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

Chen D, Li W, Du M, Wu M, Cao B - Asian-australas. J. Anim. Sci. (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science, Shanxi Agriculture University, Taigu, Shanxi 030800, China.

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.

No MeSH data available.


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.
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f1-ajas-28-2-158: 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.

Mentions: Approximately 90% of the initial reads were retained for further analysis after the filtering of low-quality reads, resulting in 56.61 million, 49.79 million, 52.60 million, and 67.04 million clean reads for the Y1-1, Y1-2, Y2-1, and Y2-2 samples, respectively. Of the total sequenced reads, more than 98% mapped to the UMD 3.1.73 reference genome for each sample. More than 87% of these clean reads uniquely mapped to specific regions of the bovine genome. Unmapped reads and reads mapped to multiple positions were excluded from further analyses (Table 1). Among the 19,994 bovine genes (protein coding) in the bovine reference genome, 16,020 were expressed in the bovine muscle samples, representing the core components of the bovine muscle transcriptome. The mean numbers of genes transcribed in the muscle transcriptomes of the L and H animals were 14,904±226.3 and 14,837±44.5 (mean± standard deviation), respectively. These transcribed genes represented 74.5% and 74.2% of the total bovine genes for the L and H animals, respectively. Strong correlations between biological replicates were also observed (R2≥0.92; Figure 1A) between individuals showing the same marbling grade. There were 713 genes that were only expressed in the L group, and there were 509 genes only expressed in the H group (Figure 1B).


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

Chen D, Li W, Du M, Wu M, Cao B - Asian-australas. J. Anim. Sci. (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4283159&req=5

f1-ajas-28-2-158: 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.
Mentions: Approximately 90% of the initial reads were retained for further analysis after the filtering of low-quality reads, resulting in 56.61 million, 49.79 million, 52.60 million, and 67.04 million clean reads for the Y1-1, Y1-2, Y2-1, and Y2-2 samples, respectively. Of the total sequenced reads, more than 98% mapped to the UMD 3.1.73 reference genome for each sample. More than 87% of these clean reads uniquely mapped to specific regions of the bovine genome. Unmapped reads and reads mapped to multiple positions were excluded from further analyses (Table 1). Among the 19,994 bovine genes (protein coding) in the bovine reference genome, 16,020 were expressed in the bovine muscle samples, representing the core components of the bovine muscle transcriptome. The mean numbers of genes transcribed in the muscle transcriptomes of the L and H animals were 14,904±226.3 and 14,837±44.5 (mean± standard deviation), respectively. These transcribed genes represented 74.5% and 74.2% of the total bovine genes for the L and H animals, respectively. Strong correlations between biological replicates were also observed (R2≥0.92; Figure 1A) between individuals showing the same marbling grade. There were 713 genes that were only expressed in the L group, and there were 509 genes only expressed in the H group (Figure 1B).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: College of Life Science, Shanxi Agriculture University, Taigu, Shanxi 030800, China.

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.

No MeSH data available.