Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience
Abstract Background Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify po...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | deu |
| Published: |
BMC
2023-12-01
|
| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-023-00860-9 |
| _version_ | 1827581863737163776 |
|---|---|
| author | Kyu-Sang Lim Jian Cheng Christopher Tuggle Michael Dyck PigGen Canada Frederic Fortin John Harding Graham Plastow Jack Dekkers |
| author_facet | Kyu-Sang Lim Jian Cheng Christopher Tuggle Michael Dyck PigGen Canada Frederic Fortin John Harding Graham Plastow Jack Dekkers |
| author_sort | Kyu-Sang Lim |
| collection | DOAJ |
| description | Abstract Background Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome of 1594 young healthy pigs with subsequent records on disease resilience. Transcriptome data were obtained by 3’mRNA sequencing and genotype data were from a 650 K genotyping array. Results Heritabilities of the expression of 16,545 genes were estimated, of which 5665 genes showed significant estimates of heritability (p < 0.05), ranging from 0.05 to 0.90, with or without accounting for white blood cell composition. Genes with heritable expression levels were spread across chromosomes, but were enriched in the swine leukocyte antigen region (average estimate > 0.2). The correlation of heritability estimates with the corresponding estimates obtained for genes expressed in human blood was weak but a sizable number of genes with heritable expression levels overlapped. Genes with heritable expression levels were significantly enriched for biological processes such as cell activation, immune system process, stress response, and leukocyte activation, and were involved in various disease annotations such as RNA virus infection, including SARS-Cov2, as well as liver disease, and inflammation. To estimate genetic correlations with disease resilience, 3205 genotyped pigs, including the 1594 pigs with transcriptome data, were evaluated for disease resilience following their exposure to a natural polymicrobial disease challenge. Significant genetic correlations (p < 0.05) were observed with all resilience phenotypes, although few exceeded expected false discovery rates. Enrichment analysis of genes ranked by estimates of genetic correlations with resilience phenotypes revealed significance for biological processes such as regulation of cytokines, including interleukins and interferons, and chaperone mediated protein folding. Conclusions These results suggest that expression levels in the blood of young healthy pigs for genes in biological pathways related to immunity and endoplasmic reticulum stress have potential to be used as genetic indicator traits to select for disease resilience. |
| first_indexed | 2024-03-08T22:42:24Z |
| format | Article |
| id | doaj.art-7bc0d0dc749e46e7b5b31246ed124cd0 |
| institution | Directory Open Access Journal |
| issn | 1297-9686 |
| language | deu |
| last_indexed | 2024-03-08T22:42:24Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj.art-7bc0d0dc749e46e7b5b31246ed124cd02023-12-17T12:04:21ZdeuBMCGenetics Selection Evolution1297-96862023-12-0155111710.1186/s12711-023-00860-9Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilienceKyu-Sang Lim0Jian Cheng1Christopher Tuggle2Michael Dyck3PigGen Canada4Frederic Fortin5John Harding6Graham Plastow7Jack Dekkers8Department of Animal Science, Iowa State UniversityDepartment of Animal Science, Iowa State UniversityDepartment of Animal Science, Iowa State UniversityDepartment of Agricultural, Food and Nutritional Science, University of AlbertaPigGen Canada Research ConsortiumCentre de Développement du Porc du Québec Inc. (CDPQ)Department of Large Animal Clinical Sciences, University of SaskatchewanDepartment of Agricultural, Food and Nutritional Science, University of AlbertaDepartment of Animal Science, Iowa State UniversityAbstract Background Disease resilience is the ability of an animal to maintain productive performance under disease conditions and is an important selection target. In pig breeding programs, disease resilience must be evaluated on selection candidates without exposing them to disease. To identify potential genetic indicators for disease resilience that can be measured on selection candidates, we focused on the blood transcriptome of 1594 young healthy pigs with subsequent records on disease resilience. Transcriptome data were obtained by 3’mRNA sequencing and genotype data were from a 650 K genotyping array. Results Heritabilities of the expression of 16,545 genes were estimated, of which 5665 genes showed significant estimates of heritability (p < 0.05), ranging from 0.05 to 0.90, with or without accounting for white blood cell composition. Genes with heritable expression levels were spread across chromosomes, but were enriched in the swine leukocyte antigen region (average estimate > 0.2). The correlation of heritability estimates with the corresponding estimates obtained for genes expressed in human blood was weak but a sizable number of genes with heritable expression levels overlapped. Genes with heritable expression levels were significantly enriched for biological processes such as cell activation, immune system process, stress response, and leukocyte activation, and were involved in various disease annotations such as RNA virus infection, including SARS-Cov2, as well as liver disease, and inflammation. To estimate genetic correlations with disease resilience, 3205 genotyped pigs, including the 1594 pigs with transcriptome data, were evaluated for disease resilience following their exposure to a natural polymicrobial disease challenge. Significant genetic correlations (p < 0.05) were observed with all resilience phenotypes, although few exceeded expected false discovery rates. Enrichment analysis of genes ranked by estimates of genetic correlations with resilience phenotypes revealed significance for biological processes such as regulation of cytokines, including interleukins and interferons, and chaperone mediated protein folding. Conclusions These results suggest that expression levels in the blood of young healthy pigs for genes in biological pathways related to immunity and endoplasmic reticulum stress have potential to be used as genetic indicator traits to select for disease resilience.https://doi.org/10.1186/s12711-023-00860-9 |
| spellingShingle | Kyu-Sang Lim Jian Cheng Christopher Tuggle Michael Dyck PigGen Canada Frederic Fortin John Harding Graham Plastow Jack Dekkers Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience Genetics Selection Evolution |
| title | Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| title_full | Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| title_fullStr | Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| title_full_unstemmed | Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| title_short | Genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| title_sort | genetic analysis of the blood transcriptome of young healthy pigs to improve disease resilience |
| url | https://doi.org/10.1186/s12711-023-00860-9 |
| work_keys_str_mv | AT kyusanglim geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT jiancheng geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT christophertuggle geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT michaeldyck geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT piggencanada geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT fredericfortin geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT johnharding geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT grahamplastow geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience AT jackdekkers geneticanalysisofthebloodtranscriptomeofyounghealthypigstoimprovediseaseresilience |