Genome-Wide Association Analysis of Semen Characteristics in Piétrain Boars.

Since artificial insemination is common practice in pig breeding, the quality and persistence of the semen are decisive for the usability of individual boars. In the current study, genome-wide association analyses were performed to investigate the genetic variability underlying phenotypic variations in semen characteristics. These traits comprise sperm morphology and sperm motility under different temporal and thermal storage conditions, in addition to standard semen quality parameters. Two consecutive samples of the fourth and fifth ejaculates from the same boar were comprehensively analyzed in a genotyped Piétrain boar population. A total of 13 genomic regions on different chromosomes were identified that contain single-nucleotide polymorphisms significantly associated with these traits. Subsequent analysis of the genomic regions revealed candidate genes described to be involved in spermatogenesis, such as FOXL3, GPER1, PDGFA, PRKAR1B, SNRK, SUN1, and TSPO, and sperm motility, including ARRDC4, CEP78, DNAAF5, and GPER1. Some of these genes were also associated with male fertility or infertility in mammals (e.g., CEP78, GPER1). The analyses based on these laboriously determined and valuable phenotypes contribute to a better understanding of the genetic background of male fertility traits in pigs and could prospectively contribute to the improvement of sperm quality through breeding approaches.

Multivariate genome-wide associations for immune traits in two maternal pig lines.

BACKGROUND: Immune traits are considered to serve as potential biomarkers for pig's health. Medium to high heritabilities have been observed for some of the immune traits suggesting genetic variability of these phenotypes. Consideration of previously established genetic correlations between immune traits can be used to identify pleiotropic genetic markers. Therefore, genome-wide association study (GWAS) approaches are required to explore the joint genetic foundation for health biomarkers. Usually, GWAS explores phenotypes in a univariate (uv), trait-by-trait manner. Besides two uv GWAS methods, four multivariate (mv) GWAS approaches were applied on combinations out of 22 immune traits for Landrace (LR) and Large White (LW) pig lines. RESULTS: In total 433 (LR: 351, LW: 82) associations were identified with the uv approach implemented in PLINK and a Bayesian linear regression uv approach (BIMBAM) software. Single Nucleotide Polymorphisms (SNPs) that were identified with both uv approaches (n = 32) were mostly associated with immune traits such as haptoglobin, red blood cell characteristics and cytokines, and were located in protein-coding genes. Mv GWAS approaches detected 647 associations for different mv immune trait combinations which were summarized to 133 Quantitative Trait Loci (QTL). SNPs for different trait combinations (n = 66) were detected with more than one mv method. Most of these SNPs are associated with red blood cell related immune trait combinations. Functional annotation of these QTL revealed 453 immune-relevant protein-coding genes. With uv methods shared markers were not observed between the breeds, whereas mv approaches were able to detect two conjoint SNPs for LR and LW. Due to unmapped positions for these markers, their functional annotation was not clarified. CONCLUSIONS: This study evaluated the joint genetic background of immune traits in LR and LW piglets through the application of various uv and mv GWAS approaches. In comparison to uv methods, mv methodologies identified more significant associations, which might reflect the pleiotropic background of the immune system more accurately. In genetic research of complex traits, the SNP effects are generally small. Furthermore, one genetic variant can affect several correlated immune traits at the same time, termed pleiotropy. As mv GWAS methods consider strong dependencies among traits, the power to detect SNPs can be boosted. Both methods revealed immune-relevant potential candidate genes. Our results indicate that one single test is not able to detect all the different types of genetic effects in the most powerful manner and therefore, the methods should be applied complementary.

Characteristics of thermal images of the mammary gland and of performance in sows differing in health status and parity.

Precision livestock farming can combine sensors and complex data to provide a simple score of meaningful productivity, pig welfare, and farm sustainability, which are the main drivers of modern pig production. Examples include using infrared thermography to monitor the temperature of sows to detect the early stages of the disease. To take account of these drivers, we assigned 697 hybrid (BHZP db. Viktoria) sows to four parity groups. In addition, by pooling clinical findings from every sow and their piglets, sows were classified into three groups for the annotation: healthy, clinically suspicious, and diseased. Besides, the udder was thermographed, and performance data were documented. Results showed that the piglets of diseased sows with eighth or higher parity had the lowest daily weight gain [healthy; 192 g ± 31.2, clinically suspicious; 191 g ± 31.3, diseased; 148 g ± 50.3 (p < 0.05)] and the highest number of stillborn piglets (healthy; 2.2 ± 2.39, clinically suspicious; 2.0 ± 1.62, diseased; 3.91 ± 4.93). Moreover, all diseased sows showed higher maximal skin temperatures by infrared thermography of the udder (p < 0.05). Thus, thermography coupled with Artificial Intelligence (AI) systems can help identify and orient the diagnosis of symptomatic animals to prompt adequate reaction at the earliest time.

