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This study aimed at estimating genetic and phenotypic relationships among feed efficiency, immune and production traits measured pre- (9–20 weeks of age) and post- (12 weeks from on-set of lay) maturity. Production traits were average daily gain (ADG) and average daily feed-intake (ADFI1) in the pre-maturity period and age at first egg (AFE), average daily feed-intake (ADFI2) and average daily egg mass (EM) in the post-maturity period. Feed efficiency comprised of residual feed intake (RFI) estimated in both periods. Natural antibodies binding to keyhole limpet hemocyanin (KLH-IgM) and specific antibodies binding to Newcastle disease virus (NDV-IgG) measured at 16 and 28 weeks of age represented immune traits pre- and post-maturity, respectively. In the growing period, 1,820 records on ADG, KLH-IgM and NDV-IgG, and 1,559 records on ADFI1 and RFI were available for analyses. In the laying period, 1,340 records on AFE, EM, KLH-IgM and NDV-IgG, and 1,288 records on ADFI2 and RFI were used in the analyses. Bi-variate animal mixed model was fitted to estimate (co)variance components, heritability and correlations among the traits. The model constituted sex, population, generation, line and genotype as fixed effects, and animal and residual effects as random variables. During the growing period, moderate to high heritability (0.36–0.68) was estimated for the production traits and RFI while the antibody traits had low (0.10–0.22) heritability estimates. Post-maturity, the production traits and RFI were moderately (0.30–0.37) heritable while moderate to high (0.25–0.41) heritability was estimated for the antibody traits. Genetic correlations between feed efficiency and production traits in both periods showed that RFI had negative genetic correlations with ADG (−0.47) and EM (−0.56) but was positively correlated with ADFI1 (0.60), ADFI2 (0.74) and AFE (0.35). Among immune and production traits, KLH-IgM and NDV-IgG had negative genetic correlations with ADG (−0.22; −0.56), AFE (−0.39; −0.42) and EM (−0.35; −0.16) but were positively correlated with ADFI1 (0.41; 0.34) and ADFI2 (0.47; 0.52). Genetic correlations between RFI with KLH-IgM (0.62; 0.33) and NDV-IgG (0.58; 0.50) were positive in both production periods. Feed intake, RFI and antibody traits measured in both production periods were positively correlated with estimates ranging from 0.48 to 0.82. Results from this study indicate selection possibilities to improve production, feed efficiency and immune-competence in indigenous chicken. The genetic correlations suggest that improved feed efficiency would be associated with high growth rates, early maturing chicken, high egg mass and reduced feed intake. In contrast, improved general (KLH-IgM) and specific (NDV-IgG) immunity would result in lower growth rates and egg mass but associated with early sexual maturation and high feed intake. Unfavorable genetic correlations between feed efficiency and immune traits imply that chicken of higher productivity and antibody levels will consume more feed to support both functions. These associations indicate that selective breeding for feed efficiency and immune-competence may have genetic consequences on production traits and should therefore be accounted for in indigenous chicken improvement programs

Abstract Background Reproductive performance plays an important role in animal welfare, health and profitability in animal husbandry and breeding. It is well established that there is a negative correlation between performance and reproduction in dairy cattle. This relationship is being increasingly considered in breeding programs. By elucidating the genetic architecture of underlying reproduction traits, it will be possible to make a more detailed contribution to this. Our study followed two approaches to elucidate this area; in a first part, variance components were estimated for 14 different calving and fertility traits, and then genome-wide association studies were performed for 13 reproduction traits on imputed sequence-level genotypes with subsequent enrichment analyses. Results Variance components analyses showed a low to moderate heritability (h2) for the traits analysed, ranging from 0.014 for endometritis up to 0.271 for stillbirth, indicating variable degrees of variation within the reproduction traits. For genome-wide association studies, we were able to detect genome-wide significant association signals for nine out of 13 analysed traits after Bonferroni correction on chromosome 6, 18 and the X chromosome. In total, we detected over 2700 associated SNPs encircling more than 90 different genes using the imputed whole-genome sequence data. Functional associations were reviewed so far known and potential candidate regions in the proximity of reproduction events were hypothesised. Conclusion Our results confirm previous findings of other authors in a comprehensive cohort including 13 different traits at the same time. Additionally, we identified new candidate genes involved in dairy cattle reproduction and made initial suggestions regarding their potential impact, with special regard to the X chromosome as a putative information source for further research. This work can make a contribution to reveal the genetic architecture of reproduction traits in context of trait specific interactions.

ABSTRACT: The objective of this study was to characterize intestinal phytate degradation and mineral utilization by 2 laying hen strains before and after the onset of egg laying using diets without or with a mineral phosphorus (P) supplement. One offspring of 10 roosters per strain (Lohmann Brown-classic [LB] and Lohmann LSL-classic [LSL]) was sacrificed before (wk 19) and after (wk 24) the onset of egg-laying activity and following 4 wk placement in a metabolic unit. Diets were corn-soybean meal-based and without supplemented P (P-) or with 1 g/kg supplemented P (P+) from monocalcium phosphate. In wk 19 and 24, the blood plasma and digesta of duodenum+jejunum and distal ileum were collected. The concentration of P in blood plasma was higher in hens fed P+ than P- (P < 0.001). In duodenum + jejunum and ileum content, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in P- than in P+ (P ≤ 0.009). In duodenum+jejunum, the concentrations of InsP6, Ins(1,2,4,5,6)P5 and Ins(1,2,3,4,5)P5 were lower in wk 24 than 19 and lower in LSL than LB hens (P < 0.001). The concentration of myo-inositol (MI) in duodenum + jejunum content was lower in wk 19 than 24 (P < 0.001). Following a 4-d total excreta collection, the retained amount of P was higher in P+ than P- (P < 0.001). Phosphorus retention was lower in LB hens fed P- than in other treatments (P × strain: P = 0.039). In the jejunal tissue, some genes related to intracellular InsP metabolism were higher expressed in LB than LSL hens. The renunciation of mineral P increased endogenous phytate degradation, but more P was retained with supplemented P. Differences in endogenous phytate degradation between the periods before and after the onset of egg laying might be attributed to different Ca concentrations in intestinal digesta caused by different Ca needs in both periods.

