An important goal in animal breeding is to improve longitudinal traits. The objective of this study was to explore for longitudinal residual feed intake (RFI) data, which estimated breeding value (EBV), or combination of EBV, to use in a breeding program. Linear combinations of EBV (summarized breeding values, SBV) or phenotypes (summarized phenotypes) derived from the eigenvectors of the genetic covariance

Bayesian genomic prediction methods were developed to simultaneously fit all genotyped markers to a set of available phenotypes for prediction of breeding values for quantitative traits, allowing for differences in the genetic architecture (distribution of marker effects) of traits. These methods also provide a flexible and reliable framework for genome-wide association (GWA) studies. The objective

The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje

The objective of the present study was to investigate how variation in the faecal microbial composition is associated with variation in average daily gain (ADG), backfat thickness (BFT), daily feed intake (DFI), feed conversion ratio (FCR), and residual feed intake (RFI), using data from two experimental pig lines that were divergent for feed efficiency. Estimates of microbiability were obtained by

There is growing interest in using genetic selection to obtain more resilient farm animals (i.e. that are minimally affected by disturbances or rapidly recover from them). The aims of this study were to: (i) estimate the genetic parameters of resilience indicator traits based on egg production data, (ii) assess whether these traits are genetically correlated in purebreds and crossbreds, and (iii) assess

After publication of this work [1], we noticed that (1) we had not clearly stated that the data are publicly available and (2) we had not cited the original paper [2]. Therefore, the following sections “Background”, “Methods”, “Availability of data and materials” and “References” are incomplete and should be amended as follows. Page 1, first paragraph of the “Background” section where we stated “that

Blood urea nitrogen (BUN) is an indicator trait for urinary nitrogen excretion. Measuring BUN level requires a blood sample, which limits the number of records that can be obtained. Alternatively, BUN can be predicted using mid-infrared (MIR) spectroscopy of a milk sample and thus records become available on many more cows through routine milk recording processes. The genetic correlation between MIR

Natural antibodies (NAb) are antibodies that are present in a healthy individual without requiring previous exposure to an exogenous antigen. Selection for high NAb levels might contribute to improved general disease resistance. Our aim was to analyse the genetic background of NAb based on a divergent selection experiment in poultry, and in particular the effect of a polymorphism in the TLR1A gene

Single-step genomic best linear unbiased prediction (ssGBLUP) allows the inclusion of information from genotyped and ungenotyped individuals in a single analysis. This avoids the need to genotype all candidates with the potential benefit of reducing overall costs. The aim of this study was to assess the effect of genotyping strategies, the proportion of genotyped candidates and the genotyping criterion

Milk samples from 10,641 dairy cattle were screened by a mass spectrometry method for extreme concentrations of the A or B isoforms of the whey protein, β-lactoglobulin (BLG), to identify causative genetic variation driving changes in BLG concentration. A cohort of cows, from a single sire family, was identified that produced milk containing a low concentration of the BLG B protein isoform. A genome-wide

Resilient animals are minimally affected by disturbances, such as diseases and heat stress, and quickly recover. Daily activity data can potentially indicate resilience, because resilient animals likely keep variations due to disturbances that threat animal homeostasis at a low magnitude. We used daily step count of cows to define resilience indicators based on theory, exploratory analysis and literature

Phosphorus is an essential nutrient in all living organisms and, currently, it is the focus of much attention due to its global scarcity, the environmental impact of phosphorus from excreta, and its low digestibility due to its storage in the form of phytates in plants. In poultry, phosphorus utilization is influenced by composition of the ileum microbiota and host genetics. In our study, we analyzed

Genomic selection has revolutionized genetic improvement in animals and plants, but little is known about its long-term effects. Here, we investigated the long-term effects of genomic selection on response to selection, genetic variance, and the genetic architecture of traits using stochastic simulations. We defined the genetic architecture as the set of causal loci underlying each trait, their allele

Semen quality and insemination success are monitored in artificial insemination bulls to ensure high male fertility rates. Only ejaculates that fulfill minimum quality requirements are processed and eventually used for artificial inseminations. We examined 70,990 ejaculates from 1343 Brown Swiss bulls to identify bulls from which all ejaculates were rejected due to low semen quality. This procedure

Heat tolerance is a trait of economic importance in the context of warm climates and the effects of global warming on livestock production, reproduction, health, and well-being. This study investigated the improvement in prediction accuracy for heat tolerance when selected sets of sequence variants from a large genome-wide association study (GWAS) were combined with a standard 50k single nucleotide

Next-generation sequencing is a promising approach for the detection of causal variants within previously identified quantitative trait loci. Because of the costs of re-sequencing experiments, this application is currently mainly restricted to subsets of animals from already genotyped populations. Imputation from a lower to a higher marker density could represent a useful complementary approach. An

Urinary nitrogen leakage is an environmental concern in dairy cattle. Selection for reduced urinary nitrogen leakage may be done using indicator traits such as milk urea nitrogen (MUN). The result of a previous study indicated that the genetic correlation between MUN in Australia (AUS) and MUN in New Zealand (NZL) was only low to moderate (between 0.14 and 0.58). In this context, an alternative is

