Analysis of Whole Genome Sequence and Genome-wide SNPs in Highly Inbred Pigs [Array]
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE157934 | GEO | 2020/12/31
REPOSITORIES: GEO
Similar Datasets
Project description:Analysis of Whole Genome Sequence and Genome-wide SNPs in Highly Inbred Pigs [Array]
| PRJNA663378 | ENA
Project description:The research on alternative and sustainable feed ingredients is a challenge to reduce the feed-food competition between humans and monogastrics, in particular pigs. Former food products (FFPs) drop out from the industrial production of food such as pasta, bread, snacks and chips. They have a high nutritional and energetic value and represent an alternative and sustainable feed ingredient. The aim of this study was to apply label-free quantitative peptidomics to assess the impact of the inclusion of FFPs on serum peptidome.
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Project description:Epigenomic mapping of DNA methylation polymorphisms segregating within an epigenetic Recombinant Inbred Line population resultant from crossing the wild-type Col-0 and DNA maintenance methyltransferase mutant, met1-3, parental lines. Each line within the epiRIL population was self-fertilized for 7 generations, 10 individual F7 plants were then bulk harvested to create the F8 generation. Here, data files for three DNA methylation profiled epiRIL lines (epi01, epi12, epi28) are deposited. The DNA methylation polymorphisms were determined using the BiMP method with the Affymetrix Arabidopsis Tiling 1.0R array. The main objective for these samples was to create an epigenomic map to analyze the inheritance of DNA methylation polymorphisms within these three epiRIL entries. Keywords: Bisulfite Methylation Profiling (BiMP) by genome tiling array
2009-04-23 | GSE13438 | GEO
Project description:Survey of gene expression in 7 brain regions at 6-8wks of age in 20 inbred strains of laboratory mice. Autism is a highly heritable neurodevelopmental disorder with no consistent neuropathological hallmarks, diagnosed through behavioral inventory rather than a biomarker. The genetic etiology of autism is complex and likely has a significant interaction with the environment. To investigate the molecular and genetic nature of autism, we modeled the core symptom of social deficits in inbred strains of mice. Using gene expression profiles and behavioral phenotyping relevant to social deficits, we have identified basic cellular functions that may be dysregulated in the brain in autism. Correlations between these two complex datasets indicate cell morphology, proliferation, and migration may be perturbed in disorders of altered social behavior. Furthermore, these data in the mouse show significant overlap with published expression profiling in lymphoblastoid lines from autistic individuals. Keywords: Comparison between inbred strains and brain regions.
2009-02-05 | GSE10415 | GEO
Project description:Inbred mini-pigs are ideal organ donors for future human xenotransplantations because of their clear genetic background, high homozygosity, and high inbreeding endurance. In this study, we chose fibroblast cells from a highly inbred pig line called Banna mini-pig inbred line (BMI) as donor nuclei for nuclear transfer, combining with transcription activator-like effector nucleases (TALENs) and successfully generated α-1,3-galactosyltransferase (GGTA1) gene biallelic knockout (KO) pigs. To validate the efficiency of TALEN vectors, in vitro-transcribed TALEN mRNAs were microinjected into one-cell stage parthenogenetically activated porcine embryos. The efficiency of indel mutations at the GGTA1-targeting loci was as high as 73.1% (19/26) among the parthenogenetic blastocysts. TALENs were co-transfected into porcine fetal fibroblasts of BMI with a plasmid containing neomycin gene. The targeting efficiency reached 89.5% (187/209) among the survived cell clones after a 10 d selection. More remarkably 27.8% (58/209) of colonies were biallelic KO. Five fibroblast cell lines with biallelic KO were chosen as nuclear donors for somatic cell nuclear transfer (SCNT). Three miniature piglets with biallelic mutations of the GGTA1 gene were achieved. Gal epitopes on the surface of cells from all the three biallelic KO piglets were completely absent. The fibroblasts from the GGTA1 null piglets were more resistant to lysis by pooled complement-preserved normal human serum than those from wild-type pigs. These results indicate that a combination of TALENs technology with SCNT can generate biallelic KO pigs directly with high efficiency. The GGTA1 null piglets with inbred features created in this study can provide a new organ source for xenotransplantation research.
