Sequencing and Characterization of Divergent Marbling Levels in the Beef Cattle (Longissimus dorsi Muscle) Transcriptome
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
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.
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.
참고문헌 (22)
- Baldwin, R. L. V., "Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers", Physiol. Genomics, 44, pp.543~550 (2012)
- Cloonan, N., "Transcriptome content and dynamics at single-nucleotide resolution", Genome Biol, 9, pp.234~ (2008)
- Cox, M. P., "SolexaQA : At-a-glance quality assessment of Illumina second-generation sequencing data", BMC Bioinformatics, 11, pp.485~ (2010)
- de Hoon, M. J. L., "Open source clustering software", Bioinformatics, 20, pp.1453~1454 (2004)
- Driver, A. M., "RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo-and in vitro-derived bovine blastocysts", BMC Genomics, 13, pp.118~ (2012)
- Grobet, L., "A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle", Nat. Genet, 17, pp.71~74 (1997)
- Hausman, G. J., "Board-invited review: the biology and regulation of preadipocytes and adipocytes in meat animals", J. Anim. Sci, 87, pp.1218~1246 (2009)
- He, H., "Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing", PloS one, 8(6), pp.e64356~ (2013)
- Huang, D. W., "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", Nat. Protoc, 4, pp.44~57 (2009)
- Kim, D., "TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions", Genome Biol, 14, pp.36~ (2013)
- Langmead, B., "Fast gapped-read alignment with Bowtie 2", Nat. Methods, 9, pp.357~359 (2012)
- Livak, K. J., "Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T))method", Methods, 25, pp.402~408 (2001)
- Marioni, J. C., "RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays", Genome Res, 18, pp.1509~1517 (2008)
- Nagalakshmi, U., "The transcriptional landscape of the yeast genome defined by RNA sequencing", Science, 320, pp.1344~1349 (2008)
- Reecy, J., "Gene expression profiling: insights into skeletal muscle growth and development", J. Anim. Sci, 84, pp.150~154 (2006)
- 't Hoen, P. A. C., "Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms", Nucl. Acids Res, 36, pp.e141~ (2008)
- Trapnell, C., "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks", Nat. Protoc, 7, pp.562~578 (2012)
- Trapnell, C., "Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation", Nat. Biotechnol, 28, pp.511~515 (2010)
- Wang, Y. H., "Gene expression patterns during intramuscular fat development in cattle", J. Anim. Sci, 87, pp.119~130 (2009)
- Wang, Y. H., "Transcriptional profiling of skeletal muscle tissue from two breeds of cattle", Mamm. Genome, 16, pp.201~210 (2005)
- Wang, Z., "RNA-Seq: A revolutionary tool for transcriptomics", Nat. Rev. Genet, 10, pp.57~63 (2009)
- Werner, T., "Next generation sequencing in functional genomics", Brief. Bioinform, 11, pp.499~511 (2010)