ABSTRACT: The cost benefits of herd genotyping and the benefits of using sexed semen have been affected by recent improvements in sexing technologies, incorporation of direct health traits in the German total merit index for Holstein cattle, deteriorating prices for purebred heifer calves and bull calves, and introduction of herd genotyping programs. Inseminating genetically superior dams with female-sexed Holstein semen increases the mean breeding value of heifer calves and can produce more Holstein heifer calves than are needed for replacement. This provides an opportunity to increase the selection response in health and production traits at the farm level. A deterministic model is introduced that predicts the increase or decrease in net profit when a farmer takes part in a herd genotyping program and follows a certain insemination strategy. The types of semen allocated to cows and heifers may be sexed or unsexed and Holstein or beef breed. Genetically superior heifers and cows are inseminated with female-sexed Holstein semen, intermediate dams with unsexed Holstein semen, and genetically inferior dams with unsexed or male-sexed beef breed semen. In general, participating in a herd genotyping program is beneficial for German Holstein breeders. The optimum proportions of cows and heifers that should be inseminated with a certain type of semen are sensitive to farm-specific peculiarities. A small price difference between crossbred bull calves and crossbred heifer calves often makes the use of male-sexed beef breed semen uneconomic. Under the conditions considered, it was found to be advantageous to inseminate approximately 50% of heifers and 10% of cows with the highest genetic merit with female-sexed Holstein semen. The optimum proportion of cows that should be inseminated with unsexed beef breed semen was found to be approximately 40%. In a herd with a low replacement rate, the selected heifers can exhibit their genetic superiority over a longer period of time, and a larger proportion of cows can be inseminated with beef breed semen. Participation in a herd genotyping program is, therefore, particularly beneficial for herds with low replacement rates.

Abstract Background Claw diseases and mastitis represent the most important health issues in dairy cattle with a frequently mentioned connection to milk production. Although many studies have aimed at investigating this connection in more detail by estimating genetic correlations, they do not provide information about causality. An alternative is to carry out Mendelian randomization (MR) studies using genetic variants to investigate the effect of an exposure on an outcome trait mediated by genetic variants. No study has yet investigated the causal association of milk yield (MY) with health traits in dairy cattle. Hence, we performed a MR analysis of MY and seven health traits using imputed whole-genome sequence data from 34,497 German Holstein cows. We applied a method that uses summary statistics and removes horizontal pleiotropic variants (having an effect on both traits), which improves the power and unbiasedness of MR studies. In addition, genetic correlations between MY and each health trait were estimated to compare them with the estimates of causal effects that we expected. Results All genetic correlations between MY and each health trait were negative, ranging from − 0.303 (mastitis) to − 0.019 (digital dermatitis), which indicates a reduced health status as MY increases. The only non-significant correlation was between MY and digital dermatitis. In addition, each causal association was negative, ranging from − 0.131 (mastitis) to − 0.034 (laminitis), but the number of significant associations was reduced to five nominal and two experiment-wide significant results. The latter were between MY and mastitis and between MY and digital phlegmon. Horizontal pleiotropic variants were identified for mastitis, digital dermatitis and digital phlegmon. They were located within or nearby variants that were previously reported to have a horizontal pleiotropic effect, e.g., on milk production and somatic cell count. Conclusions Our results confirm the known negative genetic connection between health traits and MY in dairy cattle. In addition, they provide new information about causality, which for example points to the negative energy balance mediating the connection between these traits. This knowledge helps to better understand whether the negative genetic correlation is based on pleiotropy, linkage between causal variants for both trait complexes, or indeed on a causal association.

ABSTRACT: This study aimed to evaluate various selection strategies for adoption in dual-purpose (ICD), meat (ICM) and layer (ICL) breeding goals in indigenous chicken breeding programs. The ICM goal aimed to improve live weight (LW12), daily gain (ADG) and egg weight (EW12) or together with feed efficiency and antibody response. For the ICL goal, age at first egg (AFE) and egg number (EN12) or together with feed efficiency and antibody response were targeted. In the ICD goal, the objective was to improve LW12, ADG, AFE and EN12 or together with feed efficiency and antibody response. Highest total index responses of US$ 49.83, US$ 65.71, and US$ 37.90 were estimated in indices targeting only production traits in the ICD, ICM and ICL goals, respectively. Highest index accuracy estimates of 0.77 and 0.70 were observed in indices that considered production and feed-related traits in the ICD and ICL goals, respectively, while in the ICM goal, the highest estimate of 0.96 was observed in an index targeting only production traits. Inbreeding levels ranged from 0.60 to 1.14% across the various indices considered in the breeding goals. Targeting only production traits in the ICD, ICM and ICL goals required the least number of generations of selection of 7.46, 5.50, and 8.52, respectively, to achieve predefined gains. Generally, a strategy targeting only production traits in a goal was the most optimal but resulted to unfavorable correlated responses in feed efficiency and antibody response. Addition of feed efficiency or/and antibody response in a goal was, however, not attractive due to the decline in total index response and accuracy and increase in inbreeding levels and number of generations of selection. Considering the feed availability and disease challenges in the tropics, choice of including feed efficiency or/and antibody response in the ICD, ICM and ICL goals should depend on targeted production system, resource availability to support breeding activities and magnitude of correlated responses on these traits when not included in the goals.

Abstract Background Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. Results In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits’ genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets’ high effect. Conclusion Our results confirm the connection of milk production and health traits in dairy cattle via the animals’ metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits’ connection in more detail.

Abstract Background In spite of being controversial and raising ethical concerns, the application of gene editing is more likely to be accepted when it contributes to improving animal welfare. One of the animal welfare and ethical issues in chicken breeding is chick culling, the killing of the male layer chicks after hatching due to the poor fattening performance. Although establishing dual-purpose chicken lines could solve this problem, unfavorable genetic correlations between egg and meat production traits hindered their competitiveness. Although it is also controversial in ethical terms, gene editing may accelerate genetic progress in dual-purpose chicken and alleviate the ethical concerns from chick culling. Results The simulation compared the utility improvement in dual-purpose use under two breeding schemes: one consisting in the improvement of the laying hens, and the second in the improvement of a synthetic line obtained from a layer broiler cross. In each breeding scheme, the breeding programs were simulated with and without gene editing. Polygenic breeding values and 500 simulated quantitative trait loci (QTL) with different levels of pleiotropy caused negative correlations between egg production, meat production, and overall health. The results of the simulation demonstrated that genetic gain could be accelerated by at most 81% for several generations if gene editing was used. The actual increase in genetic gain depended on the number of single nucleotide polymorphisms (SNPs) being edited per animal. The rate of genetic improvement became equal in scenarios with and without gene editing after 20 generations. This is because the remaining segregating QTL had small effects and their edition would have negative overall health effects from potential off-target edits. Although gene editing can improve genetic gain in quantitative traits, it can only be recommended as long as QTL with reasonable effect sizes are segregating and detectable. Conclusions This simulation demonstrates the potential of gene editing to accelerate the simultaneous improvement of negatively correlated traits. When the risk of negative consequences from gene editing persists, the number of SNPs to be edited should be chosen carefully to obtain the optimal genetic gain.

