus dorsi muscle (p<0.05). Furthermore, the addition of succinate to the diet altered the muscle fiber characteristics of the longissimus dorsi muscle in Tan sheep, significantly increasing the fiber diameter and cross-sectional area of type I and type IIa muscle fibers (p<0.05). The addition of 1.0% succinate to the diet altered the transcriptome of the longissimus dorsi muscle in Tan sheep, with 741 differentially expressed genes identified compared to the control group. These differentially expressed genes were involved in various pathways related to lipid metabolism, energy metabolism, and muscle development, such as insulin secretion, insulin resistance, cAMP signaling pathway, PI3K-Akt signaling pathway, and FoxO signaling, among others. In summary, succinate plays a crucial role in regulating energy metabolism, protein deposition, and glucose and lipid metabolism homeostasis in Tan sheep through insulin signaling pathways and the interaction of muscle cell factors. By modulating the expression of relevant genes, succinate improves the muscle fiber characteristics of Tan sheep, thereby enhancing production performance and meat quality.
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Project description:Studies exploring the transcriptome of stress and its effects on meat quality are very limited, particularly in goats. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats / treatment): (i) transported for 180 min, (ii) transported for 30 min, or (iii) held in pens (control) to analyze the transcriptome of stress and meat quality in goats using RNA-seq technology. Blood samples were collected before and after treatment, and meat samples were collected after humane slaughter for stress hormone, meat quality (Longissimus dorsi), and transcriptomic analysis. Plasma epinephrine concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group; however, norepinephrine concentrations were not affected by the treatment. Muscle glycogen concentrations (15 min postmortem) were lower (P < 0.01) in both 30 min and 180 min groups compared to the control group. Calpastatin levels were higher (P < 0.01) in 180 min and 30 min groups than the control group. Warner-Bratzler shear force values of loin chops were the highest in the 180 min group (4 ± 0.15, kg), lowest in the control group (3.51 ± 0.10, kg), and intermediate in the 30 min group (3.78 ± 0.09, kg; P < 0.01) both at day 1 and day 6 aging time. Additionally, desmin levels of day 6 samples were lowest in the control group, highest in 180 min group, and intermediate in 30 min group (P < 0.05). RNA-seq results showed that a total of 10,633 genes were differentially expressed (5,194 up regulated; 5,439 down regulated) among all comparisons (blood and day 1 and day 6 muscle samples). Among these differentially expressed genes (DEGs), KLF9, AMPK, FOXO3, PTX3, GADD45, PTPN1, CASP7, MAPK4, HSPA12A, and JAK-STAT were probably associated with the effects of stress on skeletal muscle proteins and involved in biological process such as cellular response to corticosteroid stimulus, endoplasmic reticulum stress, insulin resistance, DNA repair, apoptosis, MAPK cascade and regulation of proteolysis. The KEGG analysis revealed that AMPK and JAK-SAT signaling pathways and autophagy were among the top 20 enriched pathways in our treatment comparisons. The results provide an understanding of the genes and pathways involved in stress responses and related changes in postmortem muscle metabolism and meat quality characteristics in goats.
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