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

Dauben, Christina; Pröll-Cornelissen, Maren Julia; Heuß, Esther Maren; Appel, Anne K.; Henne, Hubert; Roth, Katharina; Schellander, K.; Tholen, Ernst; Große‐Brinkhaus, Christine

doi:10.1186/s12864-021-07997-1

Cited by 13 publications

(21 citation statements)

References 73 publications

(118 reference statements)

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“…Making use of highly informative genotype data, genome-wide association studies (GWAS) that use highly informative genotypes are a highly efficient approach to map loci and to detect QTL and candidate genes for complex traits (e.g., [ 1 ]). This approach enables fine mapping [ 19 ] and validation of previously identified regions in a GWAS for important traits (e.g., [ 21 ]).…”

Section: Resultsmentioning

confidence: 99%

“…Selection was conducted by applying several theoretical concepts and approaches under practical conditions. Selection steps were built on existing pedigree and real SNP genotype information within the pigFit project which focuses on piglet survival and immunocompetence [ 20 , 21 ]. Performance of the different selection strategies was assessed based on the accuracy of imputation of masked genotypes from SNP chip data.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…Data sets of purebred LR and LW subset pig populations were recorded from 2010 to 2017 and were provided by the German breeding organization BHZP GmbH as already been described in Dauben et al (2021). The animals within the nucleus populations were kept under high hygienic conditions and reflect the genetic diversity of both populations concerning their different breeding objectives.…”

Section: Animals and Phenotypic Measurementsmentioning

confidence: 99%

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

Roth

Pröll-Cornelissen

Heuß

et al. 2022

J Animal Breeding Genetics

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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.

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“…Additionally, hematological characteristics are crucial traits that are associated with immune and metabolic status and diseases in pigs. Previous studies have reported that many blood parameters are heritable in swine [ 10 , 11 ], and serval genes have been identified by GWAS, RNA-seq, and eGWAS in pigs [ 12 , 13 , 14 ]. China has long been regarded as the largest live pig and pork consumption country in the world, and the per capita pork consumption is about 20 kg.…”

Section: Introductionmentioning

confidence: 99%

Assessment of Hematologic and Biochemical Parameters for Healthy Commercial Pigs in China

Zhang

Liu

et al. 2022

Animals

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Hematologic and biochemical data are useful for indicating disease diagnosis and growth performance in swine. However, the assessment of these parameters in healthy commercial pigs is rare in China. Thus, blood samples were collected from 107 nursery pigs and 87 sows and were analyzed for 25 hematologic and 14 biochemical variables. After the rejection of the outliers and the detection of the data distribution, the correlations between the blood parameters were analyzed and the hematologic/biochemical RIs were preliminarily established using the 95% percentile RI. Correlation analysis showed that albumin was the hub parameter among the blood parameters investigated, and genes overlapping with key correlated variables were discovered. Most of the hematologic and biochemical parameters were significantly different between nursery pigs and sows. The 95% RIs of white blood cells and red blood cells were 7.18–24.52 × 109/L and 5.62–7.84 × 1012/L, respectively, for nursery pigs, but 9.34–23.84 × 109/L and 4.98–8.29 × 1012/L for sows. The 95% RIs of total protein and albumin were 43.16–61.23 g/dL and 19.35–37.86 g/dL, respectively, for nursery pigs, but 64.96–88.68 g/dL and 31.91–43.28 g/dL for sows. In conclusion, our study highlights the variability in blood parameters between nursery pigs and sows and provides fundamental data for the health monitoring of commercial pigs in China.

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

Cited by 13 publications

References 73 publications

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

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

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

Assessment of Hematologic and Biochemical Parameters for Healthy Commercial Pigs in China

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