As global demand for pork continues to rise, strategies to enhance nitrogen utilization efficiency (NUE) in pig farming have become vital for environmental sustainability. This study explored the relationship between the fecal microbiota, their metabolites, and NUE in crossbreed fattening pigs with a defined family structure. Pigs were kept under standardized conditions and fed in a two-phase feeding regime. In each phase, one fecal sample was collected from each pig. DNA was extracted from a total of 892 fecal samples and subjected to target amplicon sequencing. The results indicated an influence of sire, sampling period (SP), and sex on the fecal microbiota. Streptococcus emerged as a potential biomarker in comparing high and low NUE pigs in SP 1, suggesting a genetic predisposition to NUE regarding the fecal microbiota. All fecal samples were grouped into two enterotype-like clusters named cluster LACTO and cluster CSST. Pigs’ affiliation with enterotype-like clusters altered over time and might be sex-dependent. The stable cluster CSST demonstrated the highest NUE despite containing pigs with lower performance characteristics such as average daily gain, dry matter intake, and daily nitrogen retention. This research contributes with valuable insights into the microbiome’s role in NUE, paving the way for future strategies to enhance sustainable pig production.

Abstract Background The objective of any valid breeding program is to increase the suitability of a breed for its future purposes. The approach most often followed in animal breeding for optimizing breeding goals assumes that the sole desire of the owners is profit maximization. As this assumption is often violated, a generalized approach is needed that does not rely on this assumption. Results The generalized approach is based on the niche concept. The niche of a breed is a set of environments in which a small population of the breed would have a positive population growth rate. Its growth rate depends on demand from prospective consumers and supply from producers. The approach involves defining the niche that is envisaged for the breed and identifying the trait optima that maximize the breed’s adaptation to its envisaged niche within the set of permissible breeding goals. The set of permissible breeding goals is the set of all potential breeding goals that are compatible with animal welfare and could be reached within the planning horizon of the breeding program. In general, the breed’s adaptation depends on the satisfaction of the producers with the animals and on the satisfaction of the consumers with the products produced by the animals. When consumers buy live animals, then the breed needs to adapt to both the environments provided by the producers, and the environments provided by the consumers. The profit function is replaced by a more general adaptedness function that measures the breed’s adaptation to its envisaged niche. Conclusions The proposed approach coincides with the traditional approach if the producers have the sole desire to maximize their income, and if consumer preferences are well reflected by the product prices. If these assumptions are not met, then the traditional approach to breeding goal optimization is unlikely to result in a valid breeding goal. Using the example of companion breeds, this paper shows that the proposed approach has the potential to fill the gap.

Introduction: Genetic improvement of general resilience of dairy cattle is deemed as a part of the solution to low dairy productivity and poor cattle adaptability in sub-Saharan Africa (SSA). While indicators of general resilience have been proposed and evaluated in other regions, their applicability in SSA remains unexplored. This study sought to test the viability of utilizing log-transformed variance (LnVar), autocorrelation (rauto), and skewness (Skew) of deviations in milk yield as indicators of general resilience of dairy cows performing in the tropical environment of Kenya.Methods: Test-day milk yield records of 2,670 first-parity cows performing in three distinct agroecological zones of Kenya were used. To predict expected milk yield, quantile regression was used to model lactation curve for each cow. Subsequently, resilience indicators were defined based on actual and standardized deviations of observed milk yield from the expected milk yield. The genetic parameters of these indicators were estimated, and their associations with longevity and average test-day milk yield were examined.Results: All indicators were heritable except skewness of actual and standardized deviation. The log-transformed variance of actual (LnVar1) and standardized (LnVar2) deviations had the highest heritabilities of 0.19 ± 0.04 and 0.17 ± 0.04, respectively. Auto-correlation of actual (rauto1) and standardized (rauto2) deviations had heritabilities of 0.05 ± 0.03 and 0.07 ± 0.03, respectively. Weak to moderate genetic correlations were observed among resilience indicators. Both rauto and Skew indicators had negligible genetic correlations with both longevity and average test-day milk yield. LnVar1 and LnVar2 were genetically associated with better longevity (rg = −0.47 ± 0.26 and −0.49 ± 0.26, respectively). Whereas LnVar1 suggested that resilient animals produce lower average test-day milk yield, LnVar2 revealed a genetic association between resilience and higher average test-day milk yield.Discussion: Log transformed variance of deviations in milk yield holds a significant potential as a robust resilience indicator for dairy animals performing in SSA. Moreover, standardized as opposed to actual deviations should be employed in defining resilience indicators because the resultant indicator does not inaccurately infer that low-producing animals are inherently resilient. This study offers an opportunity for enhancing the productivity of dairy cattle performing in SSA through selective breeding for resilience to environmental stressors.

ABSTRACT: Claw diseases and mastitis represent the most important disease traits in dairy cattle with increasing incidences and a frequently mentioned connection to milk yield. Yet, many studies aimed to detect the genetic background of both trait complexes via fine-mapping of quantitative trait loci. However, little is known about genomic regions that simultaneously affect milk production and disease traits. For this purpose, several tools to detect local genetic correlations have been developed. In this study, we attempted a detailed analysis of milk production and disease traits as well as their interrelationship using a sample of 34,497 50K genotyped German Holstein cows with milk production and claw and udder disease traits records. We performed a pedigree-based quantitative genetic analysis to estimate heritabilities and genetic correlations. Additionally, we generated GWAS summary statistics, paying special attention to genomic inflation, and used these data to identify shared genomic regions, which affect various trait combinations. The heritability on the liability scale of the disease traits was low, between 0.02 for laminitis and 0.19 for interdigital hyperplasia. The heritabilities for milk production traits were higher (between 0.27 for milk energy yield and 0.48 for fat-protein ratio). Global genetic correlations indicate the shared genetic effect between milk production and disease traits on a whole genome level. Most of these estimates were not significantly different from zero, only mastitis showed a positive one to milk (0.18) and milk energy yield (0.13), as well as a negative one to fat-protein ratio (−0.07). The genomic analysis revealed significant SNPs for milk production traits that were enriched on Bos taurus autosome 5, 6, and 14. For digital dermatitis, we found significant hits, predominantly on Bos taurus autosome 5, 10, 22, and 23, whereas we did not find significantly trait-associated SNPs for the other disease traits. Our results confirm the known genetic background of disease and milk production traits. We further detected 13 regions that harbor strong concordant effects on a trait combination of milk production and disease traits. This detailed investigation of genetic correlations reveals additional knowledge about the localization of regions with shared genetic effects on these trait complexes, which in turn enables a better understanding of the underlying biological pathways and putatively the utilization for a more precise design of breeding schemes.

