Cote I.,Laval University |
Vigneault C.,LAlliance Boviteq Inc. |
Laflamme I.,Laval University |
Laquerre J.,Laval University |
And 6 more authors.
Reproduction | Year: 2011
In vitro production (IVP) of cattle embryos over the past two decades has revealed several negative impacts that have been attributed to the artificial microenvironment. Studies on embryos produced in vitro clearly point to aberrant gene expression levels. So far, the causal association between phenotype and measured gene expression has not led to substantial improvement of IVP systems. The aim of this study was to generate a unique dataset composed of microarray-derived relative transcript abundance values for blastocysts produced in ten in vitro systems differing primarily in culture medium formulation. Between-group comparisons determine the level of overall similarity among systems relative to in vivo reference embryos. The use of the dataset to contrast all in vitro treatments with the in vivo blastocysts pointed to a single common gene network. The 'boutique' array contained a panel of novel uncharacterized transcripts that were variably expressed depending on the medium in which the blastocysts were produced. These novel transcripts were differentially expressed in blastocysts even as carryover from conditions encountered 7 days earlier during oocyte maturation. All of the selected novel candidates thus expressed were from intergenic regions. The function of this long non-coding RNA remains unknown but clearly points to an additional level of complexity in early embryo development. © 2011 Society for Reproduction and Fertility.
Chen L.,University of Alberta |
Li C.,University of Alberta |
Li C.,Agriculture and Agri Food Canada |
Sargolzaei M.,University of Guelph |
Schenkel F.,LAlliance Boviteq Inc.
PLoS ONE | Year: 2014
The aim of this study was to evaluate the impact of genotype imputation on the performance of the GBLUP and Bayesian methods for genomic prediction. A total of 10,309 Holstein bulls were genotyped on the BovineSNP50 BeadChip (50 k). Five low density single nucleotide polymorphism (SNP) panels, containing 6,177, 2,480, 1,536, 768 and 384 SNPs, were simulated from the 50 k panel. A fraction of 0%, 33% and 66% of the animals were randomly selected from the training sets to have low density genotypes which were then imputed into 50 k genotypes. A GBLUP and a Bayesian method were used to predict direct genomic values (DGV) for validation animals using imputed or their actual 50 k genotypes. Traits studied included milk yield, fat percentage, protein percentage and somatic cell score (SCS). Results showed that performance of both GBLUP and Bayesian methods was influenced by imputation errors. For traits affected by a few large QTL, the Bayesian method resulted in greater reductions of accuracy due to imputation errors than GBLUP. Including SNPs with largest effects in the low density panel substantially improved the accuracy of genomic prediction for the Bayesian method. Including genotypes imputed from the 6 k panel achieved almost the same accuracy of genomic prediction as that of using the 50 k panel even when 66% of the training population was genotyped on the 6 k panel. These results justified the application of the 6 k panel for genomic prediction. Imputations from lower density panels were more prone to errors and resulted in lower accuracy of genomic prediction. But for animals that have close relationship to the reference set, genotype imputation may still achieve a relatively high accuracy. © 2014 Chen et al.
de Montera B.,Laval University |
Fournier E.,Laval University |
Shojaei Saadi H.A.,Laval University |
Gagne D.,Laval University |
And 4 more authors.
