Raw datas of the transcriptome in testes of Hezuo pigs and Landrace pigs at two different ages
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PROVIDER: PRJNA720752 | ENA |
REPOSITORIES: ENA
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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.
2022-11-18 | GSE192462 | 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.
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: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.
2018-09-06 | GSE97711 | GEO
Project description:Jinhua and Landrace pigs fecal samples Raw sequence reads
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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.
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Project description:Individual pigs [(Large White × Landrace) x Hylean Maxgro] divergent in residual feed intake were sampled for hepatic transcriptome profiling at day 140.
2017-09-18 | GSE95223 | 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
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