ABSTRACT: This study sheds light on the genetic complexity and interplay of production, body size, and metabolic health in dairy cattle. Phenotypes for body size-related traits from conformation classification (130,166 animals) and production (101,562 animals) of primiparous German Holstein cows were available. Additionally, 21,992, 16,641, and 7,096 animals were from herds with recordings of the metabolic diseases ketosis, displaced abomasum, and milk fever in first, second, and third lactation. Moreover, all animals were genotyped. Heritabilities of traits and genetic correlations between all traits were estimated and GWAS were performed. Heritability was between 0.240 and 0.333 for production and between 0.149 and 0.368 for body size traits. Metabolic diseases were lowly heritable, with estimates ranging from 0.011 to 0.029 in primiparous cows, from 0.008 to 0.031 in second lactation, and from 0.037 to 0.052 in third lactation. Production was found to have negative genetic correlations with body condition score (BCS; −0.279 to −0.343) and udder depth (−0.348 to −0.419). Positive correlations were observed for production and body depth (0.138–0.228), dairy character (DCH) (0.334–0.422), and stature (STAT) (0.084–0.158). In first parity cows, metabolic disease traits were unfavorably correlated with production, with genetic correlations varying from 0.111 to 0.224, implying that higher yielding cows have more metabolic problems. Genetic correlations of disease traits in second and third lactation with production in primiparous cows were low to moderate and in most cases unfavorable. While BCS was negatively correlated with metabolic diseases (−0.255 to −0.470), positive correlations were found between disease traits and DCH (0.269–0.469) as well as STAT (0.172–0.242). Thus, the results indicate that larger and sharper animals with low BCS are more susceptible to metabolic disorders. Genome-wide association studies revealed several significantly associated SNPs for production and conformation traits, confirming previous findings from literature. Moreover, for production and conformation traits, shared significant signals on Bos taurus autosome (BTA) 5 (88.36 Mb) and BTA 6 (86.40 to 87.27 Mb) were found, implying pleiotropy. Additionally, significant SNPs were observed for metabolic diseases on BTA 3, 10, 14, 17, and 26 in first lactation and on BTA 2, 6, 8, 17, and 23 in third lactation. Overall, this study provides important insights into the genetic basis and interrelations of relevant traits in today's Holstein cattle breeding programs, and findings may help to improve selection decisions.

Abstract Background Structural variants and tandem repeats are relevant sources of genomic variation that are not routinely analyzed in genome wide association studies mainly due to challenging identification and genotyping. Here, we profiled these variants via state-of-the-art strategies in the founder animals of four F2 pig crosses using whole-genome sequence data (20x coverage). The variants were compared at a founder level with the commonly screened SNPs and small indels. At the F2 level, we carried out an association study using imputed structural variants and tandem repeats with four growth and carcass traits followed by a comparison with a previously conducted SNPs and small indels based association study. Results A total of 13,201 high confidence structural variants and 103,730 polymorphic tandem repeats (with a repeat length of 2-20 bp) were profiled in the founders. We observed a moderate to high (r from 0.48 to 0.57) level of co-localization between SNPs or small indels and structural variants or tandem repeats. In the association step 56.56% of the significant variants were not in high LD with significantly associated SNPs and small indels identified for the same traits in the earlier study and thus presumably not tagged in case of a standard association study. For the four growth and carcass traits investigated, many of the already proposed candidate genes in our previous studies were confirmed and additional ones were identified. Interestingly, a common pattern on how structural variants or tandem repeats regulate the phenotypic traits emerged. Many of the significant variants were embedded or nearby long non-coding RNAs drawing attention to their functional importance. Through which specific mechanisms the identified long non-coding RNAs and their associated structural variants or tandem repeats contribute to quantitative trait variation will need further investigation. Conclusions The current study provides insights into the characteristics of structural variants and tandem repeats and their role in association studies. A systematic incorporation of these variants into genome wide association studies is advised. While not of immediate interest for genomic prediction purposes, this will be particularly beneficial for elucidating biological mechanisms driving the complex trait variation.

ABSTRACT: Various aspects of activity, such as spontaneous activity, explorative activity, activity in open-field tests, and hyperactivity syndrome have been explored as causal factors of feather pecking in laying hens, with no clear results. In all previous studies, mean values of activity over different time intervals were used as criteria. Incidental observation of alternated oviposition time in lines selected for high (HFP) and low feather pecking (LFP), supported by a recent study which showed differentially expressed genes related to the circadian clock in the same lines, led to the hypothesis that feather pecking may be related to a disturbed diurnal activity rhythm. Hence activity recordings of a previous generation of these lines have been reanalyzed. Data sets of a total of 682 pullets of 3 subsequent hatches of HFP, LFP, and an unselected control line (CONTR) were used. Locomotor activity was recorded in pullets housed in groups of mixed lines in a deep litter pen on 7 consecutive 13-h light phases, using a radio-frequency identification antenna system. The number of approaches to the antenna system was recorded as a measure of locomotor activity and analyzed using a generalized linear mixed model including hatch, line, time of day and the interactions of hatch × time of day and line × time of day as fixed effects. Significant effects were found for time and the interaction line × time of day but not for line. All lines showed a bimodal pattern of diurnal activity. The peak activity of the HFP in the morning was lower than that of the LFP and CONTR. In the afternoon peak all lines differed with the highest mean in the LFP followed by CONTR and HFP. The present results provide support for the hypothesis that a disturbed circadian clock plays a role in the development of feather pecking.

