Regional Regulation of Transcription in the Bovine Genome

Eukaryotic genes are distributed along chromosomes as clusters of highly expressed genes termed RIDGEs (Regions of IncreaseD Gene Expression) and lowly expressed genes termed anti-RIDGEs, interspersed among genes expressed at intermediate levels or not expressed. Previous studies based on this observation suggested a dual mechanism of gene regulation, where, in addition to transcription factors, the chromosomal domain influences the expression level of their embedded genes. The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines. Gene expression analysis of four brain tissues and the anterior pituitary of 28 cows identified 70 RIDGEs and 41 anti-RIDGEs (harbouring 3735 and 1793 bovine genes respectively) across the bovine genome which are significantly higher than expected by chance. Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not. Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES. Our findings suggest the existence of chromosomal regional regulation of transcription in the bovine genome. The genomic features observed for genes within RIDGEs and housekeeping genes in bovines agree with previous studies in several other species further strengthening the hypothesis of selective pressure to keep the highly and widely expressed genes short and compact for transcriptional efficiency. Further, positively selected genes were found non-randomly distributed on the genome with a preference for RIDGEs and regions of intermediate gene expression compared to anti-RIDGEs

Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken

Temperature stress impacts both welfare and productivity of livestock. Global warming is expected to increase the impact, especially in tropical areas. We investigated the biological mechanisms regulated by temperature stress due to the circadian temperature cycle in temperature adapted and non-adapted chicken under tropical conditions. We studied transcriptome profiles of heart, breast muscle, and spleen tissues of Ethiopian lowland chicken adapted to high circadian temperatures and non-adapted Ethiopian highland chicken under lowland conditions at three points during the day: morning, noon, and evening. Functional annotations and network analyses of genes differentially expressed among the time points of the day indicate major differences in the reactions of the tissues to increasing and decreasing temperatures, and also the two chickens lines differ. However, epigenetic changes of chromatin methylation and histone (de)acetylation seemed to be central regulatory mechanisms in all tissues in both chicken lines. Finally, all tissues showed differentially expressed genes between morning and evening times indicating biological mechanisms that need to change during the night to reach morning levels again the next day.</p

Measurable biomarkers linked to meat quality from different pig production systems

Invited reviewNom actuel de la revue : Archives Animal BreedingBiological processes underlie all livestock traits, including post-mortem meat quality traits. Biomarkersare molecular components of the biological processes showing differential expression associated with thephenotype of the trait. The phenotypes of the meat quality traits are determined by the animal’s genotype interacting with the environment affecting the expression of the genome. The “omics” technologies enable measuring the expression of the genome at all levels: transcriptome, proteome, and metabolome. Associations between the phenotype of the traits and expressions measured with the omics techniques are a first step in developing biomarkers. Biomarkers enable the monitoring, diagnosis, and prediction of changes in meat quality related to external (environmental, e.g. feed and animal management conditions) stimuli and interactions with the genotype. In this paper we review the development of biomarkers for meat quality of pigs in diverse pig breeds,environments, and pork production chains

The Importance of Endophenotypes to Evaluate the Relationship between Genotype and External Phenotype

With the exception of a few Mendelian traits, almost all phenotypes (traits) in livestock science are quantitative or complex traits regulated by the expression of many genes. For most of the complex traits, differential expression of genes, rather than genomic variation in the gene coding sequences, is associated with the genotype of a trait. The expression profiles of the animal’s transcriptome, proteome and metabolome represent endophenotypes that influence/regulate the externally-observed phenotype. These expression profiles are generated by interactions between the animal’s genome and its environment that range from the cellular, up to the husbandry environment. Thus, understanding complex traits requires knowledge about not only genomic variation, but also environmental effects that affect genome expression. Gene products act together in physiological pathways and interaction networks (of pathways). Due to the lack of annotation of the functional genome and ontologies of genes, our knowledge about the various biological systems that contribute to the development of external phenotypes is sparse. Furthermore, interaction with the animals’ microbiome, especially in the gut, greatly influences the external phenotype. We conclude that a detailed understanding of complex traits requires not only understanding of variation in the genome, but also its expression at all functional levels

Genetic variation in the porcine myogenin gene locus

ISSN:0938-8990ISSN:1432-177

Characterization, chromosomal localization, and genetic variation of the porcine heart fatty acid-binding protein gene

ISSN:0938-8990ISSN:1432-177

Tables S1-S5: Detailed information about farms and samples selected for Mainstream (M) / Artisanal (A), Bacterial colony forming units / ml milk, Breed, Number of goats on the farm, and sampling date, respectively.

Table S6: Reads per sample. Tables S7 and S8: Goat raw milk microbiome information at phylum and genera levels per sample and farm, respectively. (XLSX)</p

Goat milk colony forming units of the ten farms.

The selected samples are the same as in Figs 2 and 3. Each farm is represented with two independent samples. All raw data can be found in Table S2 in S2 File. Blue dots represent mainstream farms, green dots represent artisanal farms. Please note two missing values of farms 5 and 6, respectively, due to unreliable dilution series.</p

Box plot showing the observed variation of the lactic acid synthesizing bacteria in the goat milk microbiome.

The average value of the two management systems is similar, but the variation is higher in the artisanal farms, varying from very high (up to above 6% of the total bacterial content) to very low (almost zero).</p