Identification of novel markers of beef sensory quality and muscle growth potential
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus Bos taurus Homo sapiens
PROVIDER: GSE5561 | GEO | 2007/08/18
SECONDARY ACCESSION(S): PRJNA95407
REPOSITORIES: GEO
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Project description:The transcriptome of bovine Longissimus thoracis muscles from 15- and 19-month-old Charolais young bulls were analyzed in order to identify genes whose expression level was associated to beef quality scores, in particular to tenderness, juiciness and flavor, and to muscle growth potential. The expression of over 5000 genes was compared between high and low meat quality samples according to the three sensory traits, taken individually, and between animals with either a high or a low muscle growth potential. Keywords: meat sensory quality, growth potential Twenty-five samples were analyzed. Each sample was hybridized on 4 independent microarrays and compared to a reference pool.
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Project description:Arouquesa breed is an autochthonous Portuguese breed produced under a traditional mountain system. It is known for its Arouquesa PDO beef, a high-quality product with valued organoleptic characteristics. There is a need to improve production systems without affecting beef quality. The aim of this work is to compare the proteomics profile from the Longissimus thoracis muscle from Arouquesa animals produced under different systems. Sixty weaners were produced under the following systems: traditional (TF) and traditional with starter feed supplementation (TF+S1) with weaning and slaughtering at 8 months, the S1+S2 (weaning at 5 months and grower supplement until slaughter) and two rearing periods with finishing supplementation (TF+S3 and S3). Upon slaughter, samples of L. thoracis were taken and analyzed using a shotgun proteomics workflow. Several putative biomarkers of beef quality for the Arouquesa breed were identified: VIM, FSCN1, SERPINH1, ALDH1A1, NDUFB5, ANXA1, PDK4, CEMIP2, NDUFB9, PDLIM1, OXCT1, MYH4. These proteins were involved in actin binding, skeletal muscle development and in the mitochondrial respiratory chain and they can influence mostly meat tenderness and color. Our results demonstrate the link between production practices and putative meat quality signatures, that have potential to improve traceability of certified products.
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Project description:Background: Intramuscular fat (IMF) content is highly valued as it improves meat product quality by enhancing taste, juiciness, and tenderness. IMF content can be significantly different between breeds. Thought many lipid metabolism-related genes are stated to be associated with IMF deposition, the molecular mechanism of IMF deposition is still poorly understood. To date, no gene or mutation loci responsible for the difference of IMF content among cattle breeds has been identified. To identify transcripts with potential regulatory role in lipid accumulated in muscle tissue, RNA sequencing was performed to compare the mRNAs, lncRNAs, and circRNAs expression patterns in the longissimus dorsi muscle and back fat between Chinese buffalo and cattle. Results: A total of 12 cDNA libraries were constructed. A total of 925,441,106 and 512,507,068 raw reads were obtained from buffalo and cattle, respectively. After filtering the adaptor and low quality reads, 909,040,352 and 491,967,820 clean reads were retained. In total, 19,917 mRNAs, 43,975 lncRNAs, and 10,701 circRNAs were identified in buffalo and 19,383 mRNAs, 8,265 lncRNAs, and 18,535 circRNAs were identified in cattle.
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Project description:Purpose: The goals of this study are to determine effects of castration on gene expression in longissimus dorsi muscle by comparing transcriptome profiles and to search candidate genes related with beef quality like flavor, tenderness, juiciness and fat deposition Methods: longissimus dorsi muscle mRNA profiles of 3 bulls and 3 steers of Korean cattles were generated by RNA sequencing using Illumina NextSeq 500. After quality checking, Tophat2 software was used for read mapping, and EdgeR was used to identify differentially expressed genes (DEGs) between bulls and steers. Gene ontology pathway analysis on DEGs was conducted with DAVID tool for categorization of DEGs. Results: Using an optimized data analysis workflow, we mapped about 58 million sequence reads per sample to the bovine genome (build UMD3.1) and identified 18,027 expressed genes in the longissimus dorsi muscle of bulls and steers with TopHat2 workflow. RNA-seq data confirmed 1,146 differentially expressed genes (adjusted p-value, FDR <0.05). Conclusions: We comparatively analyzed the transcriptome profile from longissimus dorsi muscle of bulls and steers of Korean cattles using NGS and identified DEGs between bulls and steers. The functional annotation analysis of DEGs found that transcriptome profile difference in longissimus dorsi muscle by castration.
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Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture. Experiment Overall Design: Gene expression profiles were correlated with beef traits measured at the same cattle.
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Project description:To identify transcriptional markers for beef traits related to meat tenderness and moisture, we measured the transcriptome of the Longissimus dorsi skeletal muscle in 10 Korean native cattle (KNC). We analyzed the correlation between the beef transcriptome and measurements of four different beef traits, shear force (SF), water holding capacity (WHC), cooking loss (CL), and loin eye area (LEA). We obtained non-overlapping and unique panels of genes showing strong correlations (|r| > 0.8) with SF, WHC, CL, and LEA, respectively. Functional studies of these genes indicated that SF was mainly related to energy metabolism, and LEA to rRNA processing. Interestingly, our data suggested that WHC is influenced by protein metabolism. Overall, the skeletal muscle transcriptome pointed to the importance of energy and protein metabolism in determining meat quality after the aging process. The panels of transcripts for beef traits may be useful for predicting meat tenderness and moisture.
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