Genetic selection has proven to be a successful strategy for the sustainable control of gastrointestinal parasitism in sheep. However, little is known on the relationship between resistance to parasites and production traits in dairy breeds. In this study, we estimated the heritabilities and genetic correlations for resistance to parasites and milk production traits in the blond-faced Manech breed

Deterministic predictions of the accuracy of genomic estimated breeding values (GEBV) when combining information sources have been developed based on selection index theory (SIT) and on Fisher information (FI). These two approaches have resulted in slightly different results when considering the combination of pedigree and genomic information. Here, we clarify this apparent contradiction, both for

Linkage disequilibrium (LD) is commonly measured based on the squared coefficient of correlation $$\left({r}^{2}\right)$$ between the alleles at two loci that are carried by haplotypes. LD can also be estimated as the $${r}^{2}$$ between unphased genotype dosage at two loci when the allele frequencies and inbreeding coefficients at both loci are identical for the parental lines. Here, we investigated

Disease resilience is the ability to maintain performance across environments with different disease challenge loads (CL). A reaction norm describes the phenotypes that a genotype can produce across a range of environments and can be implemented using random regression models. The objectives of this study were to: (1) develop measures of CL using growth rate and clinical disease data recorded under

Multiple breed evaluation using genomic prediction includes the use of data from multiple populations, or from parental breeds and crosses, and is expected to lead to better genomic predictions. Increased complexity comes from the need to fit non-additive effects such as dominance and/or genotype-by-environment interactions. In these models, marker effects (and breeding values) are modelled as correlated

About one year ago, some of us learned that Rohan Fernando had announced his intention to retire from his position as Professor of Animal Science at Iowa State University. We felt that it would be appropriate to prepare a volume honoring his important contributions to quantitative genetics, especially to animal breeding. With that idea in mind, many of his collaborators and colleagues (past and present)

Brown trout is one of the most widespread fresh-water fish species in Europe. The evolutionary history of and phylogenetic relationships between brown trout populations are complex, and this is especially true for Italian populations, which are heavily influenced in different ways by stocking practices. The characterization of the genetic structure of Italian brown trout populations may give information

Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication resulting from consumption of contaminated poultry products. Genetic selection of animals that are more resistant to Salmonella carriage and modulation of the gut microbiota are two promising ways to decrease individual Salmonella carriage. The aims of this study were to identify the main genetic and microbial factors

The domestication of goat (Capra hircus) started 11,000 years ago in the fertile crescent. Breed formation in the nineteenth century, establishment of herd books, and selection for specific traits resulted in 10 modern goat breeds in Switzerland. We analyzed whole-genome sequencing (WGS) data from 217 modern goats and nine wild Bezoar goats (Capra aegagrus). After quality control, 27,728,288 biallelic

Deleterious recessive conditions have been primarily studied in the context of Mendelian diseases. Recently, several deleterious recessive mutations with large effects were discovered via non-additive genome-wide association studies (GWAS) of quantitative growth and developmental traits in cattle, which showed that quantitative traits can be used as proxies of genetic disorders when such traits are

Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas

Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the

Gastroinestinal nematodes (GIN) are one of the major health problem in grazing sheep. Although genetic variability of the resistance to GIN has been documented, traditional selection is hampered by the difficulty of recording phenotypes, usually fecal egg count (FEC). To identify causative mutations or markers in linkage disequilibrium (LD) to be used for selection, the detection of quantitative trait

The genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability

As a major economic trait in poultry, egg production efficiency attracts widespread interest in breeding and production. However, limited information is available about the underlying genetic architecture of egg production traits in ducks. In this paper, we analyzed six egg production-related traits in 352 F2 ducks derived from reciprocal crosses between mallard and Pekin ducks. Feed conversation ratio

Following publication of the original article [1], the authors noticed the following two errors: (1) Figures 1 and 2 are swapped, but the legends and figure numbers are correct, that is, the legend indicated for Figure 1 is in the right place but corresponds to Figure 2, and vice versa; and (2) In the Funding section, the statement: MPE is funded by Ministry of Science and Innovation-State Research

Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the

This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine

Carcass length is very important for body size and meat production for swine, thus understanding the genetic mechanisms that underly this trait is of great significance in genetic improvement programs for pigs. Although many quantitative trait loci (QTL) have been detected in pigs, very few have been fine-mapped to the level of the causal mutations. The aim of this study was to identify potential causal

Genotype-by-environment interactions for a trait can be modeled using multiple-trait, i.e. character-state, models, that consider the phenotype as a different trait in each environment, or using reaction norm models based on a functional relationship, usually linear, between phenotype and a quantitative measure of the quality of the environment. The equivalence between character-state and reaction

Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures

The possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their

The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios

Understanding whether genomic selection has been effective in livestock and when the results of genomic selection became visible are essential questions which we have addressed in this paper. Three criteria were used to identify practices of breeding programs over time: (1) the point of divergence of estimated genetic trends based on pedigree-based best linear unbiased prediction (BLUP) versus single-step