| S-EPMC3866186 | biostudies-literature
Project description:Iberian ham production includes both purebred (IB) and Duroc-crossbred (IBxDU) Iberian pigs, which show important differences in meat quality and production traits, such as muscle growth and fatness. This experiment was conducted to investigate gene expression differences, transcriptional regulation and genetic polymorphisms that could be associated with the observed phenotypic differences between IB and IBxDU pigs. Nine IB and 10 IBxDU pigs were slaughtered at birth. Morphometric measures and blood samples were obtained and samples from Biceps femoris muscle were employed for compositional and transcriptome analysis by RNA-Seq technology. Phenotypic differences were evident at this early age, including greater body size and weight in IBxDU and greater Biceps femoris intramuscular fat and plasma cholesterol content in IB newborns. We detected 150 differentially expressed genes between IB and IBxDU neonates (p < 0.01 and Fold-Change > 1. 5). Several were related to adipose and muscle tissues development (DLK1, FGF21 or UBC). The functional interpretation of the transcriptomic differences revealed enrichment of functions and pathways related to lipid metabolism in IB and to cellular and muscle growth in IBxDU. Protein catabolism, cholesterol biosynthesis and immune system were functions enriched in both genotypes. We identified transcription factors potentially affecting the observed gene expression differences. Some of them have known functions on adipogenesis (CEBPA, EGRs), lipid metabolism (PPARGC1B) and myogenesis (FOXOs, MEF2D, MYOD1), which suggest a key role in the meat quality differences existing between IB and IBxDU hams. We also identified several polymorphisms showing differential segregation between IB and IBxDU pigs. Among them, non-synonymous variants were detected in several transcription factors as PPARGC1B gene, which could be associated to altered gene function. Taken together, these results provide information about candidate genes, metabolic pathways and genetic polymorphisms potentially involved in phenotypic differences between IB and IBxDU associated to meat quality and production traits.
2016-09-25 | GSE73566 | GEO
Project description:In contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data.A total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism.This work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families.
| S-EPMC3601988 | biostudies-literature
Project description:The Piétrain pig originates from the Belgian village Piétrain some time between 1920 and 1950. Owing to its superior conformation, the Piétrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed's genetic diversity has been questioned. Therefore, this study examines Piétrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and FST analysis showed that US Piétrains differ most from European Piétrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Piétrain populations, but numerous population-specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34-126 Mb) appears nearly fixed in all Piétrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Piétrain populations. This study shows that Piétrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Piétrain populations by introgression from other Piétrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Piétrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Piétrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.
| S-EPMC7003864 | biostudies-literature
Project description:Background: Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach. Results: We observed a tendency toward a global loss of DNA methylation in the gene-body region of the skeletal muscle of the middle-aged pigs compared with the young group. We determined the genome-wide gene expression pattern in the longissimus dorsi muscle using microarray analysis and performed a correlation analysis using DMR (differentially methylated region)-mRNA pairs, and we found a significant negative correlation between the changes in methylation levels within gene bodies and gene expression. Furthermore, we identified numerous genes that show age-related methylation changes that are potentially involved in the aging process. The methylation status of these genes was confirmed using bisulfite sequencing PCR. The genes that exhibited a hypomethylated gene body in middle-aged pigs were over-represented in various proteolysis and protein catabolic processes, suggesting an important role for these genes in age-related muscle atrophy. In addition, genes associated with tumorigenesis exhibited aged-related differences in methylation and expression levels, suggesting an increased risk of disease associated with increased age. Conclusions: This study provides a comprehensive analysis of genome-wide DNA methylation patterns in aging pig skeletal muscle. Our findings will serve as a valuable resource in aging studies, promoting the pig as a model organism for human aging research and accelerating the development of comparative animal models in aging research. We collected the longissimus dorsi muscles tissue from Jinhua pigs which aged 0.5 year and seven years and study the genome-wide DNA methylation difference between the two age periods.
2014-08-02 | E-GEOD-50716 | biostudies-arrayexpress
Project description:Background Age-related physiological, biochemical and functional changes in mammalian skeletal muscle have been shown to begin at the mid-point of the lifespan. However, the underlying changes in DNA methylation that occur during this turning point of the muscle aging process have not been clarified. To explore age-related genomic methylation changes in skeletal muscle, we employed young (0.5 years old) and middle-aged (7 years old) pigs as models to survey genome-wide DNA methylation in the longissimus dorsi muscle using a methylated DNA immunoprecipitation sequencing approach. Results We observed a tendency toward a global loss of DNA methylation in the gene-body region of the skeletal muscle of the middle-aged pigs compared with the young group. We determined the genome-wide gene expression pattern in the longissimus dorsi muscle using microarray analysis and performed a correlation analysis using DMR (differentially methylated region)-mRNA pairs, and we found a significant negative correlation between the changes in methylation levels within gene bodies and gene expression. Furthermore, we identified numerous genes that show age-related methylation changes that are potentially involved in the aging process. The methylation status of these genes was confirmed using bisulfite sequencing PCR. The genes that exhibited a hypomethylated gene body in middle-aged pigs were over-represented in various proteolysis and protein catabolic processes, suggesting an important role for these genes in age-related muscle atrophy. In addition, genes associated with tumorigenesis exhibited aged-related differences in methylation and expression levels, suggesting an increased risk of disease associated with increased age. Conclusions This study provides a comprehensive analysis of genome-wide DNA methylation patterns in aging pig skeletal muscle. Our findings will serve as a valuable resource in aging studies, promoting the pig as a model organism for human aging research and accelerating the development of comparative animal models in aging research.
2014-08-02 | GSE49791 | GEO