Strong differences between the selection (indoor fattening) and production environment (pasture fattening) are expected to reduce genetic gain due to possible genotype-by-environment interactions (G × E). To investigate how to adapt a sheep breeding program to a pasture-based production environment, different scenarios were simulated for the German Merino sheep population using the R package Modular Breeding Program Simulator (MoBPS). All relevant selection steps and a multivariate pedigree-based BLUP breeding value estimation were included. The reference scenario included progeny testing at stations to evaluate the fattening performance and carcass traits. It was compared to alternative scenarios varying in the progeny testing scheme for fattening traits (station and/or field). The total merit index (TMI) set pasture-based lamb fattening as a breeding goal, i.e., field fattening traits were weighted. Regarding the TMI, the scenario with progeny testing both in the field and on station led to a significant increase in genetic gain compared with the reference scenario. Regarding fattening traits, genetic gain was significantly increased in the alternative scenarios in which field progeny testing was performed. In the presence of G × E, the study showed that the selection environment should match the production environment (pasture) to avoid losses in genetic gain. As most breeding goals also contain traits not recordable in field testing, the combination of both field and station testing is required to maximize genetic gain.

Abstract Background 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 the impact of host genetics on composition of the ileum microbiota and the relationship of the relative abundance of ileal bacterial genera with phosphorus utilization and related quantitative traits in Japanese quail. An F2 cross of 758 quails was genotyped with 4k genome-wide single nucleotide polymorphisms (SNPs) and composition of the ileum microbiota was characterized using target amplicon sequencing. Heritabilities of the relative abundance of bacterial genera were estimated and quantitative trait locus (QTL) linkage mapping for the host was conducted for the heritable genera. Phenotypic and genetic correlations and recursive relationships between bacterial genera and quantitative traits were estimated using structural equation models. A genomic best linear unbiased prediction (GBLUP) and microbial (M)BLUP hologenomic selection approach was applied to assess the feasibility of breeding for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota. Results Among the 59 bacterial genera examined, 24 showed a significant heritability (nominal p ≤ 0.05), ranging from 0.04 to 0.17. For these genera, six genome-wide significant QTL were mapped. Significant recursive effects were found, which support the indirect host genetic effects on the host’s quantitative traits via microbiota composition in the ileum of quail. Cross-validated microbial and genomic prediction accuracies confirmed the strong impact of microbial composition and host genetics on the host’s quantitative traits, as the GBLUP accuracies based on the heritable microbiota-mediated components of the traits were similar to the accuracies of conventional GBLUP based on genome-wide SNPs. Conclusions Our results revealed a significant effect of host genetics on composition of the ileal microbiota and confirmed that host genetics and composition of the ileum microbiota have an impact on the host’s quantitative traits. This offers the possibility to breed for improved phosphorus utilization based on the host genome and the heritable part of composition of the ileum microbiota.

Feather pecking in chickens is a damaging behavior, seriously impacting animal welfare and leading to economic losses. Feather pecking is a complex trait, which is partly under genetic control. Different hypotheses have been proposed to explain the etiology of feather pecking and notably, several studies have identified similarities between feather pecking and human mental disorders such as obsessive-compulsive disorder and schizophrenia. This study uses transcriptomic and phenotypic data from 167 chickens to map expression quantitative trait loci and to identify regulatory genes with a significant effect on this behavioral disorder using an association weight matrix approach. From 70 of the analyzed differentially expressed genes, 11,790 genome wide significantly associated variants were detected, of which 23 showed multiple associations (≥15). These were located in proximity to a number of genes, which are transcription regulators involved in chromatin binding, nucleic acid metabolism, protein translation and putative regulatory RNAs. The association weight matrix identified 36 genes and the two transcription factors: SP6 (synonym: KLF14) and ENSGALG00000042129 (synonym: CHTOP) as the most significant, with an enrichment of KLF14 binding sites being detectable in 40 differentially expressed genes. This indicates that differential expression between animals showing high and low levels of feather pecking was significantly associated with a genetic variant in proximity to KLF14. This multiallelic variant was located 652 bp downstream of KLF14 and is a deletion of 1-3 bp. We propose that a deletion downstream of the transcription factor KLF14 has a negative impact on the level of T cells in the developing brain of high feather pecking chickens, which leads to developmental and behavioral abnormalities. The lack of CD4 T cells and gamma-Aminobutyric acid (GABA) receptors are important factors for the increased propensity of laying hens to perform feather pecking. As such, KLF14 is a clear candidate regulator for the expression of genes involved in the pathogenic development. By further elucidating the regulatory pathways involved in feather pecking we hope to take significant steps forward in explaining and understanding other mental disorders, not just in chickens.

The objective of this study was to compare 2 laying hen strains in 5 production periods regarding phytase activity, phytate (InsP6) degradation, and myo-inositol (MI) release in the digestive tract and phosphorus (P) and calcium (Ca) utilization. One offspring of 10 nonrelated roosters per strain (Lohmann Brown-classic (LB) or Lohmann LSL-classic (LSL)) was placed in one of 20 metabolic units in a completely randomized block design in week 8, 14, 22, 28, and 58 of life. All hens were fed the same corn and soybean meal–based diet at one time, but the diet composition was adjusted to the requirements in the respective period. For 4 consecutive days, excreta were collected quantitatively at 24-hour intervals. In week 10, 16, 24, 30, and 60, the blood plasma, digesta of crop, gizzard, jejunum, ileum, and ceca, and mucosa of the jejunum was collected. The concentration of inorganic P in the blood plasma was higher in LB than in LSL hens (P = 0.026). Plasma Ca concentrations increased with each period (P

Abstract Background Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic variants and affected genes that lead to FP behavior. To achieve that we imputed low-density genotypes from two different populations of layers divergently selected for FP to sequence level by performing whole genome sequencing on founder and half-sib individuals. In order to decipher the genetic structure of FP, genome wide association studies and meta-analyses of two resource populations were carried out by focusing on the traits ‘feather pecks delivered’ (FPD) and the ‘posterior probability of a hen to belong to the extreme feather pecking subgroup’ (pEFP). Results In this meta-analysis, we discovered numerous genes that are affected by polymorphisms significantly associated with the trait FPD. Among them SPATS2L, ZEB2, KCHN8, and MRPL13 which have been previously connected to psychiatric disorders with the latter two being responsive to nicotine treatment. Gene set enrichment analysis revealed that phosphatidylinositol signaling is affected by genes identified in the GWAS and that the Golgi apparatus as well as brain structure may be involved in the development of a FP phenotype. Further, we were able to validate a previously discovered QTL for the trait pEFP on GGA1, which contains variants affecting NIPA1, KIAA1211L, AFF3, and TSGA10. Conclusions We provide evidence for the involvement of numerous genes in the propensity to exhibit FP behavior that could aid in the selection against this unwanted trait. Furthermore, we identified variants that are involved in phosphatidylinositol signaling, Golgi metabolism and cell structure and therefore propose changes in brain structure to be an influential factor in FP, as already described in human neuropsychiatric disorders.