After the publication of the original article [1], the authors noticed that there was an error. In the first paragraph of page 5, where we compare ACCLR and ACCT, the accuracy symbols have been swapped. The right sentences are: “ACCT were on average lower than ACCLR (Table 3) and more variable (Fig. 1b). This resulted in a much higher coefficient of variation for ACCT (Fig. 1c), particularly for ADG

The quality of colostrum administered to calves is based on its concentration in immunoglobulins G (IgG, g/L). Immunoglobulins A (IgA) and M (IgM) are also present but at a lower level. The gold standard reference analysis for these traits, radial immunodiffusion, is time-consuming and expensive. In order to define breeding strategies that are aimed at improving colostrum quality in dairy cattle, a

Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization

The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals

In dairy cattle, genomic selection has been implemented successfully for purebred populations, but, to date, genomic estimated breeding values (GEBV) for crossbred cows are rarely available, although they are valuable for rotational crossbreeding schemes that are promoted as efficient strategies. An attractive approach to provide GEBV for crossbreds is to use estimated marker effects from the genetic

Based on the relatively homogeneous origin of the sheep breeds in Morocco that originate mainly from Iberia, it is highly relevant to address the question of how these very diverse sheep populations differentiated from each other. The Mountains of the High Atlas and Middle Atlas are expected to constitute North–South and West–East geographical barriers, respectively, which could have shaped the history

Growth traits are of great importance for poultry breeding and production and have been the topic of extensive investigation, with many quantitative trait loci (QTL) detected. However, due to their complex genetic background, few causative genes have been confirmed and the underlying molecular mechanisms remain unclear, thus limiting our understanding of QTL and their potential use for the genetic

After publication of [1], several errors in references to equations were noted. In the Methods section entitled “\({M}_{e}\) for the reference population”, reference to Eqs. (6), (7), and (9) must be replaced by Eqs. (5), (6), and (8) in the sentence: “These two accuracies can then be combined to predict \({r}_{{G}_{r}}\), using either the Fisher approach (Eqs. (5) and (6)) or the Index approach (Eq

The domestication of wild animals has resulted in a reduction in effective population sizes, which can affect the deleterious mutation load of domesticated breeds. In addition, artificial selection contributes to the accumulation of deleterious mutations because of an increased rate of inbreeding among domesticated animals. Since founder population sizes and artificial selection differ between cattle

The single-step genomic best linear unbiased prediction (SSGBLUP) method is a popular approach for genetic evaluation with high-density genotype data. To solve the problem that pedigree and genomic relationship matrices refer to different base populations, a single-step genomic method with metafounders (MF-SSGBLUP) was put forward. The aim of this study was to compare the predictive ability and bias

Genomic selection using single nucleotide polymorphism (SNP) markers has been widely used for genetic improvement of livestock, but most current methods of genomic selection are based on SNP models. In this study, we investigated the prediction accuracies of haplotype models based on fixed chromosome distances and gene boundaries compared to those of SNP models for genomic prediction of phenotypic

Improving feedlot performance, carcase weight and quality is a primary goal of the beef industry worldwide. Here, we used data from 3408 Australian Angus steers from seven years of birth (YOB) cohorts (2011–2017) with a minimal level of sire linkage and that were genotyped for 45,152 SNPs. Phenotypic records included two feedlot and five carcase traits, namely average daily gain (ADG), average daily

Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White

We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step. We used stochastic simulation to estimate true genetic gain realised at a

Goat, one of the first domesticated livestock, is a worldwide important species both culturally and economically. The current goat reference genome, known as ARS1, is reported as the first nonhuman genome assembly using 69× PacBio sequencing. However, ARS1 suffers from incomplete X chromosome and highly fragmented Y chromosome scaffolds. Here, we present a very high-quality de novo genome assembly

India is the largest milk producer globally, with the largest proportion of cattle milk production coming from smallholder farms with an average herd size of less than two milking cows. These cows are mainly undefined multi-generation crosses between exotic dairy breeds and indigenous Indian cattle, with no performance or pedigree recording. Therefore, implementing genetic improvement based on genetic

Various regions of the chicken genome have been under natural and artificial selection for thousands of years. The substantial diversity that exits among chickens from different geographic regions provides an excellent opportunity to investigate the genomic regions under selection which, in turn, will increase our knowledge about the mechanisms that underlie chicken diversity and adaptation. Several

Efficient breeding programs are difficult to implement in honeybees due to their biological specificities (polyandry and haplo-diploidy) and complexity of the traits of interest, with performances being measured at the colony scale and resulting from the joint effects of tens of thousands of workers (called direct effects) and of the queen (called maternal effects). We implemented a Monte Carlo simulation

Body weight (BW) is an economically important trait in the broiler (meat-type chickens) industry. Under the assumption of polygenicity, a “large” number of genes with “small” effects is expected to control BW. To detect such effects, a large sample size is required in genome-wide association studies (GWAS). Our objective was to conduct a GWAS for BW measured at 35 days of age with a large sample size