BMC Genomics | Year: 2013
Background: It was recently established that changes in methylation during development are dynamic and involve both methylation and demethylation processes. Yet, which genomic sites are changing and what are the contributions of methylation (5mC) and hydroxymethylation (5hmC) to this epigenetic remodeling is still unknown. When studying early development, options for methylation profiling are limited by the unavailability of sufficient DNA material from these scarce samples and limitations are aggravated in non-model species due to the lack of technological platforms. We therefore sought to obtain a representation of differentially 5mC or 5hmC loci during bovine early embryo stages through the use of three complementary methods, based on selective methyl-sensitive restriction and enrichment by ligation-mediated PCR or on subtractive hybridization. Using these strategies, libraries of putative methylation and hydroxymethylated sites were generated from Day-7 and Day-12 bovine embryos.Results: Over 1.2 million sequencing reads were analyzed, resulting in 151,501 contigs, of which 69,136 were uniquely positioned on the genome. A total of 101,461 putative methylated sites were identified. The output of the three methods differed in genomic coverage as well as in the nature of the identified sites. The classical MspI/HpaII combination of restriction enzymes targeted CpG islands whereas the other methods covered 5mC and 5hmC sites outside of these regions. Data analysis suggests a transition of these methylation marks between Day-7 and Day-12 embryos in specific classes of repeat-containing elements.Conclusions: Our combined strategy offers a genomic map of the distribution of cytosine methylation/hydroxymethylation during early bovine embryo development. These results support the hypothesis of a regulatory phase of hypomethylation in repeat sequences during early embryogenesis. © 2013 de Montera et al.; licensee BioMed Central Ltd.
Baldoceda L.,University Laval |
Gilbert I.,University Laval |
Gagne D.,University Laval |
Vigneault C.,LAlliance Boviteq Inc. |
And 3 more authors.
Reproduction, Fertility and Development | Year: 2016
Some embryos exhibit better survival potential to cryopreservation than others. The cause of such a phenotype is still unclear and may be due to cell damage during cryopreservation, resulting from overaccumulation and composition of lipids. In cattle embryos, in vitro culture conditions have been shown to impact the number of lipid droplets within blastomeres. Thus far, the impact of breed on embryonic lipid content has not been studied. In the present study were compared the colour, lipid droplet abundance, lipid composition, mitochondrial activity and gene expression of in vivo-collected Jersey breed embryos, which are known to display poor performance post-freezing, with those of in vivo Holstein embryos, which have good cryotolerance. Even when housed and fed under the same conditions, Jersey embryos were found to be darker and contain more lipid droplets than Holstein embryos, and this was correlated with lower mitochondrial activity. Differential expression of genes associated with lipid metabolism and differences in lipid composition were found. These results show genetic background can impact embryonic lipid metabolism and storage. © CSIRO 2016.
D'Amours O.,Laval University |
Bordeleau L.-J.,Laval University |
Frenette G.,Laval University |
Blondin P.,LAlliance Boviteq Inc. |
And 2 more authors.
Reproduction | Year: 2012
Previously, we showed that binder of sperm 1 (BSP1) and epididymal sperm binding protein 1 (ELSPBP1) proteins are more abundant in the immotile bovine sperm subpopulation following cryopreservation. In this study, we investigated the association of BSP1 and ELSPBP1 with sperm in relation to their ability to survive the cryopreservation process. Fresh and cryopreserved semen samples from the same ejaculate collected from nine Holstein bulls were incubated with a fixable viability probe, fixed and permeabilised and then immunolabelled with rabbit anti-BSP1, rabbit anti-ELSPBP1 or rabbit IgG as negative control. Spermatozoa were then incubated with Alexa 488-conjugated secondary antibody and Hoechst 33342. For each sample, 10 000 'Hoechst positive' events were analysed by flow cytometry. Alternatively, sperm populations were obtained by fluorescence-activated cell sorting. In freshly ejaculated live sperm, two distinct BSP1 detection patterns were revealed: a first population where BSP1 is present along the flagellar region (P1 subpopulation) and a second population where BSP1 is localised on both the flagellar and the acrosomal regions (P3 subpopulation). The dead population presented a BSP1 distribution similar to P3 but with a more intense fluorescence signal (P4 subpopulation). In the corresponding cryopreserved samples, all sperm in the P3 subpopulation were dead while only a small proportion of the P1 subpopulation was dead (P2 subpopulation). ELSPBP1 was detected only in dead spermatozoa and in comparable proportions in both freshly ejaculated and cryopreserved semen. These results show that the presence of BSP1 over the acrosomal region characterises spermatozoa sensitive to cryopreservation and that ELSPBP1 characterises spermatozoa that are already dead at ejaculation. © 2012 Society for Reproduction and Fertility.