Integrated mRNA and miRNA profiles expression of liver between Jinhua and Landrace pigs
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ABSTRACT:
PROVIDER: PRJNA512179 | ENA |
REPOSITORIES: ENA
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Project description:Jinhua and Landrace pigs fecal samples Raw sequence reads
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Project description:Backfat thickness is one of the most important traits of commercially raised pigs. Meishan pigs are renowned for having thicker backfat than Landrace pigs. To examine the genetic factors responsible for the differences, we first produced female crossbred pig lines by mating Landrace (L) × Large White (W) × Duroc (D) females (LWD) with Landrace (L) or Meishan (M) boars (i.e., LWD × L = LWDL for Landrace offspring and LWD × M = LWDM of the Meishan offspring). We confirmed that LWDM pigs indeed had a thicker backfat than LWDL pigs. Next, we performed gene expression microarray analysis (in both genetic lines) to examine differentially expressed genes (DEGs) in energy metabolism-related tissues, subcutaneous adipose (fat), liver, and longissimus dorsi muscle tissues. We analyzed the annotation of DEGs (2-fold cutoff) to functionally categorize them by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. The number of DEGs in muscle tissues of both lines was much less than that in fat and liver tissues, indicating that DEGs was much lesser in muscle tissues (in both genetic lines) than in fat and liver tissues, thus indicating that DEGs in muscle tissues may not contribute much to differences in backfat thickness. In contrast, several genes related to muscle (in fat tissue) and fatty acid and glucose metabolism (in the liver) were more upregulated in LWDM pigs than LWDL pigs, indicating that those DEGs might be responsible for differences in backfat thickness. The different genome-wide, gene expression profiles in the fat, liver, and muscle tissues between breeds can provide useful information for pig breeders.
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Project description:Using Jinhua and Landrace pigs as fat and lean models, we present a comprehensive transcriptome-wide m6A profiling in adipose and muscle tissues from these two pig breeds.The results show m6A is widely spread and highly conserved in pig mRNA. m6A occurs in the conserved sequence motif of GGACU and exhibits a unique topology in pig. m6A peak enrichment correlates positively with gene expression, and transcripts with m6A at 5’UTR or CDS are correlated with gene activation than those at 3’UTR. Common m6A peaks in both layer of backfat from Landrace (L-LB) and Jinhua (J-LB) pigs are involved in lipid metabolism, while common m6A peaks in both longissimus dorsi muscle from Landrace (L-LDM) and Jinhua (J-LDM) mapped to muscle development, suggesting m6A-containing genes are involved in many biological processes especially related to tissue-specific functions.
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Project description:Hezuo pigs are known in China for early sexual maturity. In this study, we obtained transcriptome data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some genes related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.
2021-08-31 | GSE171756 | GEO
Project description:Hezuo pigs are known in China for early sexual maturity. In this study, we obtained small RNA-Seq data from testicular tissues of 30-day-old and 120-day-old Hezuo and Landrace pigs. Through comparative analysis of their differences, we searched for some miRNAs related to the regulation of precocious sexual traits in male cooperating pigs and revealed their molecular regulatory mechanisms, which can then provide references for the diagnosis and treatment of precocious sexual diseases in humans and for accelerating the breeding of high-fertility animals.
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Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types.
