Genetic determinism of sheep prolificacy
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PROVIDER: PRJEB35553 | ENA |
REPOSITORIES: ENA
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Project description:In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
2018-06-26 | GSE105092 | GEO
Project description:Transcriptomics and functional bioinformatics were used to investigate the potential interactions of undernutrition and the presence of the conceptus at the time of maternal recognition of pregnancy on uterine indicators of metabolism and reproduction. Adult Rasa Aragonesa ewes were allocated to one of two planes of nutrition during 28 days: maintenance energy intake (control; 5 cyclic, 6 pregnant ewes) providing 7.8 MJ of metabolisable energy per ewe and 0.5 maintenance intake (undernourished; 6 cyclic, 7 pregnant ewes) providing 3.9 MJ of metabolisable energy per ewe. RNA from uterine tissue was harvested at slaughter on day 14 of estrus or pregnancy, and hybridized to the Agilent 15K Sheep Microarray chip. Functional bioinformatics analyses were performed using the Dynamic Impact Approach (DIA) and Ingenuity Pathway Analysis. Among metabolic pathways, citrate cycle, oxidative phosphorylation, pentose and glucuronate interconversions and biosynthesis of unsaturated fatty acids were upregulated in control pregnant compared with control cyclic ewes. However, these pathways were not altered in undernourished ewes. The presence of an embryo in undernourished ewes upregulated fatty acid and glycogenic amino acid metabolism. RIG-I and Toll like receptors and chemokine signaling pathways were upregulated by the presence of the embryo in both control and undernourished ewes, but in the latter group the impact was lower. Undernutrition alone upregulated carbohydrate metabolism, but different pathways were altered in cyclic versus pregnant ewes. Citrate cycle, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions were upregulated in undernourished cyclic compared with control cyclic ewes. Glycolysis/gluconeogenesis, pyruvate and propanoate metabolism, beta-alanine and phenylalanine metabolism were upregulated in undernourished pregnant compared with control pregnant ewes, whereas biosynthesis of unsaturated fatty acids and replication and repair were downregulated. Undernutrition alone led to an overall weak activation of immune system pathways both in cyclic and pregnant ewes. However, undernourished cyclic compared with control cyclic ewes had a high activation of NOD-like and RIG-1 like receptor signaling pathways, whereas undernourished pregnant compared with control pregnant ewes only had a weak upregulation of T cell receptor signaling pathways. Overall, data revealed that metabolic and immune adaptations of the uterus to nutrient restriction are dependent on the presence of the conceptus.
2018-03-01 | GSE108176 | GEO
Project description:An F2 cross between two highly divergent porcine breeds for most productive traits, including prolificacy, was generated. F2 sows were classified as of high or low prolificacy based on phenotypic records of four consecutive parities (total number of piglets born and number of piglets born alive were recorded). At the fifth gestation, sows were slaughtered at day 30-32 of gestation, and the number of corpora lutea and number of embryos were registered. Samples from different tissues were snap frozen in liquid nitrogen for further studies. Uterus samples were used for total RNA extraction and hybridized on the affymetrix porcine genechip for comparison between high and low prolificacy F2 sows.
2014-12-01 | GSE49398 | GEO
Project description:The knowledge of the genetic architecture behind feed efficiency would allow to breed more efficient animals maximizing farm profitability and reducing the environmental impact of animal production. This study analyzes high throughput gene expression data from milk samples to determine key genes and biological mechanisms associated to feed efficiency in dairy sheep.A detailed description of the sheep management practices and calculations for the feed efficiency index (FEI) are detailed in 10.3168/jds.2020-19061. For these analyses, we selected animals with divergent FEI values from a group of 40 lactating Assaf ewes. RNA-Seq was performed on milk somatic cell samples from 8 high feed efficiency sheep (H-FE), FEI = −0.29 (SD = 0.23), RFI = −0.16 (SD = 0.25), and 8 low feed efficiency sheep (L-FE), FEI = 0.81 (SD = 0.24), RFI = 0.19 (SD = 0.24)).