Genetic parameters of immune traits for Landrace and Large White pig breeds.

Improving the immunocompetence towards pathogens represents a desirable objective of breeding strategies to increase resilience. However, the immune system is complex and the genetic foundation of the underlying components is not yet clarified. In the present study, we focused on 22 blood parameters of 1,144 Landrace (LR) and Large White (LW) piglets at the age of 6-7 weeks. The immune profiles covered immune cells, red blood cell characteristics and cytokines. Genetic parameters based on pedigree information along with possible environmental effects were estimated. Litter effects play an important role in the expression of immune parameters of their young progenies. Hence, litter impacts on the piglet's immune profile including the immune parameters of the dam itself were investigated by different models. To incorporate the complexity of the immune network, the data were further investigated with a principal component analysis. Immune traits showed low to high breed-specific heritabilities (h2 ). Strong positive rg were estimated among red blood cell characteristics (0.77-0.99) and among cytokines (0.48-0.99). Neutrophils and lymphocytes illustrated a high negative rg (-0.96 to -0.98). The litter impact on piglet's immunity was examined and strengthened already observed breed differences. In LR, h2 (0.22-0.15) and litter effect (c2 ) (0.52-0.44) for IFN-γ decreased after statistical consideration of maternal impact. In LW, a decrease in h2 (0.32-0.18) for IFN-γ and an increase in c2 (0.54-0.56) were observed. Here, sufficient correlations were detected within various immune traits and functional biological networks of principal components. Most immune traits are heritable and are promising to cover global breed-specific immunocompetence in pigs. The analysis of immune traits has to be extended in order to find an optimal range and to characterize relationships between immunity and performance to gain an improved immune system without accidental losses in productivity.

Comparison of the choice of animals for re-sequencing in two maternal pig lines.

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 analysis of the literature shows that several strategies are available to select animals for re-sequencing. This study demonstrates an animal selection workflow under practical conditions. Our approach considers different data sources and limited resources such as budget and availability of sampling material. The workflow combines previously described approaches and makes use of genotype and pedigree information from a Landrace and Large White population. Genotypes were phased and haplotypes were accurately estimated with AlphaPhase. Then, AlphaSeqOpt was used to optimize selection of animals for re-sequencing, reflecting the existing diversity of haplotypes. AlphaSeqOpt and ENDOG were used to select individuals based on pedigree information and by taking into account key animals that represent the genetic diversity of the populations. After the best selection criteria were determined, a subset of 57 animals was selected for subsequent re-sequencing. In order to evaluate and assess the advantage of this procedure, imputation accuracy was assessed by setting a set of single nucleotide polymorphism (SNP) chip genotypes to missing. Accuracy values were compared to those of alternative selection scenarios and the results showed the clear benefits of a targeted selection within this practical-driven approach. Especially imputation of low-frequency markers benefits from the combined approach described here. Accuracy was increased by up to 12% compared to a randomized or exclusively haplotype-based selection of sequencing candidates.

Genome-wide associations for immune traits in two maternal pig lines.

BACKGROUND: In recent years, animal welfare and health has become more and more important in pig breeding. So far, numerous parameters have been considered as important biomarkers, especially in the immune reaction and inflammation. Previous studies have shown moderate to high heritabilities in most of these traits. However, the genetic background of health and robustness of pigs needs to be extensively clarified. The objective of this study was to identify genomic regions with a biological relevance for the immunocompetence of piglets. Genome-wide Association Studies (GWAS) in 535 Landrace (LR) and 461 Large White (LW) piglets were performed, investigating 20 immune relevant traits. Besides the health indicators of the complete and differential blood count, eight different cytokines and haptoglobin were recorded in all piglets and their biological dams to capture mediating processes and acute phase reactions. Additionally, all animals were genotyped using the Illumina PorcineSNP60v2 BeadChip. RESULTS: In summary, GWAS detected 25 genome-wide and 452 chromosome-wide significant SNPs associated with 17 immune relevant traits in the two maternal pig lines LR and LW. Only small differences were observed considering the maternal immune records as covariate within the statistical model. Furthermore, the study identified across- and within-breed differences as well as relevant candidate genes. In LR more significant associations and related candidate genes were detected, compared with LW. The results detected in LR and LW are partly in accordance with previously identified quantitative trait loci (QTL) regions. In addition, promising novel genomic regions were identified which might be of interest for further detailed analysis. Especially putative pleiotropic regions on SSC5, SSC12, SSC15, SSC16 and SSC17 are of major interest with regard to the interacting structure of the immune system. The comparison with already identified QTL gives indications on interactions with traits affecting piglet survival and also production traits. CONCLUSION: In conclusion, results suggest a polygenic and breed-specific background of immune relevant traits. The current study provides knowledge about regions with biological relevance for health and immune traits. Identified markers and putative pleiotropic regions provide first indications in the context of balancing a breeding-based modification of the porcine immune system.

