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Bio-Markers Measured on Young Healthy Pigs to Select for Disease Resilience.

紀錄類型:	書目-電子資源 : Monograph/item
正題名/作者:	Bio-Markers Measured on Young Healthy Pigs to Select for Disease Resilience./
作者:	Chen, Yulu.
出版者:	Ann Arbor : ProQuest Dissertations & Theses, : 2021,
面頁冊數:	228 p.
附註:	Source: Dissertations Abstracts International, Volume: 83-04, Section: B.
Contained By:	Dissertations Abstracts International83-04B.
標題:	Bioinformatics. -
電子資源:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=28496279
ISBN:	9798460406159

Bio-Markers Measured on Young Healthy Pigs to Select for Disease Resilience.
Chen, Yulu.

Bio-Markers Measured on Young Healthy Pigs to Select for Disease Resilience. - Ann Arbor : ProQuest Dissertations & Theses, 2021 - 228 p.

Source: Dissertations Abstracts International, Volume: 83-04, Section: B.

Thesis (Ph.D.)--Iowa State University, 2021.

This item must not be sold to any third party vendors.

Infectious diseases cause large economic losses in the swine industry. Disease resilience is the ability to maintain performance under pathogen exposure and may be an effective way to reduce the impact of the disease. However, disease resilience it is difficult to select for because breeding populations are raised in high-health bio-secure environments. Selection for resilience in high-health breeding populations could be accomplished through an indicator trait that can be measured on healthy animals. To be effective, such indicator traits for disease resilience need to heritable and genetically correlated with resilience. The overall goal of this dissertation was to study different bio-markers that can be measured on young healthy pigs to select for disease resilience, including immune traits and different omics information. All bio-marker data and phenotype data came from a natural disease challenge model for wean-to-finish pigs.Natural antibodies (NAb) are produced without previous exposure and are part of the innate immune system. To investigate the potential of NAb levels in blood from young healthy pigs as indicators of disease resilience, the genetic basis of NAb levels to different pathogen-associated molecular patterns (including lipopolysaccharides, lipoteichoic acid, peptidoglycan, and keyhole limpet hemocyanin) and their relationships (both phenotypic and genetic) with disease resilience were estimated in Chapter 2 of this thesis. NAb titers were found to be heritable (0.12 to 0.53), with IgM isotype NAb having higher heritability estimates (0.12 to 0.24) than IgG isotype NAb (0.33 to 0.53). In the phenotypic association study, pigs that died had lower NAb titers than pigs that survived. In the genetic correlation studies, the NAb titers were found to be genetically correlated with resilience traits but with large standard errors. Genome-wide association studies identified novel candidate genes for NAb in the significant genome region. Alltogether, the levels of NAb in plasma of young healthy pigs were shown to have potential as indicators of disease resilience, especially IgM isotype NAb binding keyhole limpet hemocyanin.In Chapter 3, we investigated whether protein levels in plasma from young healthy pigs could be the indicators for disease resilience. Proteins are the functional components that drive the majority of biological processes and the plasma proteome provides a window into the current status of the organism because it contains blood proteins and tissue proteins. To identify effective plasma protein indicators for disease resilience, quantitative analyses were conducted of the abundances of 377 proteins in 912 plasma samples from young healthy pigs, at both the phenotypic and genetic levels. The abundances of 100 proteins were significantly heritable and abundances of several proteins were found to be associated with disease resilience, genetically and/or phenotypically. Gene set enrichment analysis was used to identify associations across proteins with different disease resilience traits. For both the phenotypic and genetic enrichment analyses, many significant enriched terms were related to the immune system and these terms were unfavorably associated with disease resilience. In conclusion, this study contributes to improving our understanding of the genetic basis of the plasma proteome in young healthy pigs and shows that there is great potential for the abundance of some proteins in plasma from young healthy pigs to be used as indicators for disease resilience.In Chapter 4, the potential of types of omics data, including genomics, transcriptomics, proteomics, and metabolomics, that were available on 836 young healthy pigs, to predict subsequent disease resilience was investigated. Specifically, we used omics data obtained before exposure to pathogens to predict disease resilience and compared the predictive power of different combinations of omics information for prediction using best linear unbiased prediction (BLUP) mixed linear models. Adding more omics data to genomics in BLUP mixed linear models increased the predictive ability compared with using genomics information alone, where a combination of transcriptomics, metabolomics, and genomics in BLUP mixed linear model usually had a good predictive ability. However, including more omics levels did not always increase the accuracy. For categorial disease resilience variables, the different omics data were also integrated using generalized canonical correlation analysis. Results showed that integrating more omics data increased the ability to correctly classify the animals compared with using one omics data alone. In conclusion, it is very promising to incorporate omics information into pig breeding programs to select for disease resilience.Overall, different bio-markers in plasma from young healthy pigs were studied to select for disease resilience in this dissertation. Most of them showed good potential to be the indicators or predictors for disease resilience.

