Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle (Longissimus dorsi Muscle) Transcriptome - PubMed (original) (raw)

Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle (Longissimus dorsi Muscle) Transcriptome

Dong Chen et al. Asian-Australas J Anim Sci. 2015 Feb.

Abstract

Marbling is an important trait regarding the quality of beef. Analysis of beef cattle transcriptome and its expression profile data are essential to extend the genetic information resources and would support further studies on beef cattle. RNA sequencing was performed in beef cattle using the Illumina High-Seq2000 platform. Approximately 251.58 million clean reads were generated from a high marbling (H) group and low marbling (L) group. Approximately 80.12% of the 19,994 bovine genes (protein coding) were detected in all samples, and 749 genes exhibited differential expression between the H and L groups based on fold change (>1.5-fold, p<0.05). Multiple gene ontology terms and biological pathways were found significantly enriched among the differentially expressed genes. The transcriptome data will facilitate future functional studies on marbling formation in beef cattle and may be applied to improve breeding programs for cattle and closely related mammals.

Keywords: Beef Cattle; Marbling; RNA-Sequencing; Transcriptome.

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Figures

Figure 1

Figure 1

Bioinformation for the 4 samples. (A) Correlations of 4 samples; (B) venn diagram showing the shared and unique genes among the high (H) and low (L) groups. The two groups of longissimus dorsi tissues (H and L) share over 14,000 genes. Total unique transcripts = 1,222; Y1 = 713; Y2 = 509; (C) clustering of the list of differentially expressed genes between the L and H groups.

Figure 2

Figure 2

Top 20 functional gene ontology annotations for the differentially expressed genes (DEGs). Bar graphs (A), (B), and (C) show the three independent gene ontology (GO) information categories of biological processes, molecular functions and cellular components, respectively. In each bar graph, the abscissa represents the number of DEGs, and the ordinate shows the ID numbers of the GO terms. All GO categories listed exhibit enrichment with p<0.05.

Figure 3

Figure 3

Comparisons of the RNA sequencing and quantitative polymerase chain reaction expression ratios (low and high groups) for the selected genes.

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