Gene expression during testis development in Duroc boars
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE39322 | GEO | 2013/09/01
SECONDARY ACCESSION(S): PRJNA170758
REPOSITORIES: GEO
Similar Datasets
Project description:The aim of the study was to combine understanding between a timeline for molecular and macroscopic functions in the testis of the Duroc boar. To achieve this, cluster and pathway analysis was performed based on microarray transcripts from four pubertal timepoints with known steroidogenic status and known morphological maturation status. Gene expression study of testes biopsies from Duroc boars, taken at age 12, 16, 20 and 27 weeks of age, using in-house printed porcine two-colour cDNA microarrays.
2013-09-01 | E-GEOD-39322 | biostudies-arrayexpress
Project description:Chromatin packaging in sperm protects it against DNA fragmentation, and the importance of proper chromatin packaging for boar fertility outcome has become increasingly evident. Little is known however about the molecular mechanisms underlying differences in sperm DNA fragmentation and an understanding of the genes controlling this sperm parameter could help in selecting the best boars for AI use. The aim of this study was to identify differentially expressed genes in testis of Norsvin Landrace and Duroc boars with good and bad sperm DNA fragmentation using transcriptome sequencing and to use the data for polymorphism search. RNA sequence reads were obtained using Illumina technology and mapped by TopHat using the Ensembl pig database. Differentially expressed genes and pathways were analyzed using the R Bioconductor packages edgeR and goseq respectively. Using a false discovery rate of 0.05, 309 and 375 genes were found displaying significant differences in expression level between the good and bad condition in Landrace and Duroc respectively. Of the differentially expressed genes, 72 were found in common for the two breeds. Gene ontology analysis revealed that terms common for the two breeds included extracellular matrix, extracellular region and calcium ion binding. Additionally, different metabolic processes were enriched in Landrace and Duroc, whereas immune response ontologies were found to be important in Landrace. SNP detection in Landrace/Duroc identified 53182/53931 variants in 10924/10748 transcripts and of these, 1573/1827 SNPs occurred in 189/241 unique genes that were also differentially expressed. Possible high impact variants were detected using SnpEff. Transcriptome sequencing identified differentially expressed genes and nucleotide variants related to differences in sperm DNA fragmentation, and functional annotation of the genes pointed towards important biochemical pathways. This study provides insights into the genetic network underlying this trait and is a first step towards using sperm DNA fragmentation for predicting boar fertility.
2017-09-01 | GSE74934 | GEO
Project description:Sus scrofa strain:Duroc and wild boar Transcriptome or Gene expression
| PRJNA173041 | ENA
Project description:Recents studies in mammalian genomes have uncovered the extent of copy number variation (CNV) that contributes to phenotypic diversity, including health and disease status. Here we report the first glimpse of CNVs in the pig genome covering part of the chromosomes 4, 7, 14 and 17 already sequenced and assembled. We used a custom tiling oligonucleotide array with a median probe spacing of 409 bp to screen 12 unrelated Duroc boar founders of a vast-family material. After a strict CNV calling pipeline it was identified 40 copy number variable regions covering all the four chromosomes, with some overlapping segmental duplications and pig unigenes. This CNV snapshot analysis lays the groundwork for a better understanding of porcine phenotypes and genotypes for the identification of important economic traits. Keywords: comparative genome hybridization, CNV, Sus Scrofa, Nimblegen tiling array A custom 385k tiling-path array CGH was designed (Nimblegen Systems) to cover the preliminary Sus Scrofa assembly for chromosomes 4, 7, 14 and 17, from the August 2007 release (http://www.sanger.ac.uk/Projects/S_scrofa/), which was the newest version at the time of the experiment. From a pig family-material comprising 14 boar founders, 700 sows and about 12.000 offspring, 12 Duroc boar founders (A, B, C, D, E, G, H, J, K, L, M and N) were selected to function as test animals. An unrelated boar of the Hampshire breed was selected as the common reference. Each of the 12 boars were hybridized twice (technical replicates, 24 arrays) against the common reference.
2010-06-21 | E-GEOD-10753 | biostudies-arrayexpress
Project description: Not available
| S-EPMC5011730 | biostudies-literature
Project description: Not available
| S-EPMC7578402 | biostudies-literature
Project description:Boar taint is a major obstacle when using uncastrated male pigs for swine production. One of the main compounds causing this taint is androstenone, a pheromone produced in porcine testis. Here we use microarrays to study the expression of thousands of genes simultaneously in testis of high and low androstenone boars. The study allows identification of genes and pathways associated with elevated androstenone levels. Testicular tissue was collected from 60 boars, 30 with extreme high and 30 with extreme low levels of androstenone, from each of the two breeds Duroc and Norwegian Landrace. The samples were hybridised to porcine arrays containing 26.877 cDNA clones, detecting 563 and 160 genes that were differentially expressed (p < 0.01) in Duroc and Norwegian Landrace, respectively. Of these significantly up- and down-regulated clones, 72 were found to be common for the two breeds, suggesting both general and breed specific mechanisms in regulation of, or response to androstenone levels in boars. Ten of the most significant genes were chosen for verification of expression patterns by quantitative real competitive PCR and real-time PCR. As expected, our results point towards steroid hormone metabolism and biosynthesis as important biological processes for the androstenone levels, but other potential pathways were identified as well. Among these were oxidoreductase activity, ferric iron binding, iron ion binding and electron transport activities. Genes belonging to the cytochrome P450 and hydroxysteroid dehydrogenase families were highly up-regulated, in addition to several genes encoding different families of conjugation enzymes. Furthermore, a number of genes encoding transcription factors were found both up- and down-regulated. The high number of clones belonging to ferric iron and iron ion binding suggests an importance of these genes, and the association between these pathways and androstenone levels is not previously described. This study contributes to the understanding of the complex genetic system controlling and responding to androstenone levels in pig testis. The identification of new pathways and genes involved in the biosynthesis and metabolism of androstenone is an important first step towards finding molecular markers to reduce boar taint. Keywords: high vs low Testicle samples from animals with extreme androstenone values, 30 high and 30 low from each of the two breeds Norwegian Landrace and Duroc, were used for the experiment. Each microarray was hybridised with one high and one low androstenone sample from the same breed, giving a total of 30 arrays for each breed.
2007-11-26 | E-GEOD-7409 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4749976 | biostudies-literature
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