The use of endogenous retroviruses as markers to describe the genetic relationships among some local Swedish sheep breeds

The present modern sheep is believed to have evolved from its wild ancestors 2.5 million years ago. Furthermore archeological evidence suggest that sheep has been domesticated by man since 8500-9000 years BC for their beneficial products to man including; milk, meat, skin and wool. Through centuries, sheep have been spread from the center of domestication to different parts of the world where they have adapted to environmental factors in such areas giving rise to what is known today as local or indigenous breeds. Indigenous breeds are generally characterized by the presence of horns in both rams and ewes, dark and coarse fleece and moulting coat. Such local breeds in Sweden include; Dala Fur sheep, Gestrike sheep, Helsinge sheep, Klövsjö sheep, Svärdsjö sheep, Åsen sheep, Roslagen sheep, Värmland sheep, Gotland sheep and Gute sheep. Though there have been some studies on some of these breeds, information on genetic distinctiveness between them remains scarce. The sheep genome contains more than 30 polymorphic endogenous proviruses (enJSRV) that are related to the Jaagsiekte retrovirus (JSRV), a Beta retrovirus known for causing Ovine Pulmonary Adenocarcinoma. These proviruses are remains of exogenous retroviruses that infected germ cells of ancestors or great grandparents and have been passed on in a Mendelian manner to the present day sheep. Some of these endogenous proviruses have been found to have different functions in sheep species including the protection of hosts from infection by related defective exogenous viruses and also aid in conception and implantation during reproduction. Recently these polymorphic loci have been used to study the domestication trend of sheep and genetic distinctiveness between some sheep breeds. The aim of the current study was to use 6 of the polymorphic proviruses to define genetic difference between five local Swedish breeds. The presence or absence of each of these proviruses in the studied individuals was tested using polymerase chain reaction (PCR) and agarose gel-electrophoresis on genomic DNA of 66 individuals. Results were analyzed based on the frequencies of the individual loci in the tested samples, retrotype or provirus combination frequencies and a principal component analysis was performed based on the provirus frequencies to visualize genetic distances between studied breeds. The study revealed a close genetic relationship sheep between Gute, Swedish fine wool sheep and Roslag. Furthermore we also found a strong genetic closeness between Värmland and Klövsjö sheep breeds. Although all the local Swedish breeds tested were found to have genomes of ancestral or primitive makeup, Värmland and Klövsjö were more primitive than others. Further comparison of each breed with Texel showed that Swedish fine wool sheep was more close to the Texel breed than any other breed in the study. However, the number of samples used and their distribution among herds was small. Hence, more samples are needed for a larger study to allow for better conclusions on the genetic diversity or relatedness between these breeds and other Swedish breeds not included in our study

Transcriptome analyses reveal reduced hepatic lipid synthesis and accumulation in more feed efficient beef cattle

peer-reviewedThe genetic mechanisms controlling residual feed intake (RFI) in beef cattle are still largely unknown. Here we performed whole transcriptome analyses to identify differentially expressed (DE) genes and their functional roles in liver tissues between six extreme high and six extreme low RFI steers from three beef breed populations including Angus, Charolais, and Kinsella Composite (KC). On average, the next generation sequencing yielded 34 million single-end reads per sample, of which 87% were uniquely mapped to the bovine reference genome. At false discovery rate (FDR)  2, 72, 41, and 175 DE genes were identified in Angus, Charolais, and KC, respectively. Most of the DE genes were breed-specific, while five genes including TP53INP1, LURAP1L, SCD, LPIN1, and ENSBTAG00000047029 were common across the three breeds, with TP53INP1, LURAP1L, SCD, and LPIN1 being downregulated in low RFI steers of all three breeds. The DE genes are mainly involved in lipid, amino acid and carbohydrate metabolism, energy production, molecular transport, small molecule biochemistry, cellular development, and cell death and survival. Furthermore, our differential gene expression results suggest reduced hepatic lipid synthesis and accumulation processes in more feed efficient beef cattle of all three studied breeds

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Abstract Background Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. Results Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10−5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. Conclusions This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data

Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle

Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, l-glutamine, succinic acid, pyruvic acid, l-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, d-glucose, and glycerol), 2 (l-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10(–5)), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits

Data Literacy: A catalyst for improving research publication productivity of Kyambogo University Academic Staff

Objective: The aim of this study is to explore how data literacy can influence the research and publications productivity of Kyambogo University academic staff.Methods: The study employed a literature review to collect detailed information. It observed lessons, and studied patterns of the phenomenon to explore data literacy initiatives that can be used by Kyambogo University academic staff to improve their research publications productivity and also to mitigate the accrued challenges.&nbsp;Results: The paper explored eight initiatives through which data literacy skills could enhance the research productivity of Kyambogo University academic staff. These were awareness and promoting freedom of using open data, engaging students in data literacy activities, pedagogical reflection, datafication of single and joint academic staff publications, visualization of data, storytelling, ethical use of data, and preservation of research data.&nbsp;Conclusions: While this paper relies on the context of the Kyambogo University academic staff, the authors posit that these data literacy skills can be embraced by universities in developing economies; especially those struggling with poor research and publications productivity. The paper further identifies areas where universities in developing economies, in conjunction with their libraries, can improve the academic staff pedagogy and compliance to eScience through polishing their data literacies

Applying multi-omics data to study the genetic background of bovine respiratory disease infection in feedlot crossbred cattle

Bovine respiratory disease (BRD) is the most common and costly infectious disease affecting the wellbeing and productivity of beef cattle in North America. BRD is a complex disease whose development is dependent on environmental factors and host genetics. Due to the polymicrobial nature of BRD, our understanding of the genetic and molecular mechanisms underlying the disease is still limited. This knowledge would augment the development of better genetic/genomic selection strategies and more accurate diagnostic tools to reduce BRD prevalence. Therefore, this study aimed to utilize multi-omics data (genomics, transcriptomics, and metabolomics) analyses to study the genetic and molecular mechanisms of BRD infection. Blood samples of 143 cattle (80 BRD; 63 non-BRD animals) were collected for genotyping, RNA sequencing, and metabolite profiling. Firstly, a genome-wide association study (GWAS) was performed for BRD susceptibility using 207,038 SNPs. Two SNPs (Chr5:25858264 and BovineHD1800016801) were identified as associated (p-value 2, logCPM>2, and FDR<0.01), 101 differentially expressed (DE) genes were identified. These DE genes significantly (p-value <0.05) enriched several immune responses related functions such as inflammatory response. Additionally, we performed expression quantitative trait loci (eQTL) analysis and identified 420 cis-eQTLs and 144 trans-eQTLs significantly (FDR <0.05) associated with the expression of DE genes. Interestingly, eQTL results indicated the most significant SNP (Chr5:25858264) identified via GWAS was a cis-eQTL for DE gene GPR84. This analysis also demonstrated that an important SNP (rs209419196) located in the promoter region of the DE gene BPI significantly influenced the expression of this gene. Finally, the abundance of 31 metabolites was significantly (FDR <0.05) different between BRD and non-BRD animals, and 17 of them showed correlations with multiple DE genes, which shed light on the interactions between immune response and metabolism. This study identified associations between genome, transcriptome, metabolome, and BRD phenotype of feedlot crossbred cattle. The findings may be useful for the development of genomic selection strategies for BRD susceptibility, and for the development of new diagnostic and therapeutic tools