Transcriptome analysis of adductor muscle color in Boihai Red Scallop
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ABSTRACT:
PROVIDER: PRJNA505266 | ENA |
REPOSITORIES: ENA
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Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study, transcriptomic was conducted on orange and white adductor muscle tissues. Transcriptomic analysis showeds 416 differentially expressed genes (DEGs) were identified between white and orange adductor muscle tissues in Boihai Red Scallop, with 216 up regulated and 200 down. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
2019-04-15 | GSE122451 | GEO
Project description:Boihai Red is new strains of inter-specific hybridizing the bay scallop (Argopecten irradians irradians) with the Peruvian scallop (Argopecten purpuratus). Orange color variant of adductor muscle have been developed through successive selective breeding in this strain. In the present study,proteomic were conducted on orange and white adductor muscle tissues.Notably, 74 differentially expressed proteins (DEPs) were identified by lable free proteomics, including 36 up and 38 down regulated. In DEGs, apolipophorin, CYP450 and tyrosinase were expressed highly in orange adductor muscle tissues, which related to carotenoids or melanin. In DEPs, high expression of VPS and TIF in orange adductor muscle tissues indicated that proteins outside the carotenoid pathway might also affect carotenoid biosynthesis. In addition, RAB11A related to melanin was also expressed highly in orange adductor muscle tissues at protein level. It is probable that not only carotenoids, but also melanin act on orange color of adductor muscle. This study provides valuable genetic resources for understanding underlying mechanisms and pathways of adductor muscle color.
2019-11-12 | PXD011708 | Pride
Project description:We performed the first quantitative proteomics analysis of differences between striated (fast) and catch (slow) adductor muscle in Yesso scallop (Patinopecten yessoensis), with the goal to uncover muscle specific genes and proteins, as well as enzymes of metabolic pathways in fast and slow adductor muscle of scallops. The present findings highlight the functional roles of muscle contractile proteins, calcium signaling pathways, membrane and extracellular matrix proteins, and glycogen metabolism involved in the different contractile and metabolic properties between fast and slow muscles. The present findings will help better understand the molecular basis underlying muscle contraction and its physiological regulation in invertebrates.
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Project description:Background: Earlobe color is a typical external trait in chicken. There are some previous studies showing that the chicken white/red earlobe color is a polygenic and sex-linked trait in some breeds, but its molecular genetic and histological mechanisms still remain unclear. Methods: We herein utilized histological section, genome-wide association study (GWAS) and RNA-seq, further to investigate the potential histological and molecular genetic mechanisms of white/red earlobe formation in Qiangyuan Partridge chicken (QYP). Results: through histological section analysis, we found the dermal papillary layer of red earlobes had many more blood vessels than that of white earlobes. And we identified a total of 44 SNPs from Chromosome 1, 2, 3, 4, 9, 10, 11, 13, 19, 20, 23 and Z, that was significantly associated with the chicken white/red earlobe color from GWAS, along with 73 significantly associated genes obtained (e.g., PIK3CB, B4GALT1 and TP63), supporting the fact that the white/red earlobe color was also polygenic and sex-linked in QYP. Importantly, PIK3CB and B4GALT1 are both involved in the biological process of angiogenesis, which may directly give rise to the chicken white earlobe formation through regulating blood vessel density in chicken earlobe. Additionally, through contrast of RNA-seq profiles between white earlobe skins and red earlobe skins, we further identified TP63 and CDH1 differentially expressed. Combined with the existing knowledge of TP63 in epithelial development and tumor angiogenesis, we propose that down-regulated TP63 in white earlobes may play roles in thickening the skin and decreasing the vessel numbers in dermal papillary layer, thereby contributing to the white earlobe formation via paling the redness of the skin in QYP, but the specific mechanism remains further clarified. Conclusion: our findings advance the existing understanding of the white earlobe formation, as well as provide new clues to understand the molecular mechanism of chicken white/red earlobe color formation.
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Project description:In meat animal production, favourable meat traits such as color and, in the pig in particular, tenderness have been found to closely associate with the greater abundance of red or highly oxidative fibres. Red muscles possess higher lipid concentration (intra- and inter-fibre fat) which is associated with more tender and juicy meat. In addition, individuals with muscles that are abundant in oxidative type I fibres are associated with favourable metabolic health, and are less likely to predispose to obesity and insulin resistance. Collectively, understanding the molecular processes that govern the expression of specific fiber types and the phenotypic characteristics of muscles is important in agricultural and medical fields. In this study, a genome-wide investigation of the porcine differential expression between two red (soleus, SE) and white (longissimus dorsi, LD) muscle was conducted using the Affymetrix GeneChip® Porcine Genome Array containing oligonucleotides representing approximately 24123 transcripts from 20201 S. scrofa genes
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Project description:In meat animal production, favourable meat traits such as color and, in the pig in particular, tenderness have been found to closely associate with the greater abundance of red or highly oxidative fibres. Red muscles possess higher lipid concentration (intra- and inter-fibre fat) which is associated with more tender and juicy meat. In addition, individuals with muscles that are abundant in oxidative type I fibres are associated with favourable metabolic health, and are less likely to predispose to obesity and insulin resistance. Collectively, understanding the molecular processes that govern the expression of specific fiber types and the phenotypic characteristics of muscles is important in agricultural and medical fields. In this study, a genome-wide investigation of the porcine differential expression between two red (soleus, SE) and white (longissimus dorsi, LD) muscle was conducted using the Affymetrix GeneChip® Porcine Genome Array containing oligonucleotides representing approximately 24123 transcripts from 20201 S. scrofa genes Three meishan gilts from the same litter were slaughtered at the 150 days of age by electrical stunning and exsanguination, in compliance with national regulations applied in commercial slaughtering. Immediately after slaughter, two muscles with different locations, functions, and biochemical properties were sampled: the longissimus at the last rib level, a fast twitch glycolytic muscle involved in voluntary movements of the back, and the deep portion of the SE, a oxydolytic muscle.
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