The aim of the present study was to analyze interplay between gastrointestinal tract (GIT) microbiota, host genetics, and complex traits in pigs using extended quantitative-genetic methods. design consisted 207 that were housed slaughtered under standardized conditions, phenotyped for daily gain, feed intake, conversion rate. genotyped with a standard 60 K SNP chip. GIT microbiota composition analyzed by 16S rRNA gene amplicon sequencing technology. Eight from 49 investigated bacteria genera...

Selecting animals for breeding in the optimum way plays an essential role management of genetic resources and selective livestock species. It requires to compute contribution each selection candidate next generation. Current software packages (OCS) are not able handle main conflicting objectives animal programs simultaneously, which includes increase gain, or maintain diversity, recover original background endangered breeds with historic introgression, diversity at native alleles.The free R...

Summary Genomic selection refers to the use of dense, genome-wide markers for prediction breeding values (BV) and subsequent individuals. It has become a standard tool in livestock plant accelerating genetic gain. The core genomic is large number marker effects from limited observations. Various Bayesian methods that successfully cope with this challenge are known. Until now, main research emphasis been on additive effects. Dominance coefficients quantitative trait loci (QTLs), however, can...

Currently, genomic prediction in cattle is largely based on panels of about 54k single nucleotide polymorphisms (SNPs). However with the decreasing costs and current advances next-generation sequencing technologies, whole-genome sequence (WGS) data large numbers individuals within reach. Availability such provides new opportunities for selection, which need to be explored. This simulation study investigated how much predictive ability gained by using WGS under scenarios QTL (quantitative...

Genomic selection has become a standard tool in dairy cattle breeding. However, for other animal species, implementation of this technology is hindered by the high cost genotyping. One way to reduce routine costs genotype candidates with an SNP (single nucleotide polymorphism) panel reduced density. This strategy investigated present paper. Methods are proposed approximation positions, SNPs be included low-density panel, imputation, and estimation accuracy genomic breeding values. The...

Most traits in animal breeding, including feed efficiency pigs, are affected by many genes with small effect and have a moderately high heritability between 0.1 0.5, which enables efficient selection. Since the microbiota composition gastrointestinal tract is also partly heritable was shown to substantial on efficiency, host affect phenotype not only directly altering metabolic pathways, but indirectly changing composition. The mi of breeding value gi an i conditional expectation its value,...

Summary Knowledge of the genetic architecture a quantitative trait is useful to adjust methods for prediction genomic breeding values and discover extent which common assumptions in locus (QTL) mapping experiments value estimation are violated. It also affects our ability predict long-term response selection. In this paper, we focus on additive dominance effects QTL. We derive formulae that can be used estimate number QTLs affect parameters distribution their from variance components,...

Population management has the primary task of maximizing long-term competitiveness a breed. Breeds compete with each other for being able to supply consumer demands at low costs and also funds from conservation programs. The competition preference is won by breeds high genetic gain total merit who maintained sufficiently diversity, whereas value. value breed could be improved increasing its contribution gene pool species. This may include recovery original background maintenance diversity...

In recent decades, local varieties of domesticated animal species have been frequently crossed with economically superior breeds which has resulted in considerable genetic contributions from migrants. Optimum contribution selection by maximizing gene diversity while constraining breeding values the offspring or vice versa could eventually lead to extinction historic migration because maximization would be achieved migrant contributions. Therefore, other objective functions are needed for...

In recent years, research in animal breeding has increasingly focused on the topic of resilience, which is expected to continue future due need for high-yielding, healthy, and robust animals. this context, an established approach calculation resilience indicator traits with time series analyses. Examples are variance autocorrelation daily milk yield dairy cows. We applied methodology German cow population. Data from 3 breeds Holstein, Fleckvieh Brown Swiss were obtained, included 13949...

Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance diversity. However, this diversity may be caused by high migrant contributions (MC) in population due to introgression material from other breeds, which can threaten conservation small local populations. Therefore, breeding objectives should not only focus on gains but also maintaining originality native alleles. This study aimed at investigating whether...

