Ontology highlight
ABSTRACT:
PROVIDER: PRJNA690838 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13434414_1.fastq.gz | Fastqsanger.gz | |||
| SRR13434414_2.fastq.gz | Fastqsanger.gz | |||
| SRR13434415_1.fastq.gz | Fastqsanger.gz | |||
| SRR13434415_2.fastq.gz | Fastqsanger.gz | |||
| SRR13434416_1.fastq.gz | Fastqsanger.gz |
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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:An M307 G/A point mutation of FUT1 gene has been considered as a usful marker to select the piglets that are sensitive(GG/AG genotype) or resistant(AA) to Escherichia coli F18 in foreign pig breeds.However,it is not suitable to Chinese native breeds. Duodenal tissues were collected from 8 full-sib pairs of Sutai pigs (a new hybrid between the Duroc and Taihu breeds) at the age of 28-day differing in adhesion phenotype to find the differential genes that can be used as the candidate genes fit for Chinese native breeds. piglets at the age of 28-day sensitive (GG/AG genotype) to Escherichia coli F18 vs resistant(AA) ones.Biological replicates:8 full-sib pairs of Sutai pigs (4 pairs for GG/AA genotype of FUT1 gene, 4 pairs for AG/AA genotype)
2011-01-26 | E-GEOD-26854 | biostudies-arrayexpress
Project description:Purpose: This study conducted RNA-Seq analysis on Dingyuan pig individuals with different intramuscular fat content and backfat thickness, in order to find genes that specifically regulate subcutaneous fat and intramuscular fat deposition in pigs
2021-07-08 | GSE179457 | GEO
Project description:An M307 G/A point mutation of FUT1 gene has been considered as a usful marker to select the piglets that are sensitive(GG/AG genotype) or resistant(AA) to Escherichia coli F18 in foreign pig breeds. However,it is not suitable to Chinese native breeds. Duodenal tissues were collected from 3 full-sib pairs of Sutai pigs (a new hybrid between the Duroc and Taihu breeds) at the age of 28-day differing in adhesion phenotype to find the differential miRNAs that can provide the basis for analyzing the different mechanisms of E.coli F18 resistance between foreign and Chinese native breeds,as well as for breeding for disease resistance in Chinese native breeds in the future. piglets at the age of 28-day sensitive(GG genotype) to Escherichia coli F18 vs resistant(AA) ones.Biological replicates:3 full-sib pairs of Sutai pigs(3 pairs for GG/AA genotype of FUT1 gene).One GG sample (512 piglet) was sequenced twice to verify the result. 2385 piglet and 2383 piglet were a pair of full-sib with AA and GG genotype at M307 positionof FUT1 gene, respectively. Unfortunately, the sequencing of 2385 was a failure and was excluded. 2385 piglet has an AA genotype of the FUT1 gene
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Project description:Fat deposition is a prominent economic trait and complex process in pigs. Ningxiang pig, one of the four famous indigenous breeds in China, is characterized by high fat content. The underlying gene expression pattern in different developmental periods of backfat tissue remains unclear, and the purpose of this investigation is to explore the potential molecular regulators of backfat tissue development in Ningxiang pigs. Histological analysis of backfat tissue showed that adipocyte area increased and adipocyte number decreased with the development of backfat tissue in different stages (60d, 120d, 180d, 240d, 300d, and 360d). Meanwhile, a total of 1024 differentially expressed genes were identified in five comparison groups (120d vs 60d, 180d vs 120d, 240d vs 180d, 300d vs 240d, and 360d vs 300d). And then strongly co-expressed genes in modules were clustered by Weighted gene co-expression network analysis (WGCNA). Among these modules, turquoise, red, pink, paleturquoise, darkorange, and darkgreen module had close correlation with 60d, 120d, 180d, 240d, 300d, and 360d developmental stage, respectively, while tan, black and turquoise module had intimate relation with backfat thickness, adipocyte area and adipocyte number, respectively. Furthermore, GO and KEGG enrichment were analyzed in each module, the gene co-expression network was constructed, and the hub genes were described. According to the co-expression network, 13 genes (ACSL1, ACOX1, FN1, DCN, CHST13, COL1A1, COL1A2, COL6A3, COL5A1, COL14A1, OAZ3, DNM1, and SELP) were recognized as hub genes. Further analysis revealed that ACSL1 and ACOX1 might perform considerable function in early developmental stage of backfat tissue before 60d. FN1, DCN, COL1A1, COL1A2, COL5A1, COL6A3, and COL14A1 have unignorable position around 120d developmental stage. Besides, the functional relevance associated with SELP and backfat thickness, DNM1 and adipocyte area needs to be elucidated. In addition, QCR analysis validated the strong consistency of genes expressions with RNA-seq data, manifesting the reliability and accuracy of our study. The present research preliminarily depicted the gene co-expression network for each period of backfat developmental stage in Ningxiang pigs, which not only help to understand the integrated mechanism underlying backfat tissue development and lipid metabolism, but also promotes the progress of genetic improvement in pigs.
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Project description:Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs. examining the complexity of pig transcriptome in three organs from a female full-sib pair
2010-12-20 | E-GEOD-25923 | biostudies-arrayexpress
Project description:An M307 G/A point mutation of FUT1 gene has been considered as a usful marker to select the piglets that are sensitive(GG/AG genotype) or resistant(AA) to Escherichia coli F18 in foreign pig breeds.However,it is not suitable to Chinese native breeds. Duodenal tissues were collected from 8 full-sib pairs of Sutai pigs (a new hybrid between the Duroc and Taihu breeds) at the age of 28-day differing in adhesion phenotype to find the differential genes that can be used as the candidate genes fit for Chinese native breeds.
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Project description:A comprehensive profile of microRNAs in the backfat tissue from castrated and intact full-sib pair male pigs
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Project description:The identification of the molecular mechanisms regulating pathways associated to the potential of fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. MicroRNAs (miRNAs) interactions with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is well far from saturation and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations are still fragmentary. We characterized by RNA-seq the small RNAs (sRNAs) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs, 14 up-regulated (including ssc-miR-132 ,ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p, and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p, and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network resulted to be expressed from backfat related pig QTLs. These results are informative on the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs, and facilitate the perspective implementation of innovative strategies of pig genetic improvement based on genomic markers.
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