The discovery of single nucleotide polymorphisms (SNP) and the subsequent genotyping of large numbers of animals have enabled large-scale analyses to begin to understand the biological processes that underpin variation in animal populations. In beef cattle, genome-wide association studies using genotype arrays have revealed many quantitative trait loci (QTL) for various production traits such as growth, efficiency and meat quality. Most studies regarding meat quality have focused on marbling, which is a key trait associated with meat eating quality. However, other important traits like meat color, texture and fat color have not commonly been studied. Developments in genome sequencing technologies provide new opportunities to identify regions associated with these traits more precisely. The objective of this study was to estimate variance components and identify significant variants underpinning variation in meat quality traits using imputed whole genome sequence data. Phenotypic and genomic data from 2,110 Hanwoo cattle were used. The estimated heritabilities for the studied traits were 0.01, 0.16, 0.31, and 0.49 for fat color, meat color, meat texture and marbling score, respectively. Marbling score and meat texture were highly correlated. The genome-wide association study revealed 107 significant SNPs located on 14 selected chromosomes (one QTL region per selected chromosome). Four QTL regions were identified on BTA2, 12, 16, and 24 for marbling score and two QTL regions were found for meat texture trait on BTA12 and 29. Similarly, three QTL regions were identified for meat color on BTA2, 14 and 24 and five QTL regions for fat color on BTA7, 10, 12, 16, and 21. Candidate genes were identified for all traits, and their potential influence on the given trait was discussed. The significant SNP will be an important inclusion into commercial genotyping arrays to select new breeding animals more accurately.

STUDY QUESTIONIn comparison to in vivo development, how do different conditions of in vitro culture (‘one step’ versus ‘sequential medium’) impact DNA methylation and hydroxymethylation in preimplantation embryos?SUMMARY ANSWERUsing rabbit as a model, we show that DNA methylation and hydroxymethylation are both affected by in vitro culture of preimplantation embryos and the effect observed depends on the culture medium used.WHAT IS KNOWN ALREADYCorrect regulation of DNA methylation is essential for embryonic development and DNA hydroxymethylation appears more and more to be a key player. Modifications of the environment of early embryos are known to have long term effects on adult phenotypes and health; these probably rely on epigenetic alterations.STUDY DESIGN SIZE, DURATIONThe study design we used is both cross sectional (control versus treatment) and longitudinal (time-course). Each individual in vivo experiment used embryos flushed from the donor at the 2-, 4-, 8-, 16- or morula stage. Each stage was analyzed in at least two independent experiments. Each individual in vitro experiment used embryos flushed from donors at the 1-cell stage (19 h post-coïtum) which were then cultured in parallel in the two tested media until the 2-, 4-, 8- 16-cell or morula stages. Each stage was analyzed in at least three independent experiments. In both the in vivo and in vitro experiments, 4-cell stage embryos were always included as an internal reference.PARTICIPANTS/MATERIALS, SETTING, METHODSImmunofluorescence with antibodies specific for 5-methylcytosine (5meC) and 5-hydroxymethylcytosine (5hmeC) was used to quantify DNA methylation and hydroxymethylation levels in preimplantation embryos. We assessed the expression of DNA methyltransferases (DNMT), of ten eleven translocation (TET) dioxigenases and of two endogenous retroviral sequences (ERV) using RT-qPCR, since the expression of endogenous retroviral sequences is known to be regulated by DNA methylation. Three repeats were first done for all stages; then three additional repetitions were performed for those stages showing differences or tendencies toward differences between the different conditions in the first round of quantification.MAIN RESULTS AND THE ROLE OF CHANCEThe kinetics of DNA methylation and hydroxymethylation were modified in in vitro cultured embryos, and the observed differences depended on the type of medium used. These differences were statistically significant. In addition, the expression of TET1 and TET2 was significantly reduced in post-embryonic genome activation (EGA) embryos after in vitro culture in both tested conditions. Finally, the expression of two retroviral sequences was analyzed and found to be significantly affected by in vitro culture.LIMITATIONS REASONS FOR CAUTIONOur study remains mostly descriptive as no direct link can be established between the epigenetic changes observed and the expression changes in both effectors and targets of the studied epigenetic modifications. The results we obtained suggest that gene expression could be a...

Genetic mapping to identify genes and alleles associated with or causing economically important quantitative trait variation in livestock animals such as pigs is a major goal in animal genetic improvement. Despite recent advances in high-throughput genotyping technologies, the resolution of genetic mapping in pigs remains poor due in part to the low density of genotyped variant sites. In this study, we overcame this limitation by developing a reference haplotype panel for pigs based on 2259 whole genome-sequenced animals representing 44 pig breeds. We evaluated software combinations and breed composition to optimize the imputation procedure and achieved an average concordance rate in excess of 96%, a non-reference concordance rate of 88%, and an r2 of 0.85. We demonstrated in two case studies that genotype imputation using this resource can dramatically improve the resolution of genetic mapping. A public web server has been developed to allow the pig genetics community to fully utilize this resource. We expect this resource to facilitate genetic mapping and accelerate genetic improvement in pigs.