Abstract It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes affect quantitative traits. The microbial architecture describes impact of composition on trait variation number effect distribution features. In present study feed-related traits phosphorus calcium utilization, daily gain, feed intake per gain ratio in domestic poultry model species Japanese quail were assessed mixed linear models. ileum was characterized 16S rRNA amplicon sequencing...

In this study, the effect of different measurements ancestral inbreeding on birthweight, calving ease and stillbirth were analysed. Three models used to estimate inbreeding, estimated regression coefficient phenotypic data was quantify inbreeding. The first model included only one measurement whereas second classical coefficients alternative coefficient. third coefficients, interaction between dam. Phenotypic for study collected from February 1998 December 2008 three large commercial milk...

Summary During the past decades, migrant contributions have accumulated in many local breeds. Cross‐breeding was carried out to mitigate risk of inbreeding depression and improve performance However, breeding activities for breeds were not as intensive target oriented popular high‐yielding Therefore, even if improved, gap between increased traits. Furthermore, genetic originality declined due increasing This study examined importance breed influences realization progress beef traits German...

Feather pecking (FP) in laying hens is a well-known and multi-factorial behaviour with genetic background. In selection experiment, two lines were developed for 11 generations high (HFP) low (LFP) feather pecking, respectively. Starting the second generation of selection, there was constant difference mean number FP bouts between both lines. We used data from this experiment to perform quantitative analysis map signatures.Pedigree phenotypic available last six Univariate analyses conducted...

Abstract The long-term performance of different selection strategies was evaluated via simulation using the example a local cattle breed, German Angler cattle. Different optimum contribution (OCS) approaches to maximize genetic gain were compared reference scenario without and truncation selection. kinships migrant (MC) estimated from genomic data. Truncation achieved highest but decreased diversity considerably at native alleles. It also caused increase in MCs. Traditional OCS, which only...

The purpose of a selection index is that its use to select animals for breeding maximizes the profit breed in future generations. general quantity predicts satisfaction owners with their breed, and consumers products are produced by breed. Many traits, such as conformation traits product quality have intermediate optima. Traditional theory applies only directional cannot achieve any further improvement once trait means reached A well-founded needed extends established cover well stabilizing...

Genotype-by-environment interaction (GxE) has been widely reported in dairy cattle. One way to analyze GxE is apply reaction norm models. The first derivative of a the environmental sensitivity (ES). In present study we conducted large-scale, genome-wide association analysis identify single-nucleotide polymorphisms (SNPs) that affect general production (GP) and ES milk traits German Holstein population. Sire estimates for GP were calculated from approximately 13 million daughter records by...

Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended towards accounting dominance effects and improved prediction accuracy persistence selection. The current study investigated power precision of genome-wide studies by means stochastic simulations applied these methods dairy cattle...

Summary Improvement in growth and meat quality is one of the main objectives sire line pig breeding programmes. Mapping quantitative trait loci for these traits using experimental crosses a linkage‐based approach has been performed frequently past. The Piétrain breed often was involved as founder to establish crosses. This selected muscularity leanness but shows relatively poor quality. It used breed. With advent genome‐wide dense SNP chips genomic research, it possible also conduct...

Genomic analyses commonly explore the additive genetic variance of traits. The non-additive variance, however, is usually small but often significant in dairy cattle. This study aimed at dissecting eight health traits that recently entered total merit index Germany and somatic cell score (SCS), as well four milk production by analysing dominance components. heritabilities were low for all (between 0.033 mastitis 0.099 SCS), moderate 0.261 energy yield 0.351 yield). For traits, contribution...

Feather pecking (FP) is a longstanding serious problem in commercial flocks of laying hens. It highly polygenic trait and the genetic background still not completely understood. In order to find genomic regions influencing FP, selection signatures between hen lines divergently selected for high low feather were mapped using intra-population iHS inter-population FST approach. addition, existence an extreme subgroup FP hens (EFP) across both has been demonstrated by fitting mixture negative...