2023-02-14 | E-MTAB-12355 | biostudies-arrayexpress
Project description:Prolificacy related traits are of great economical interest in the pig industry. microRNAs (miRNAs) are post-transcriptional regulators of gene expression important for reproductive processes. In pigs, the roles of ovarian miRNAs during gestation remain unknown although the ovaries are essential during gestation. It has been hypothesised that ovarian miRNAs could participate during the porcine gestation and, moreover, they could influence the prolificacy levels of sows. The miRNA expression profile was compared in the ovaries of pregnant Iberian x Meishan F2 sows displaying extreme phenotypes regarding prolificacy levels defined as the number of embryos (NE) attached to the uterus at 30-32 days of gestation. miR-146a-5p and miR-142-3p were differentially expressed between high (NEM-bM-^IM-%13) and low (NEM-bM-^IM-$11) prolificacy sows. In silico functional analyses of the predicted mRNA targets for these miRNAs revealed that miR-146a-5p targets were mainly involved in the immune system response important for the establishment of the maternal-foetal tolerance, implantation and maintenance of pregnancy. On the other hand, miR-142-3p targets participated in different biological processes that would contribute to the homeostasis maintenance to ensure a correct functional development of the ovaries. miRNAs associated with prolificacy levels could regulate negatively, by a novel post-transcriptional mechanism, their predicted mRNA targets, PPM1K, TLR1 and CPEB2 which have been reported as differentially expressed in the ovaries of pregnant sows regarding the prolificacy levels. Furthermore, among predicted mRNA targets for miRNAs associated with prolificacy, four genes, differentially expressed in the ovaries of pregnant sows regarding prolificacy levels, (LRRK1, BAT1, CPEB2, CCL8) are proposed to be good candidate genes for litter size due to their location within confidence intervals for prolificacy QTL described previously. Overall, it is suggested that the up-regulation of miR-146a-5p and miR-142-3p in the ovaries of pregnant sows could help in the establishment of a uterine environment, which would favor the embryonic development. Total RNA was isolated from uterus of Iberian x Meishan F2 pregnant sows divided into two groups: High prolificacy sows (n=3) and Low prolificacy sows (n=3). RNA was labeled with the Cy3-like Hy3M-bM-^DM-" dye, mixed with a pool of RNA from the six samples labeled with the Cy5-like Hy5M-bM-^DM-" dye, and hybridized to two-color miRCURYM-bM-^DM-" arrays from ExiqonM-BM-..
2012-12-01 | E-GEOD-41068 | biostudies-arrayexpress
Project description:In the current study, five late gestation multiparous ewes were restricted to a 30% feeding level to create a model of malnutrition, while five other ewes were fed normally as controls. All ewes were sacrificed and cecal samples were collected for transcriptome sequencing to study metabolic changes.
2023-03-22 | GSE221270 | GEO
Project description:In the present study, we studied the effect of dietray zinc (Zn) supplementation on the transcriptome profile of lactating ewes. The main objective was to evaluate the effect of Zn-supplementation on the overall transcriptome and the altered pathways and biological processes in lactating ewes. A previously custom-designed oligo microarray platform (GPL20576) was used to profile the transcriptome of 15 ewes at two time points [T0 (before supplementation) and T40 (after 40-days supplementation period; n = 30). The Isolated and purified total RNAs were individually hybridized to the custom (4x44k) DNA microarray. The comparison of control and treated animal transcriptomes revealed a large set of differentially expressed genes. Functional analysis showed several pathways and biological processes that have been altered following Zn-supplementation to the diet.
