Ontology highlight
ABSTRACT:
PROVIDER: PRJNA642992 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12115300_1.fastq.gz | Fastqsanger.gz | |||
| SRR12115300_2.fastq.gz | Fastqsanger.gz | |||
| SRR12115301_1.fastq.gz | Fastqsanger.gz | |||
| SRR12115301_2.fastq.gz | Fastqsanger.gz | |||
| SRR12115302_1.fastq.gz | Fastqsanger.gz |
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Project description:It is well recognized that the quality of boar sperm is severely influenced by higher temperature in summer, thereby reducing the productivity of semen. cDNA microarray is a high throughput technique frequently used in genome-wide screening for specific genes related a known phenotype or disease. A testis cDNA microarray was established for the investigation of the differentially expressed genes, responding to a short heat stimulus, in enriched germ cells isolated from immature pigs where the first wave of spermatogenesis was just initiated. Two cDNA libraries were constructed from the testis tissues of two mature Duroc boars with or without whole body heat shock treatment. About 27,000 single colonies were randomly picked for one-direction sequencing. After the trimming of vector derived sequences, 22,969 high quality ESTs were obtained, which assembled into 3,207 contigs and 9,541 singletons, representing 12,748 tentative unique transcripts. A porcine testis cDNA microarray was established with single spot of the amplified cDNA plus 20 spots of positive and negative controls. We conducted a cell model experiment to screen the differentially expressed genes responding to a short heat shock. Small population of genes was up- or down-regulated with at least 1.5-fold of differences, including transcriptional factors, kinases, phosphatases, binding proteins and some transcripts with unknown functions. Further examination on these genes might contribute to a clear picture on the heat-tolerance of spermatogenesis in boar and benefit the breeding of boars with elite semen quality in all reasons. Keywords: stress response
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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.
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Project description:In this study, differentially expressed (DE)piRNAs of fresh and frozen-thawed sperm with different freeze tolerance compacity from giant panda and boar were evaluated. The results showed 1160 (22 down-regulated and 1138 up-regulated) and 384 (110 up-regulated and 274 down-regulated) differentially expressed (DE) piRNAs were identified in giant panda and boar sperm, respectively. Gene ontology (GO) enrichment analysis revealed that the target DE mRNAs of DE piRNAs were mainly enriched in biological regulation, cellular process and metabolic process in giant panda and boar sperm. Moreover, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the target DE mRNAs of DE piRNAs were only distributed on DNA replication and cAMP signaling pathway in giant panda, but cAMP, cGMP and MAPK signaling pathway in boar sperm which were considered as part of olfactory transduction pathway.Conclusion:Olfactory transduction related pathways maybe contributed to different freeze tolerance compacity between giant panda and boar sperm, which will benefit to further understand the molecular mechanism of sperm cryoinjury and freezability.
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Project description:Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
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