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.

Old breeds, new solutions? Effects of two different traditional sire breeds on skin lesions, tail lesions, tail losses, performance and behaviour of rearing pigs

Some studies indicated a relationship between modern, fast-growing, lean-meat-producing hybrid pigs and the occurrence of tail-biting, one of the major issues of conventional pig husbandry. Therefore, this study investigated the effects of different local, traditional sire breeds on the behaviour and performance of rearing pigs. Between December 2019 and November 2020, a total of 1 561 piglets were weaned from hybrid sows (Bundes Hybrid Zucht Programm (BHZP) Landrace × BHZP Large White) that were paired with either Swabian-Hall (SH), Bentheim Black Pied (BB) or BHZP-Piétrain (Pi) boars. Tails of the piglets were left intact (43.5%) or docked (56.5%), and male piglets were castrated. Piglets were conventionally reared on fully slatted plastic flooring in mixed-sex groups. Starting one day after weaning, skin lesions were scored once per pig, and tail lesions and losses were scored weekly until the end of rearing. The average daily gain was documented for the suckling and rearing period. The activity behaviour of eight focal pens was analysed using video recordings. Differences between modern and traditional breeds were found in this study for so-called aggressive and non-aggressive biting pronounced by skin and tail lesions and tail losses. Significantly fewer BB pigs had severe skin lesions on the front body than SH or Pi pigs (P < 0.05). Additionally, piglets that were classified as light (<5.6 kg) at weaning showed skin lesion scores of 0 more often than piglets that were classified with a medium (≥5.6-≤8.3 kg) or heavy (>8.3 kg) weaning weight (P < 0.05). In the first half of the rearing period, significantly more BB pigs were assessed as having no tail lesions and tail losses than SH and Pi pigs (P < 0.01). However, these differences disappeared in the second half of rearing. Either docked or undocked Pi pigs had significantly higher average daily gains than SH and BB pigs (P < 0.05). The activity of the focal pens was not influenced by the sire breed or tail lesion class, which might be due to the limited sample size of eight pens. To conclude, the use of the traditional sire breed BB has the potential to reduce injurious behaviour in the offspring. However, adjustments to the housing and feeding should be taken to further reduce the incidence of tail lesions and losses and to enhance performance.

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 r_g 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 r_g (-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.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-021-07997-1).

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 (r_g) between boar taint and fertility were different in LR and LW breeds. In LR an unfavorable r_g of 0.31 (±0.15) was observed between androstenone and number of piglets born alive, whereas this r_g 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 r_g of 0.08 (±0.13) indicates no relationship between the traits, whereas the r_g 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.

Associations of functional candidate genes derived from gene-expression profiles of prenatal porcine muscle tissue with meat quality and muscle deposition

Ten genes (ANK1, bR10D1, CA3, EPOR, HMGA2, MYPN, NME1, PDGFRA, ERC1, TTN), whose candidacy for meat-quality and carcass traits arises from their differential expression in prenatal muscle development, were examined for association in 1700 performance-tested fattening pigs of commercial purebred and crossbred herds of Duroc, Pietrain, Pietrain x (Landrace x Large White), Duroc x (Landrace x Large White) as well as in an experimental F(2) population based on a reciprocal cross of Duroc and Pietrain. Comparative sequencing revealed polymorphic sites segregating across commercial breeds. Genetic mapping results corresponded to pre-existing assignments to porcine chromosomes or current human-porcine comparative maps. Nine of these genes showed association with meat-quality and carcass traits at a nominal P-value of < or = 0.05; PDGFRA revealed no association reaching the P < or = 0.05 threshold. In particular, HMGA2, CA3, EPOR, NME1 and TTN were associated with meat colour, pH and conductivity of loin 24 h postmortem; CA3 and MYPN exhibited association with ham weight and lean content (FOM) respectively at P-values of < 0.003 that correspond to false discovery rates of < 0.05. However, none of the genes showed significant associations for a particular trait across all populations. The study revealed statistical-genetic evidence for association of the functional candidate genes with traits related to meat quality and muscle deposition. The polymorphisms detected are not likely causal, but markers were identified that are in linkage disequilibrium with causal genetic variation within particular populations.

Genetische Fundierung von AutoFOM-Merkmalen

Abstract. Title of the paper: Genetic foundation of AutoFOM-traits Since the beginning of the year 2000 the payment System of pig carcasses in some slaughter houses in northwest Germany is based on the recordings of the fully automated carcass Classification system AutoFOM. Besides legal information 'estimated lean meat percentage' relative exact details of the weights of important valuable cuts are available. Genetic parameters of the AutoFOM lean carcass cut information, ham-, chop-, Shoulder- and belly weights as well as lean meat percentage of the belly cut were estimated. Using the field data of the pig breeding organisations BHZP (n = 2224) and SNW (n = 3601) the estimated heritabilties of these carcass cuts vary between 0.13 and 0.27 (BHZP) and 0.13 and 0.31 (SNW), respectively. The estimated heritabilities of the AutoFOM carcass traits of station-tested pigs were more pronounced for the dam lines German Landrace and Large White (n = 1693) and Piétrain Al-boars mated to Fl sows (n = 1053). The estimates ranged from 0.27 to 0.59 (dam lines) and 0.05 to 0.40 (Pi Al-boars), respectively. Using the records of Station tested purebred Pietrain pigs (n = 1693) the heritabilities of the AutoFOM carcass cuts did not exceed 0.10. The genetic correlation between the different AutoFOM carcass traits exceed the absolute value of 0.8. In a similar way, the genetic correlation between the "estimated lean meat percentage" used in the test Station and the AutoFOM carcass traits were close to unity. We concluded that AutoFOM traits of slaughter pigs provide a useful information for the selection of Al-boars. Moreover, with regard to the Station testing of dam lines AutoFOM carcass informations derived from AutoFOM are a useful supplementation. Because of the low heritability, only a marginal additional benefit could be expected for the genetic ranking of Pi-boars using AutoFOM carcass cut records of purebred Station tested progenies.

Variation des Fleischanteiles im Bauch von Schweinen aus Mutterlinien

Abstract. Title of the paper: Variation of lean content in pig beilies of dam lines Magnetic resonance imaging (MRI) was applied to determine the tissue composition of 157 bellies of castrated male pigs belonging to two dam-lines of the German Hybrid Pig Breeding Programme. All pigs were taken from the routine testing scheme. The analysis of carcass traits showed that pigs of line 03 were clearly leaner than those of line 01. Only in backfat thickness no significant difference could be observed. For the belly, a clear difference of 7% was found in percentage of lean. Lean content of the belly was also estimated by means of various multiple regressions using carcass traits. Percentage of lean predicted by the official equation used in German performance testing on the one hand and by means of MRI on the other hand was different particularly in line 03. A correlation of r = 0.67 and r = 0.82 between lean content determined by means of MRI and multiple regression was found for line 01 and line 03, respectively. To study the Variation between sires, variance components were estimated. Differences between sires were higher in lean content of the belly compared to backfat thickness, a trait which has been used in selection for a long time.