2017-10-22 | GSE74779 | GEO
Project description:Prolificacy related traits are of great economical interest in the pig industry. microRNAs (miRNAs) are post-transcriptional regulators of gene expression important for reproductive processes. In pigs, the roles of ovarian miRNAs during gestation remain unknown although the ovaries are essential during gestation. It has been hypothesised that ovarian miRNAs could participate during the porcine gestation and, moreover, they could influence the prolificacy levels of sows. The miRNA expression profile was compared in the ovaries of pregnant Iberian x Meishan F2 sows displaying extreme phenotypes regarding prolificacy levels defined as the number of embryos (NE) attached to the uterus at 30-32 days of gestation. miR-146a-5p and miR-142-3p were differentially expressed between high (NE≥13) and low (NE≤11) prolificacy sows. In silico functional analyses of the predicted mRNA targets for these miRNAs revealed that miR-146a-5p targets were mainly involved in the immune system response important for the establishment of the maternal-foetal tolerance, implantation and maintenance of pregnancy. On the other hand, miR-142-3p targets participated in different biological processes that would contribute to the homeostasis maintenance to ensure a correct functional development of the ovaries. miRNAs associated with prolificacy levels could regulate negatively, by a novel post-transcriptional mechanism, their predicted mRNA targets, PPM1K, TLR1 and CPEB2 which have been reported as differentially expressed in the ovaries of pregnant sows regarding the prolificacy levels. Furthermore, among predicted mRNA targets for miRNAs associated with prolificacy, four genes, differentially expressed in the ovaries of pregnant sows regarding prolificacy levels, (LRRK1, BAT1, CPEB2, CCL8) are proposed to be good candidate genes for litter size due to their location within confidence intervals for prolificacy QTL described previously. Overall, it is suggested that the up-regulation of miR-146a-5p and miR-142-3p in the ovaries of pregnant sows could help in the establishment of a uterine environment, which would favor the embryonic development.
2012-12-01 | GSE41068 | GEO
Project description:This research investigates the influence of nutritional protein restriction (NPR) during prepuberty on FE and the milk transcriptome of dairy Assaf ewes during their first lactation. Additionally, it evaluates the differences in the milk transcriptome between lactating ewes with divergent FE using the feed conversion ratio (FCR) and residual feed intake (RFI) indices and assesses milk gene expression as a predictor of FE.
2024-03-01 | E-MTAB-13619 | biostudies-arrayexpress
Project description:Cortisol administration during late gestation in ewes, modeling maternal stress, resulted in transcriptomic changes suggesting altered maturation and metabolic changes to the offspring heart. Pregnant ewes were treated with 0.5 mg/kg/day cortisol from 115 days gestation to term lambs were studied over the next 2 weeks. Left ventricular free wall (LV) and intraventricular septum (IVS) were collected at 2 weeks of age (lambs of control, untreated ewes: n=8, lambs of ewes treated with 0.5 mg/kg/day: n=8). In this model we found that neonatal plasma glucose was increased and plasma insulin was decreased compared to those in the control group. LV free wall thickness was increased in the 2 week old lamb. In this study, we have used transcriptomic modeling to better understand the programming effect of this maternal cortisolemia in the 2 week old hearts. This is a time when both terminal differentiation and a shift in the metabolism of the heart from carbohydrates to lipid oxidation are thought to be complete. The transcriptomics indicates downregulation of RNA related pathways, but upregulation of ubiquitin-mediated proteolysis and protein targeting to the mitochondria in in the intraventricular septum (IVS) and left ventricle (LV) in lambs of cortisol-infused ewes compared to untreated control ewes. In IVS pathways the AMPK pathway and adipocytokine signaling pathways were also modeled as downregulated in lambs of cortisl-treated ewes Genes for peroxisomal activity are modeled as decreased in LV and IVS; our previous metabolomic study of the newborn hearts from the 1 mg/kg/d study indicated changes in the plasmogens and phospholipids that are peroxisomal products. Our results suggest that pathways for lipid metabolismas well as cell proliferation and cardiac remodeling have altered activity postnatally after the in utero cortisol exposure. Together, this model is consistent with the observed increase in cardiac wall thickness at necropys and altered glucose metabolism observed in vivo, and predicts that in utero exposure to excess maternal cortisol causes postnatal cardiac hypertrophy and altered responses to oxidative stress.
2019-07-10 | GSE131537 | GEO