Identification of novel markers of beef sensory quality and muscle growth potential
Ontology highlight
ABSTRACT:
ORGANISM(S): Bos taurus Mus musculus 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: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.
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