Abstract
BackgroundSkeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing.ResultsAccording to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways.ConclusionsThis study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.
Highlights
Skeletal muscle growth and development are closely associated with the quantity and quality of pork production
RNA sequencing (RNA-seq) of longissimus dorsi (LD) muscle samples To systematically identify the expressed mRNA and their spatiotemporal expression profiles during skeletal muscle growth and development in pigs, cDNA libraries were constructed from LD muscle samples of 12 Tibetan pigs at 0, 14, 30, and 60 days, representing the four important developmental stages: D0 (No D0_1, D0_2, D0_3), D14 (No 14D_1, 14D_2, 14D_3), M1 (No 1M_1, 1M_2, 1M_ 3), and M2 (No 2M_1, 2M _2, 2M _3)
Identifying the differentially expressed genes (DEGs) As a result of the pairwise comparisons between the libraries of LD muscle samples at the four developmental stages, 4115 genes were detected in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01 (Fig. 1, Table S2)
Summary
Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. Siengdee et al [16] conducted a comparative study to explore the muscle miRNA expression profiles and clarify the breedassociated regulation of miRNAs in Landrace and Pietrain pig breeds. The mRNA transcriptome profiles of skeletal muscle tissue have been compared across different developmental stages, including the prenatal [17] and postnatal [18] between western pig breeds, and embryonic to postnatal periods between Chinese indigenous pigs and western pigs [9, 19]. Few studies have systematically examined the differences in transcriptome profiles at different developmental stages in piglets, dynamic transcript analyses from the embryonic to postnatal periods have been reported in sheep [22] and chickens [23]
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