2010-04-22 | GSE21412 | GEO
Project description:The anterior pituitary is the most important endocrine organ modulating animal postnatal growth, mainly by controlling growth hormone (GH) gene transcription, synthesis, and secretion. As an ideal model for animal postnatal growth studies, the Bama minipig is characterized as having a lower growth performance and fewer individual differences compared with larger pig breeds. In this study, anterior pituitaries from Bama minipig and Landrace pig were used for miRNA and mRNA expression profile analysis using miRNA microarrays and mRNA-seq. Consequently, a total of 222 miRNAs and 12,909 transcripts were detected, and both miRNAs and mRNAs in the two breeds showed high correlation (r > 0.97). Additionally, 41 differentially expressed miRNAs and 2,254 transcripts were identified. Pathways analysis indicated that 32 pathways significantly differed in the two breeds. Importantly, two GH-regulation-signalling pathways, cAMP and inositol 1, 4, 5-triphosphate (IP3), and multiple GH-secretion-related transcripts were significantly down-regulated in Bama minipigs. Moreover, target prediction by two algorithms (TargetScan and RNAhybrid) indicated that most miRNA–mRNA target pairs (63.68–71.33%) presented a negatively correlated expression pattern. A possible network among miRNAs, mRNAs, and GH-regulation pathways was also proposed. These data will be helpful in understanding the possible molecular mechanisms involved in animal postnatal growth. 2 pooled samples were analyzed. A pool of 3 pig anterior pituitary was used for Bama minpigs and Landrace pigs,respectively.
2015-05-05 | E-GEOD-68489 | biostudies-arrayexpress
Project description:The aim of this study was to identify differentially expressed genes and pathways in longissimus dorsi (LD) of pigs at 40 and 70 d of gestation (stages encompassing the transition from primary to secondary fiber formation) in U.S. commercial crossbred pigs (Yorkshire x Landrace) and Brazilian native Piau pigs. We confirmed the expression patterns for a subset of genes by qRT-PCR. Pathway analysis revealed functionally related genes, and indicated commonalities and differences between the breed types and developmental ages evaluated. Results from qRT-PCR analysis confirmed the expression patterns observed on the array for most of the genes tested (85%). This study reveals transcriptional profiles in LD at 40 and 70 d gestation for commercial and Piau pigs, which helps elucidate phenotypic differences between these breed types. This study utilized the Swine Protein-Annotated Oligonucleotide Microarray which contains 20,400 70-mer oligonucleotides (http://www.pigoligoarray.org). Total RNA was isolated from fetuses obtained from gilts at each gestational age (n=3 crossbred gilts; n=4 Piau gilts) and RNA from 3 fetuses per litter was pooled. Samples were evaluated with a connected loop design using 13 slides such that six breed comparisons and seven age comparisons were performed. Fluorescence intensity data was LOESS normalized and analyzed with a mixed model.
2010-04-22 | E-GEOD-21412 | biostudies-arrayexpress
Project description:The anterior pituitary is the most important endocrine organ modulating animal postnatal growth, mainly by controlling growth hormone (GH) gene transcription, synthesis, and secretion. As an ideal model for animal postnatal growth studies, the Bama minipig is characterized as having a lower growth performance and fewer individual differences compared with larger pig breeds. In this study, anterior pituitaries from Bama minipig and Landrace pig were used for miRNA and mRNA expression profile analysis using miRNA microarrays and mRNA-seq. Consequently, a total of 222 miRNAs and 12,909 transcripts were detected, and both miRNAs and mRNAs in the two breeds showed high correlation (r > 0.97). Additionally, 41 differentially expressed miRNAs and 2,254 transcripts were identified. Pathways analysis indicated that 32 pathways significantly differed in the two breeds. Importantly, two GH-regulation-signalling pathways, cAMP and inositol 1, 4, 5-triphosphate (IP3), and multiple GH-secretion-related transcripts were significantly down-regulated in Bama minipigs. Moreover, target prediction by two algorithms (TargetScan and RNAhybrid) indicated that most miRNA–mRNA target pairs (63.68–71.33%) presented a negatively correlated expression pattern. A possible network among miRNAs, mRNAs, and GH-regulation pathways was also proposed. These data will be helpful in understanding the possible molecular mechanisms involved in animal postnatal growth. mRNA profiling in the anterior pituitary from two different pig breeds.2 pooled samples were analyzed. A pool of 3 pig anterior pituitary was used for Bama minpigs(YB) and Landrace pigs(YC),respectively.
2015-05-05 | E-GEOD-68490 | biostudies-arrayexpress