Abstract Background Feather pecking (FP) in laying hens reduces animal welfare and leads to economic losses for the layer industry. FP is considered a heritable condition that is influenced by dysregulation of neurotransmitter homeostasis, the gut microbiome, and the immune system. To identify genes and biological pathways responsible for FP behavior we compared the brain transcriptomes of 48 hens divergently selected for FP. In addition, we tested if high feather peckers (HFP) and low feather peckers (LFP) respond differently to light since light has been shown to trigger FP behavior. Results Of approximately 48 million reads/sample an average of 98.4% were mapped to the chicken genome (GRCg6a). We found 13,070 expressed genes in the analyzed brains of which 423 showed differential expression between HFP and LFP. Genes of uncertain function and non-coding RNAs were overrepresented among those transcripts. Functional analyses revealed the involvement of cholinergic signaling, postsynaptic activity, membrane channels, and the immune system. After the light stimulus, 28 genes were found to be differentially expressed. These included an interaction cluster of core components of the circadian clock. However, differences in the response to light between HFP and LFP were not detectable. Conclusions Genes involved in cholinergic signaling, channel activity, synaptic transmission, and immune response were found to be involved in FP behavior. We propose a model in which the gut microbiota modulates the immune system, which in turn affects cholinergic signaling. This might have an influence on monoamine signaling with possible involvement of GABA or glutamate signaling.

It is well known that mammals and avian gut microbiota compositions are shaped by the host genomes and affect quantitative traits. The microbial architecture describes the impact of the microbiota composition on quantitative trait variation and the number and effect distribution of microbiota features. In the present study the gut microbial architecture of feed-related traits phosphorus and calcium utilization, daily gain, feed intake and feed per gain ratio in the domestic poultry model species Japanese quail were assessed by mixed linear models. The ileum microbiota composition was characterized by 16S rRNA amplicon sequencing techniques of growing individuals. The microbiability of the traits was on a similar level as the narrow sense heritability and was highly significant except for calcium utilization. The animal microbial correlation of the traits was substantial. Microbiome-wide association analyses revealed several traits associated and highly significant microbiota features, both on the bacteria genera as well as on the operational taxonomic unit level. Most features were significant for more than one trait, which explained the high microbial correlations. It can be concluded that the traits are polymicrobial determined with some microbiota features with larger effects and many with small effects. The results are important for the development of hologenomic selection schemes for feed-related traits in avian breeding programs that are targeting the host genome and the metagenome simultaneously.

Numerically small breeds have often been upgraded with mainstream breeds. This historic introgression predisposes the breeds for joint genomic evaluations with mainstream breeds. The linkage disequilibrium structure differs between breeds. The marker effects of a haplotype segment may, therefore, depend on the breed from which the haplotype segment originates. An appropriate method for genomic evaluation would account for this dependency. This study proposes a method for the computation of genomic breeding values for small admixed breeds that incorporate phenotypic and genomic information from large introgressed breeds by considering the breed origin of alleles (BOA) in the evaluation. The proposed BOA model classifies haplotype segments according to their origins and assumes different but correlated SNP effects for the different origins. The BOA model was compared in a simulation study to conventional within-breed genomic best linear unbiased prediction (GBLUP) and conventional multi-breed GBLUP models. The BOA model outperformed within-breed GBLUP as well as multi-breed GBLUP in most cases.

In order to gain insight into the genetic architecture of economically important traits in pigs and to derive suitable genetic markers to improve these traits in breeding programs, many studies have been conducted to map quantitative trait loci. Shortcomings of these studies were low mapping resolution, large confidence intervals for quantitative trait loci-positions and large linkage disequilibrium blocks. Here, we overcome these shortcomings by pooling four large F2 designs to produce smaller linkage disequilibrium blocks and by resequencing the founder generation at high coverage and the F1 generation at low coverage for subsequent imputation of the F2 generation to whole genome sequencing marker density. This lead to the discovery of more than 32 million variants, 8 million of which have not been previously reported. The pooling of the four F2 designs enabled us to perform a joint genome-wide association study, which lead to the identification of numerous significantly associated variant clusters on chromosomes 1, 2, 4, 7, 17 and 18 for the growth and carcass traits average daily gain, back fat thickness, meat fat ratio, and carcass length. We could not only confirm previously reported, but also discovered new quantitative trait loci. As a result, several new candidate genes are discussed, among them BMP2 (bone morphogenetic protein 2), which we recently discovered in a related study. Variant effect prediction revealed that 15 high impact variants for the traits back fat thickness, meat fat ratio and carcass length were among the statistically significantly associated variants.

Improved utilization of phytates and mineral phosphorus (P) in monogastric animals contributes significantly to preserving the finite resource of mineral P and mitigating environmental pollution. In order to identify pathways and to prioritize candidate genes related to P utilization (PU), the genomic heritability of 77 and 80 trait-dependent expressed miRNAs and mRNAs in 482 Japanese quail were estimated and eQTL (expression quantitative trait loci) were detected. In total, 104 miR-eQTL (microRNA expression quantitative traits loci) were associated with SNP markers (false discovery rate less than 10%) including 41 eQTL of eight miRNAs. Similarly, 944 mRNA-eQTL were identified at the 5% False discovery rate threshold, with 573 being cis-eQTL of 36 mRNAs. High heritabilities of miRNA and mRNA expression coincide with highly significant eQTL. Integration of phenotypic data with transcriptome and microbiome data of the same animals revealed genetic regulated mRNA and miRNA transcripts (SMAD3, CAV1, ENNPP6, ATP2B4, miR-148a-3p, miR-146b-5p, miR-16-5p, miR-194, miR-215-5p, miR-199-3p, miR-1388a-3p) and microbes (Candidatus Arthromitus, Enterococcus) that are associated with PU. The results reveal novel insights into the role of mRNAs and miRNAs in host gut tissue functions, which are involved in PU and other related traits, in terms of the genetic regulation and inheritance of their expression and in association with microbiota components.

