Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue

Abstract

Transcriptome profiles established using high-throughput sequencing can be effectively used for screening genome-wide differentially expressed genes (DEGs). RNA sequences (from RNA-seq) and microRNA sequences (from miRNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small-ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE) miRNAs, we drafted a network of 46 genes and 18 miRNAs for regulating muscle growth and a network of 15 genes and 16 miRNAs for regulating lipid deposition. We identified that CAV2, MYOZ2, FRZB, miR-29b, miR-122, miR-145-5p and miR-let-7c, etc, were key genes or miRNAs regulating muscle growth, and FASN, SCD, ADORA1, miR-4332, miR-182, miR-92b-3p, miR-let-7a and miR-let-7e, etc, were key genes or miRNAs regulating lipid deposition. The quantitative expressions of eight DEGs and seven DE miRNAs measured with real-time PCR certified that the results of differential expression genes or miRNAs were reliable. Thus, 18,208 genes and 320 miRNAs were positively expressed in porcine longissimus dorsi muscle. We obtained 85 genes and 18 miRNAs related to muscle growth and 27 genes and 16 miRNAs related to lipid deposition, which provided new insights into molecular mechanism of the economical traits in pig.

iTRAQ-based proteomic analysis reveals key proteins affecting muscle growth and lipid deposition in pigs

“…In our previous study, two indigenous Chinese pig breeds (DSP and TP) had significantly lower body weights and higher intramuscular fat (IMF) than those of two introduced pig breeds (LL and YY)25. In the present study, we found that the diameter of muscle fascicles was markedly smaller in TP and DSP than in LL and YY, indicating differential muscle development between Chinese and introduced pig breeds.…”

“…In our previous study, we identified genes related to growth and lipid deposition from the transcriptome profiles of LD muscles of pigs25. In the present study, we performed iTRAQ-based quantitative proteome analysis of the Chinese indigenous (TP and DSP) and introduced (YY and LL) pig breeds to identify functional proteins associated with muscle growth and lipid deposition pathways.…”

MTCH2 promotes adipogenesis in intramuscular preadipocytes via an m 6 A‐YTHDF1‐dependent mechanism

“…Adipogenesis of intramuscular preadipocytes has been determined via genetics (4), epigenetics, and transcriptomic mechanisms (5,6). Epigenetic imprinting through DNA methylation (7)(8)(9), microRNAs (10,11), and noncoding RNAs (12) play important roles in preadipocytes adipogenesis.…”

“…However, this process could be reversed by fat mass and obesity-associated protein (FTO) (17) or AlkBH5 (18). In addition, the YTH domain family (YTHDF) proteins YTHDF1-3 (19)(20)(21) and YTHDC1 (22) are believed to modulate m 6 A residues on mRNAs, thus regulating various aspects of RNA metabolism such as mRNA transcription (20,23), splicing (22), and stability (19). Previous studies reported that m 6 A modification down-regulates adipogenesis in porcine adipocytes (24), and it may affect adipogenesis by regulating alternative RNA splicing (25).…”

Elucidating a molecular mechanism that the deterioration of porcine meat quality responds to increased cortisol based on transcriptome sequencing

“…A large number of candidate genes between the psoas and the longissimus dorsi (LD) were obtained by cDNA microarray chip of porcine skeletal muscle18. A total of 315 differentially expressed genes (DEGs), including 240 genes annotated to the DAVID database, were obtained by comparing the LD sequencing results of the Chinese pig and imported pig19. In our research group, a significant number of DEGs associated with labor onset have been obtained via comparison of sequencing data from a shorter gestation period and a normal gestation period20.…”