Genomic background and genetic relationships between boar taint and fertility traits in German Landrace and Large White.

BACKGROUND: Due to ethical reasons, surgical castration of young male piglets in their first week of life without anesthesia will be banned in Germany from 2021. Breeding against boar taint is already implemented in sire breeds of breeding organizations but in recent years a low demand made this trait economically less important. The objective of this study was to estimate heritabilities and genetic relationships between boar taint compounds androstenone and skatole and maternal/paternal reproduction traits in 4'924 Landrace (LR) and 4'299 Large White (LW) animals from nucleus populations. Additionally, genome wide association analysis (GWAS) was performed per trait and breed to detect SNP marker with possible pleiotropic effects that are associated with boar taint and fertility. RESULTS: Estimated heritabilities (h2) were 0.48 (±0.08) for LR (0.39 ± 0.07 for LW) for androstenone and 0.52 (±0.08) for LR (0.32 ± 0.07 for LW) for skatole. Heritabilities for reproduction did not differ between breeds except age at first insemination (LR: h2 = 0.27 (±0.05), LW: h2 = 0.34 (±0.05)). Estimates of genetic correlation (rg) between boar taint and fertility were different in LR and LW breeds. In LR an unfavorable rg of 0.31 (±0.15) was observed between androstenone and number of piglets born alive, whereas this rg in LW (- 0.15 (±0.16)) had an opposite sign. A similar breed-specific difference is observed between skatole and sperm count. Within LR, the rg of 0.08 (±0.13) indicates no relationship between the traits, whereas the rg of - 0.37 (±0.14) in LW points to an unfavorable relationship. In LR GWAS identified QTL regions on SSC5 (21.1-22.3 Mb) for androstenone and on SSC6 (5.5-7.5 Mb) and SSC14 (141.1-141.6 Mb) for skatole. For LW, one marker was found on SSC17 at 48.1 Mb for androstenone and one QTL on SSC14 between 140.5 Mb and 141.6 Mb for skatole. CONCLUSION: Knowledge about such genetic correlations could help to balance conventional breeding programs with boar taint in maternal breeds. QTL regions with unfavorable pleiotropic effects on boar taint and fertility could have deleterious consequences in genomic selection programs. Constraining the weighting of these QTL in the genomic selection formulae may be a useful strategy to avoid physiological imbalances.

Experimental studies on effects of diet on Lawsonia intracellularis infections in fattening boars in a natural infection model.

BACKGROUND: Lawsonia intracellularis is one of the most economically important pathogens in swine production. This study tested the hypothesis that the composition of diets for pigs has an impact on the excretion of L. intracellularis in a natural infection model. RESULTS: Fifty boars (~ 90 kg BW) from a SPF-farm with a strict hygiene and management regime for reducing the spread of an L. intracellularis infection up to the beginning of the final fattening period were transported, regrouped and randomly allotted to groups of five animals each at the research facility. After a 1-week acclimatisation period groups were fed one of five diets 4 weeks before slaughter. These were either a finely ground pelleted diet (FP) or a coarsely ground meal diet (CM), both consisting of wheat (40.0%), barley (39.3%), soybean meal (16.0%), soybean oil (2.0%) and minor components. In the other meal diets parts of wheat, barley and soybean meal were substituted either with 22% cracked corn (CORN), 16.9% dried whey (WHEY) or 30% raw potato starch (RPS). The animals had a comparable serological status in a blocking-ELISA immediately before the start and at the end of the feeding experiment. Values increased significantly during the trial. In all subgroups (FP/CM/CORN/WHEY/RPS), shedding was detected in week 0 (genome equivalents = GE; log10 GE L. intracellularis/g faeces: 2.46 ± 2.64/3.58 ± 2.54/3.43 ± 2.37/2.30 ± 3.16/2.58 ± 2.73). The average number of L. intracellularis microbes in faeces during the trial period did not differ between the groups (log10 GE L. intracellularis/g faeces: 3.40 ± 1.53/3.01 ± 1.41/3.80 ± 1.71/3.98 ± 2.20/4.08 ± 2.13). In animals fed the WHEY-diet, significantly lower counts of L. intracellularis were found in the caecal content. The acetate content in the caecum was negatively correlated with the serological results at the end of the trial (r = - 0.36; P = 0.010). Butyrate concentrations in the caecal content were negatively correlated with the number of L. intracellularis in the caecum (r = - 0.32; P = 0.023). CONCLUSION: Therefore, this study provides preliminary evidence that there might be specific dietary effects on the course of a L. intracellularis infection.