Sus scrofa domesticus breed:Duroc*Landrace*Yorkshire crossbred
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1266884 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR33752100_1.fastq.gz | Fastqsanger.gz | |||
| SRR33752100_2.fastq.gz | Fastqsanger.gz | |||
| SRR33752097_1.fastq.gz | Fastqsanger.gz | |||
| SRR33752097_2.fastq.gz | Fastqsanger.gz | |||
| SRR33752098_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Sus scrofa domesticus breed:Duroc*Landrace*Yorkshire crossbred Raw sequence reads
| PRJNA1267022 | ENA
Project description:Sus scrofa strain:Duroc, Landrace, Yorkshire Metagenome
| PRJNA263439 | ENA
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison
2013-01-01 | GSE12927 | GEO
Project description:The experiment aimed at studying gene expression differences in longissimus dorsi muscle from pigs from two groups: High versus low intramuscular fat (IMF). The animals were selected from a crossbred population of Landrace x Yorkshire/Landrace x Duroc animals, where we have previously found a highly significant QTL for IMF (Grindflek et al. 2001: "Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross", Mammalian Genome 12(4): 299-304), and by microarray analysis we hoped to identify candidate genes for the QTL and/or pathways that are affected by the genes responsible for the QTL. Keywords: phenotype comparison Direct dye-swap design, with 14 animals in each group (high IMF and low IMF) on 14 separate arrays
2013-01-01 | E-GEOD-12927 | 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.
2010-04-22 | GSE21412 | GEO
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:Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions amongst causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc - 80 SNPs, Landrace - 146 SNPs) and high feed efficient group (Duroc - 198 SNPs, Landrace - 232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.
2020-03-23 | GSE144064 | GEO
Project description:The goal was to obtain the differential transcriptome in the deep cones between shallow and deep wounds and between the Yorkshire and Duroc breeds over time.
2011-12-31 | GSE26095 | GEO
Project description:Crossbreeding has been an effective method to improve crossbred performance in pig industry. To have a global view of a classic three-way crossbreeding system of Duroc x (Landrace x Yorkshire) (DLY), we identified SNPs for each pig breed and crossbred individual originated from a DLY pig family to estimate the influence of purebreds on crossbred offspring using whole-genome sequencing. To confirm the accuracy of the SNPs identified by whole-genome sequencing, therefore, we performed the porcine 60K BeadChip genotyping array (Illumina) for each sequenced pig individual.
2018-12-05 | GSE123327 | GEO
Project description:BackgroundThe health and welfare of pigs used in biomedical research is essential to research quality and compliance with the 3Rs (replacement, reduction, and refinement). Hematological variables are objective markers to quantitatively determine health issues and evaluate physiological differences before and after experimental procedures. There are no recent validated hematologic reference intervals (RIs) published for Danish crossbred Landrace Yorkshire Duroc (LYD) pigs to aid researchers and veterinarians in their decision-making. The objective of this study was to establish hematologic RIs for LYD pigs used for biomedical research. Blood samples were collected from healthy female LYD pigs (35-65 kg) and analyzed using the in-house ProCyte Dx Hematology Analyzer. Means with 90% confidence intervals for lower and upper limits were calculated according to guidelines by the American Society of Veterinary Clinical Pathology.ResultsInspection of 141 pigs led to 133 blood samples available for analyses after exclusions due to clinical signs of disease, inadequate tube filling or presence of macroscopic clots. Thirty-two samples reported platelet abnormalities and upon further investigation these samples were excluded when calculating RIs for platelets and platelet indices. Other measurements were not affected. The RI for red blood cells, hemoglobin, hematocrit and white blood cells were 5.10-7.00 × 106/µL, 9.36-12.29 g/dL, 30.46-40.47%, and 11.73-25.00 × 103/µL, respectively.ConclusionsOur study provides RIs for hematological variables in LYD pigs, revealing significant differences from published RIs of other breeds. These findings highlight the influence of factors like age, breed and health status on measurements, emphasizing the importance of using breed-specific RIs. This research supports the 3Rs, guiding better animal care and enhancing overall research quality.
| S-EPMC11853315 | biostudies-literature