ISBN: 9798460406159Subjects--Topical Terms:

553671
Bioinformatics.
Subjects--Index Terms:

Bio-markers

Bio-Markers Measured on Young Healthy Pigs to Select for Disease Resilience.
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520 $a Infectious diseases cause large economic losses in the swine industry. Disease resilience is the ability to maintain performance under pathogen exposure and may be an effective way to reduce the impact of the disease. However, disease resilience it is difficult to select for because breeding populations are raised in high-health bio-secure environments. Selection for resilience in high-health breeding populations could be accomplished through an indicator trait that can be measured on healthy animals. To be effective, such indicator traits for disease resilience need to heritable and genetically correlated with resilience. The overall goal of this dissertation was to study different bio-markers that can be measured on young healthy pigs to select for disease resilience, including immune traits and different omics information. All bio-marker data and phenotype data came from a natural disease challenge model for wean-to-finish pigs.Natural antibodies (NAb) are produced without previous exposure and are part of the innate immune system. To investigate the potential of NAb levels in blood from young healthy pigs as indicators of disease resilience, the genetic basis of NAb levels to different pathogen-associated molecular patterns (including lipopolysaccharides, lipoteichoic acid, peptidoglycan, and keyhole limpet hemocyanin) and their relationships (both phenotypic and genetic) with disease resilience were estimated in Chapter 2 of this thesis. NAb titers were found to be heritable (0.12 to 0.53), with IgM isotype NAb having higher heritability estimates (0.12 to 0.24) than IgG isotype NAb (0.33 to 0.53). In the phenotypic association study, pigs that died had lower NAb titers than pigs that survived. In the genetic correlation studies, the NAb titers were found to be genetically correlated with resilience traits but with large standard errors. Genome-wide association studies identified novel candidate genes for NAb in the significant genome region. Alltogether, the levels of NAb in plasma of young healthy pigs were shown to have potential as indicators of disease resilience, especially IgM isotype NAb binding keyhole limpet hemocyanin.In Chapter 3, we investigated whether protein levels in plasma from young healthy pigs could be the indicators for disease resilience. Proteins are the functional components that drive the majority of biological processes and the plasma proteome provides a window into the current status of the organism because it contains blood proteins and tissue proteins. To identify effective plasma protein indicators for disease resilience, quantitative analyses were conducted of the abundances of 377 proteins in 912 plasma samples from young healthy pigs, at both the phenotypic and genetic levels. The abundances of 100 proteins were significantly heritable and abundances of several proteins were found to be associated with disease resilience, genetically and/or phenotypically. Gene set enrichment analysis was used to identify associations across proteins with different disease resilience traits. For both the phenotypic and genetic enrichment analyses, many significant enriched terms were related to the immune system and these terms were unfavorably associated with disease resilience. In conclusion, this study contributes to improving our understanding of the genetic basis of the plasma proteome in young healthy pigs and shows that there is great potential for the abundance of some proteins in plasma from young healthy pigs to be used as indicators for disease resilience.In Chapter 4, the potential of types of omics data, including genomics, transcriptomics, proteomics, and metabolomics, that were available on 836 young healthy pigs, to predict subsequent disease resilience was investigated. Specifically, we used omics data obtained before exposure to pathogens to predict disease resilience and compared the predictive power of different combinations of omics information for prediction using best linear unbiased prediction (BLUP) mixed linear models. Adding more omics data to genomics in BLUP mixed linear models increased the predictive ability compared with using genomics information alone, where a combination of transcriptomics, metabolomics, and genomics in BLUP mixed linear model usually had a good predictive ability. However, including more omics levels did not always increase the accuracy. For categorial disease resilience variables, the different omics data were also integrated using generalized canonical correlation analysis. Results showed that integrating more omics data increased the ability to correctly classify the animals compared with using one omics data alone. In conclusion, it is very promising to incorporate omics information into pig breeding programs to select for disease resilience.Overall, different bio-markers in plasma from young healthy pigs were studied to select for disease resilience in this dissertation. Most of them showed good potential to be the indicators or predictors for disease resilience.
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