CLARITY: a Shiny app for interactive visualisation of the bovine physical-genetic map.

The arrangement of markers on the genome can be defined in either physical or linkage terms. While a physical map represents the inter-marker distances in base pairs, a genetic (or linkage) map pictures the recombination rate between pairs of markers. High-resolution genetic maps are key elements for genomic research, such as fine-mapping of quantitative trait loci, but they are also needed for creating and updating chromosome-level assemblies of whole-genome sequences.

Better, Not Just More-Contrast in Qualitative Aspects of Reward Facilitates Impulse Control in Pigs.

Delay-of-gratification paradigms, such as the famous "Marshmallow Test," are designed to investigate the complex cognitive concepts of self-control and impulse control in humans and animals. Such tests determine whether a subject will demonstrate impulse control by choosing a large, delayed reward over an immediate, but smaller reward. Documented relationships between impulsive behavior and aggression in humans and animals suggest important implications for farm animal husbandry and welfare, especially in terms of inadequate social behavior, tail biting and maternal behavior.

Evaluating the temporal and situational consistency of personality traits in adult dairy cattle.

Recent research suggests that personality, defined as consistent individual behavioral variation, in farm animals could be an important factor when considering their health, welfare, and productivity. However, behavioral tests are often performed individually and they might not reflect the behavioral differences manifested in every-day social environments. Furthermore, the contextual and longer-term temporal stability of personality traits have rarely been investigated in adult dairy cattle.

Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle.

Background: While autozygosity as a consequence of selection is well understood, there is limited information on the ability of different methods to measure true inbreeding. In the present study, a gene dropping simulation was performed and inbreeding estimates based on runs of homozygosity (ROH), pedigree, and the genomic relationship matrix were compared to true inbreeding. Inbreeding based on ROH was estimated using SNP1101, PLINK, and BCFtools software with different threshold parameters.

Integrating milk metabolite profile information for the prediction of traditional milk traits based on SNP information for Holstein cows.

In this study the benefit of metabolome level analysis for the prediction of genetic value of three traditional milk traits was investigated. Our proposed approach consists of three steps: First, milk metabolite profiles are used to predict three traditional milk traits of 1,305 Holstein cows. Two regression methods, both enabling variable selection, are applied to identify important milk metabolites in this step.

Including non-additive genetic effects in Bayesian methods for the prediction of genetic values based on genome-wide markers.

Background: Molecular marker information is a common source to draw inferences about the relationship between genetic and phenotypic variation. Genetic effects are often modelled as additively acting marker allele effects. The true mode of biological action can, of course, be different from this plain assumption.