Livestock breeding has shifted during the past decade toward genomic selection. For the estimation of breeding values in purebred breeding schemes, genomic best linear unbiased prediction has become the method of choice. Systematic crossbreeding with the aim to utilize heterosis and breed complementary effects is widely used in livestock breeding, especially in pig and poultry breeding. The goal is to improve the performance of the crossbred animals. Due to genotype-by-environment interactions, imperfect linkage disequilibrium, and the existence of dominance and imprinting, purebred and crossbred performances are not perfectly correlated. Hence, more complex genomic models are required for crossbred populations. This study reviews and compares such models. Compared to purebred genomic models, the reviewed models were of much higher complexity due to the inclusion of dominance effects, breed-specific effects, imprinting effects, and the joint evaluation of purebred and crossbred performance data. With the model assessment work conducted until now, it is not possible to come to a clear recommendation as to which existing method is most suitable for a specific breeding program and a specific genetic trait architecture. Since it is expected that a superior method includes all the different genetic effects in a single model, a dominance model with imprinting and breed-specific SNP effects is proposed. Further progress could be made by assuming realistic covariance structures between the genetic effects of the different breeding lines, and by using larger marker panels and mixture distributions for the SNP effects.

Abstract Background During the last two decades, many QTL (quantitative trait locus) mapping experiments in pigs have been conducted using F2 crosses established from two outbred founder breeds. The founder breeds were frequently chosen from the Asian and European type breeds. A combination of next-generation sequencing, SNP (single nucleotide polymorphism) genotyping technology using SNP-chips, and genotype imputation techniques, can be used to infer the sequence information of all F2 individuals in a cost-effective way. The aim of the present simulation study was to analyze the power and precision of genome-wide association studies (GWASs) with whole-genome sequence data in several types of F2 crosses, including pooled crosses. Methods Based on a common historical population, three breeds representing two European type breeds (EU1 and EU2) and one Asian type breed (AS) were simulated. Two F2 designs of 500 individuals each were simulated. The cross EU1xEU2 (ASxEU2) was simulated using the phylogenetically closely related breeds EU1 and EU2 (or distantly related breeds AS and EU2) as the founder breeds. The simulated genomes comprised ten chromosomes, each with a length of 1 Morgan and whole-genome sequence information. A polygenic trait with a heritability of 0.5, which was affected by approximately 20 QTL per Morgan, was simulated. GWASs were conducted using single marker mixed linear models, either within the crosses or in their pooled datasets. Additionally, the studies were conducted in the breed EU2, which was a founder breed in both simulated crosses. Results The power to map QTL was high (low) in the ASxEU2 (EU1xEU2) cross and was highest when the data of both crosses were analyzed jointly. By contrast, the mapping precision was the highest in the EU1xEU2 cross. Pooling data led to a precision that was in between the precision of the EU1xEU2 cross and the ASxEU2 cross. A higher mapping precision was observed for QTL segregating within a founder breed. Conclusions These results suggest that the existing F2 crosses are promising databases for QTL mapping when the founder breeds are closely related or several crosses can be pooled. This conclusion is particularly applicable for QTL that segregate in a founder breed.

The long-term performance of different selection strategies was evaluated via simulation using the example of a local cattle breed, German Angler cattle. Different optimum contribution selection (OCS) approaches to maximize genetic gain were compared to a reference scenario without selection and truncation selection. The kinships and migrant contribution (MC) were estimated from genomic data. Truncation selection achieved the highest genetic gain but decreased diversity considerably at native alleles. It also caused the highest increase in MCs. Traditional OCS, which only constrains kinship, achieved almost the same genetic gain but also caused a small increase of MC and remarkably reduced the diversity of native alleles. When MC was required not to increase and the increase of kinship at native alleles was restricted, the MC levels and the diversity at native alleles were well managed, and the genetic gain was only slightly reduced. However, genetic progress was substantially lower in the scenario that aimed to recover the original genetic background. Truncation selection and traditional OCS selection both reduce the genetic originality of breeds with historical introgression. The inclusion of MC and kinship at native alleles as additional constraints in OCS showed great potential for conservation. Recovery of the original genetic background is possible but requires many generations of selection and reduces the genetic progress in performance traits. Hence, constraining MCs at their current values can be recommended to avoid further reduction of genetic originality.

Abstract Background Optimum contribution selection (OCS) is effective for increasing genetic gain, controlling the rate of inbreeding and enables maintenance of genetic diversity. However, this diversity may be caused by high migrant contributions (MC) in the population due to introgression of genetic material from other breeds, which can threaten the conservation of small local populations. Therefore, breeding objectives should not only focus on increasing genetic gains but also on maintaining genetic originality and diversity of native alleles. This study aimed at investigating whether OCS was improved by including MC and modified kinships that account for breed origin of alleles. Three objective functions were considered for minimizing kinship, minimizing MC and maximizing genetic gain in the offspring generation, and we investigated their effects on German Angler and Vorderwald cattle. Results In most scenarios, the results were similar for Angler and Vorderwald cattle. A significant positive correlation between MC and estimated breeding values of the selection candidates was observed for both breeds, thus traditional OCS would increase MC. Optimization was performed under the condition that the rate of inbreeding did not exceed 1% and at least 30% of the maximum progress was achieved for all other criteria. Although traditional OCS provided the highest breeding values under restriction of classical kinship, the magnitude of MC in the progeny generation was not controlled. When MC were constrained or minimized, the kinship at native alleles increased compared to the reference scenario. Thus, in addition to constraining MC, constraining kinship at native alleles is required to ensure that native genetic diversity is maintained. When kinship at native alleles was constrained, the classical kinship was automatically lowered in most cases and more sires were selected. However, the average breeding value in the next generation was also lower than that obtained with traditional OCS. Conclusions For local breeds with historical introgressions, current breeding programs should focus on increasing genetic gain and controlling inbreeding, as well as maintaining the genetic originality of the breeds and the diversity of native alleles via the inclusion of MC and kinship at native alleles in the OCS process.

Population management has the primary task of maximizing the long-term competitiveness of a breed. Breeds compete with each other for being able to supply consumer demands at low costs and also for funds from conservation programs. The competition for consumer preference is won by breeds with high genetic gain for total merit who maintained a sufficiently high genetic diversity, whereas the competition for funds is won by breeds with high conservation value. The conservation value of a breed could be improved by increasing its contribution to the gene pool of the species. This may include the recovery of its original genetic background and the maintenance of a high genetic diversity at native haplotype segments. The primary objective of a breeding program depends on the genetic state of the population and its intended usage. In this paper, we review the key genetic parameters that are relevant for population management, compare the methods for estimating them, derive the formulas for predicting their value at a future time, and clarify their usage in various types of breeding programs that differ in their main objectives. These key parameters are kinships, native kinships, breeding values, Mendelian sampling variances, native contributions, and mutational effects. Population management currently experiences a transition from using pedigree-based estimates to marker-based estimates, which improves the accuracies of these estimates and thereby increases response to selection. In addition, improved measures of the factors that determine the competitiveness of a breed and utilize auxiliary parameters, such as Mendelian sampling variances, mutational effects, and native kinships, enable to improve further upon historic recommendations for genetic population management.

