UNDERSTANDING THE ROLE OF THE GENOME, MICROBIOME, AND EPIGENOME ON THE TRANSGENERATIONAL EFFECTS OF IN UTERO HEAT STRESS IN PIGS.

Ourcentral hypothesisis that the risk factors for producing offspring that display the negative IUHS phenotypes across generations are controlled, to some extent, bymaternal and direct genetic and epigenetic components, the microbial makeup of individuals, and their interaction.This proposal aims to develop amulti-omics functional approachto identify genomic, epigenomic, microbial, and metabolomic biomarkers that will enable more accurate identification of sows at minimal risk of producing offspring that display the negative IUHS phenotypes in explaining tolerance and resilience to IUHS.Identifying appropriate biomarkers to aid genomic prediction models and optimize the use of genomic information routinely generated in commercial pig breeding farms is a crucial priority for the swine industry. The successful identification of sows at minimal risk of producing offspring that display the negative IUHS phenotypes depends on the availability of phenotypes and biomarkers that are heritable andWithin this proposal, we will disentangle the leading biological causes of the adverse effects of IUHS on the postnatal health, performance, and welfare of pigs through a comprehensive transgenerational multi-omics characterization of animals with divergent genetic merit for producing offspring that suffer from negative IUHS phenotypes.The specific objectives of the proposal, therefore, are as follows:Objective 1: To quantify the role of microbiota maturation in sows at a high or low risk of producing offspring displaying negative IUHS phenotypes.We hypothesize that microbiome composition and development play a significant role in shaping heat tolerance and postulate that genetic differences in maturation rate among pigs could be used as an additional criterion to select individuals better able to cope with heat stress.Objective 2: To develop a functional trans-generational multi-omics approach to identify genomic, microbiota, epigenomic, and metabolomic biomarkers that enable identifying sows at minimal risk of producing offspring IUHS leveraging phenotypes from an integrated behavioral and physiological model in genetically divergent animals.A group of divergently selected animals predicted to be atHigh RiskorLow Riskof producing offspring that display the negative IUHS phenotypeshas been generated from previous studies (see preliminary results). Here genomic, transcriptomic, and metabolomic variants measuredin parallel in the host and microbial communitiesacross three generations will be obtained from individuals genomically divergent for heat tolerance, for which in-depth behavioral and physiological assessments are being obtained. Furthermore, there is strong evidence of stable and heritable epigenetic markers (e.g., DNA methylation) impacting health, adaptation, heat tolerance, and performance. However, there are no trans-generational studies investigating how the DNA methylation patterns in pigs are related to climatic resilience, especially IUHS. We hypothesize that IUHS drives postnatal phenotypic changes by altering DNA methylation of key regulatory gene pathways associated with heat tolerance and other biological functions. As part of this objective, DNA methylation will be measuredthroughout the entire three generations of the experiment.Furthermore, a growing body of evidence links microbial composition to transgenerational effects on host phenotypes, directly affecting the parental generation's immune and metabolic functions and altering the progeny's methylation status. Most of these studies have been conducted in model organisms, and evidence of these potentially fundamental mechanisms is currently almost nonexistent in swine. Our research will assess methylation status and microbial composition (meta)transcriptome and (meta)metabolome on F1, F2, and F3 individuals. We will first determine whether genetically divergent individuals for heat tolerance also have different methylation and microbial profiles, whether epigenomic changes are passed across generations and whether the microbiome has a role in this mechanism. The epigenomic profiles and change patterns will then be correlated with whole-genome polymorphisms (SNPs), transcriptome, metabolome, and microbial compositions to identify biomarkers affecting epigenomic changes so that a greater emphasis can be placed on significant variants when predicting heat tolerance in pigs (i.e., biology-driven genomic prediction methods). Furthermore, F3 generation pregnant replacement gilts (derived from Objective 2) will be exposed to the same temperature cycles as their dams.