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Importance of heat tolerance adaptation in pigs

Nowadays, heat stress is a major concern for pig production due to the increasing presence of the pig industry in tropical countries and the consequences of climate change especially on the frequency and severity of heat waves in more temperate countries. Heat stress has negative impacts on well-being and performance and in pigs and subsequent negative effects of pig farm profitability. Promoting a system less sensible to climate change is mandatory for the sustainability of pig industry. Within a pig population, there is great phenotypic individual variability in responses to heat. While some of this variability is genetic, adaptation to heat probably involves a large number of genes that interact with each other with environmental factors. The biological mechanisms involved in the individual variability of heat sensitivity are still poorly understood in pigs. This variability has raise little attention in breeding programs until now, and is a potential that can be used to select more robust animals, and/or to improve current farm practices. The first objective of this thesis work is to improve knowledge of these mechanisms by using gene expression data measured in different tissues in different experiments that used very contrasting experimental modalities or large cohorts of animals. The second objective of this project is to identify and validate biomarkers to classify animals according to their sensitivity to heat.

Understanding adaptation mechanisms and proposal of biomarkers

Understanding of mechanisms of the heat adaptation can be achieved through the analysis of gene expression data from pan-genomic microarrays. This approach allows a description of the mechanisms at different levels, which is a necessity for the comprehension of these physiological responses that show longitudinal and between-organs variations.
This PhD work is based on the data obtained from three experimental designs; the first one including multi-tissues and multi-breeds data, a second one with longitudinal data, and a last one with a bigger sample size for improving and validating results from the first two designs. Moreover, the first and the second design will make it possible to detect strong predictors of adaptation levels of pigs in response to heat, and the third experimental design will be used to validate the capacity of the biomarkers to predict the physiological status of a heat-stressed animal (acute or chronic). Each experiment includes transcriptomic, physiological and other omics data (mostly metabolomics) that could be used during this PhD.
The first experiment is being analyzed under different point of view, through a differential analysis using a mixed model, and with a blocking sPLS-DA and also the Bayesian method mash, that allow the testing and the estimation of many effects in many conditions.

Guilhem Huau is working on this subject since October 2021 for 3 years. He is supervised by Laurence Liaubet (UMR GenPhyse) and David Renaudeau in the Alinut team.

Contact

Guilhem Huau (doctorant) : guilhem.huau[at]inrae.fr
David Renaudeau (directeur de thèse) : david.renaudeau[at]inrae.fr
Laurence Liaubet (directrice de thèse) : laurence.liaubet[at]inrae.fr