Mitochondria are essential components of eukaryotes as they are involved in several organismic key processes such as energy production, apoptosis and cell growth. Despite their importance for the metabolism and physiology of all eukaryotic organisms, the impact of mitochondrial haplotype variation has only been studied for very few species. In this study we sequenced the mitochondrial genome of 180 individuals from two different strains of laying hens. The resulting haplotypes were combined with performance data such as body weight, feed intake and phosphorus utilization to assess their influence on the hens in five different life stages. After detecting a surprisingly low level of genetic diversity, we investigated the nuclear genetic background to estimate whether the low mitochondrial diversity is representative for the whole genetic background of the strains. Our results highlight the need for more in-depth investigation of the genetic compositions and mito-nuclear interaction in individuals to elucidate the basis of phenotypic performance differences. In addition, we raise the question of how the lack of mitochondrial variation developed, since the mitochondrial genome represents genetic information usually not considered in breeding approaches.

Background: Feather pecking is a well-known problem in layer flocks that causes animal welfare restrictions and contributes to economic losses. Birds’ gut microbiota has been linked to feather pecking. This study aims to characterize the microbial communities of two laying hen lines divergently selected for high (HFP) and low (LFP) feather pecking and investigates if the microbiota is associated with feather pecking or agonistic behavior. Methods: Besides phenotyping for the behavioral traits, microbial communities from the digesta and mucosa of the ileum and caeca were investigated using target amplicon sequencing and functional predictions. Microbiability was estimated with a microbial mixed linear model. Results: Ileum digesta showed an increase in the abundance of the genus Lactobacillus in LFP, while Escherichia was abundant in HFP hens. In the caeca digesta and mucosa of the LFP line were more abundant Faecalibacterium and Blautia. Tryptophan metabolism and lysine degradation were higher in both digesta and mucosa of the HFP hens. Linear models revealed that the two lines differ significantly in all behavior traits. Microbiabilities were close to zero and not significant in both lines and for all traits. Conclusions: Trait variation was not affected by the gut microbial composition in both selection lines.

In this study, we aimed to investigate the ileum digesta of a large cohort of Japanese quail fed the same diet, with similar environmental conditions. We also address how P utilization (PU), Ca utilization (CaU), and bird performance (feed intake (FI), feed conversion (FC), and body weight gain (BWG)) modify intestinal microbiota of male and female quail. Despite the great number of samples analyzed (760), a core microbiome was composed of five bacteria. The Unc. Lactobacillus, Unc. Clostridaceae 1, Clostridium sensu stricto, Escherichia coli, and Streptococcus alactolyticus were detected in all samples and contributed to more than 70% of the total community. Depending on the bird predisposition for PU, CaU, FI, BWG, and FC, those species were present in higher or lower abundances. There was a significant gender effect on the ileal microbial community. While females had higher abundances of Lactobacillus, males were more colonized by Streptococcus alactolyticus. The entire cohort was highly colonized by Escherichia coli (8%–15%), an enteropathogenic bacteria. It remains unclear, if microbiota composition followed the mechanisms that caused different PU, CaU, FI, FC, and BWG or if the change in microbiota composition and function caused the differences in PU, CaU, and performance traits.

Feather pecking (FP) is a longstanding serious problem in commercial flocks of laying hens. It is a highly polygenic trait and the genetic background is still not completely understood. In order to find genomic regions influencing FP, selection signatures between laying hen lines divergently selected for high and low feather pecking were mapped using the intra-population iHS and the inter-population FST approach. In addition, the existence of an extreme subgroup of FP hens (EFP) across both selected lines has been demonstrated by fitting a mixture of negative binomial distributions to the data and calculating the posterior probability of belonging to the extreme subgroup (pEFP) for each hen. A genomewide association study (GWAS) was performed for the traits pEFP and FP delivered (FPD) with a subsequent post GWAS analysis. Mapping of selection signatures revealed no clear regions under selection. GWAS revealed a region on Chromosome 1, where the existence of a QTL influencing FP is likely. The candidate genes found in this region are a part of the GABAergic system, which has already been linked to FP in previous studies. Despite the polygenic nature of FP, selection on these candidate genes may reduce FP.

Genome-wide association studies (GWAS) have been widely used in the genetic dissection of complex traits. As more genomic data is being generated within different commercial or resource pig populations, the challenge which arises is how to collectively investigate the data with the purpose to increase sample size and implicitly the statistical power. This study performs an individual population GWAS, a joint population GWAS and a meta-analysis in three pig F2 populations. D1 is derived from European type breeds (Piétrain, Large White and Landrace), D2 is obtained from an Asian breed (Meishan) and Piétrain, and D3 stems from a European Wild Boar and Piétrain, which is the common founder breed. The traits investigated are average daily gain, backfat thickness, meat to fat ratio and carcass length. The joint and the meta-analysis did not identify additional genomic clusters besides the ones discovered via the individual population GWAS. However, the benefit was an increased mapping resolution which pinpointed to narrower clusters harboring causative variants. The joint analysis identified a higher number of clusters as compared to the meta-analysis; nevertheless, the significance levels and the number of significant variants in the meta-analysis were generally higher. Both types of analysis had similar outputs suggesting that the two strategies can complement each other and that the meta-analysis approach can be a valuable tool whenever access to raw datasets is limited. Overall, a total of 20 genomic clusters that predominantly overlapped at various extents, were identified on chromosomes 2, 7 and 17, many confirming previously identified quantitative trait loci. Several new candidate genes are being proposed and, among them, a strong candidate gene to be taken into account for subsequent analysis is BMP2 (bone morphogenetic protein 2).

Damaging behaviors, like feather pecking (FP), have large economic and welfare consequences in the commercial laying hen industry. Selective breeding can be used to obtain animals that are less likely to perform damaging behavior on their pen-mates. However, with the growing tendency to keep birds in large groups, identifying specific birds that are performing or receiving FP is difficult. With current developments in sensor technologies, it may now be possible to identify laying hens in large groups that show less FP behavior and select them for breeding. We propose using a combination of sensor technology and genomic methods to identify feather peckers and victims in groups. In this review, we will describe the use of “-omics„ approaches to understand FP and give an overview of sensor technologies that can be used for animal monitoring, such as ultra-wideband, radio frequency identification, and computer vision. We will then discuss the identification of indicator traits from both sensor technologies and genomics approaches that can be used to select animals for breeding against damaging behavior.