Characteristics and differences of genes in different meat cuts from Chalu black pigs

In this study, pork intramuscular fat (IMF) content and tenderness, myosin heavy chain (MYH) isoform expression was characterized in four cuts including longissimus dorsi muscle (LDM), trapezius muscle (TM), hamstring muscle (HM) and pork belly (PB). Then transcription expression profiles were compared in LDM, TM, HM and PB of Chulu black pig using RNA sequencing technologies (RNA-Seq). We profiled the transcriptome of HM, LDM, PB and TM isolated from pigs with approximately 100kg body weight and identified expressed 21280 transcription units. Of the them, 292-1589 DEGs genes were differentially expressed between four cuts. Using analysis of upset Venn graph, the 47, 305, 395 and 10 unique DEGs were respectively screened for HM, LDM, PB and TM. The enriched pathways in unique DEGs of HM mainly related to “organismal systems and inflammatory mediator regulation of TRP channels”, “neurotrophins signaling pathway” and “cellular senescence”. In unique DEGs of LDM, pathways included “glycolysis / Gluconeogenesis”, “carbon metabolism”, “HIF-1 signaling pathway”, “glucagon signaling pathway”, “pentose phosphate pathway” and “PPAR signaling pathway” were significantly enriched. In PB, the specific DEGs enriched in the human disease, cellular process and organismal systems pathways. Only two significantly enriched pathways including “inflammatory mediator regulation of TRP channels” and “axon guidance” were found in unique DEGs of TM. The findings suggested that the cuts differences of the pork are not only related to amino acid metabolism and lipid metabolism, but also closely associated with muscle fibers type and the formation of flavor precursor substances. The cut specific gene expression patterns finally decided the VOCs profile in pork constituting the unique aroma of each meat cuts of ChaLu black pork. Overall design: The mRNA profiles of Longissimus dorsi muscle (LDM), trapezius muscle (TM), hamstring muscle (HM) and pork belly (PB) in Chalu black pig were generated by using RNA sequencing technologies (RNA-Seq). Forty cDNA libraries representing LDM, TM, HM, PB groups were constructed for mRNA transcriptome analysis.