A genome-wide screen for resilient responses in growing pigs

Laghouaouta, Houda; Fraile, Lorenzo; Suárez-Mesa, Rafael; Ros‐Freixedes, Roger; Estany, J.; Pena, Ramona N.

doi:10.1186/s12711-022-00739-1

Cited by 5 publications

(1 citation statement)

References 71 publications

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“…Owing to what stated above, multiple studies have been undertaken to elucidate the genetic mechanisms responsible for resilience. These investigations have employed diverse approaches, ranging from highthroughput phenotypic technologies [13,16] to conventional data collection systems [17,18]. All of these studies underscore how it exists a direct genetic control of resilience.…”

Section: Introductionmentioning

confidence: 99%

A first characterization of the Microbiota-Resilience Link in Swine

Mancin

Maltecca

Huang

et al. 2023

Preprint

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Background The gut microbiome plays a crucial role in understanding complex biological mechanisms, including host resilience to stressors. Investigating the microbiota-resilience link in animals and plants holds relevance in addressing challenges like adaptation of agricultural species to a warming environment. This study aims to characterize the microbiota-resilience connection in swine. As resilience is not directly observable, we estimated it using four distinct indicators based on daily feed consumption variability, assuming animals with greater intake variation may face challenges in maintaining stable physiological status. These indicators were analyzed both as linear and categorical variables. In our first set of analyses, we explored the microbiota-resilience link using PERMANOVA, α-diversity analysis, and Discriminant Analysis. Additionally, we quantified the ratio of estimated microbiota variance to total phenotypic variance (microability). Finally, we conducted a Partial Least Squares Discriminant Analysis (PLS-DA) to assess the classification performance of the microbiota with indicators expressed in classes. Results This study offers four key insights. Firstly, among all indicators, two effectively captured resilience. Secondly, our analyses revealed robust relationship between microbial composition and resilience in terms of both composition and richness. We found decreased α-diversity in less resilient animals, while specific Amplicon Sequence Variants (ASVs) and KEGG pathways associated with inflammatory responses were negatively linked to resilience. Thirdly, considering resilience indicators in classes, we observed significant differences in microbial composition primarily in animals with lower resilience. Lastly, our study indicates that gut microbial composition can serve as a reliable biomarker for distinguishing individuals with lower resilience. Conclusion Our comprehensive analyses have highlighted the host-microbiota and resilience connection, contributing valuable insights to the existing scientific knowledge. The practical implications of PLS-DA and microability results are noteworthy. PLS-DA suggests that host-microbiota interactions could be utilized as biomarkers for monitoring resilience. Furthermore, the microability findings show that leveraging host-microbiota insights may improve the selection of resilient animals, supporting their adaptive capacity in response to changing environmental conditions. These practical implications offer promising avenues for enhancing animal well-being and adaptation strategies in the context of environmental challenges faced by livestock populations.

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Section: Introductionmentioning

confidence: 99%

A first characterization of the Microbiota-Resilience Link in Swine

Mancin

Maltecca

Huang

et al. 2023

Preprint

View full text Add to dashboard Cite

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Genome-wide Association Studies of Novel Resilience Traits Identify Important Immune QTL Regions and Candidate Genes in Duroc Pigs

Li,

Pu,

MacHugh

et al. 2024

Journal of Integrative Agriculture

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Sequence variants associated with resilient responses in growing pigs

Laghouaouta,

Laplana,

Ros‐Freixedes

et al. 2024

J Animal Breeding Genetics

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The current work aimed to identify genomic regions and candidate genes associated with resilience in pigs. In previous work, we proposed the body weight deviation from the expected growth curve (ΔBW) and the increase of the positive acute‐phase protein haptoglobin (ΔHP) after a vaccine challenge as resilience indicators which may be improved through selective breeding in pigs. Individuals with steady growth rate and minor activation of haptoglobin (high ΔBW and low ΔHP values) were considered resilient. In contrast, pigs with perturbed growth rate and high activation of haptoglobin (low ΔBW and high ΔHP values) were considered susceptible. Both ∆BW and ∆HP were simultaneously considered to select the most resilient (N = 40) and susceptible (N = 40) pigs. A genome‐wide association study was carried out for the pigs' response classification to the challenge test using whole‐genome sequence data (7,760,720 variants). Eleven associated genomic regions were identified, harbouring relevant candidate genes related to the immune response (such as pro‐ and anti‐inflammatory responses) and growth pathways. These associated genomic regions harboured 41 potential functional mutations (frameshift, splice donor, splice acceptor, start loss and stop loss/gain) in candidate genes. Overall, this study advances our knowledge about the genetic determinism of resilience, highlighting its polygenic nature and strong relationship with immunity and growth.

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A genome-wide screen for resilient responses in growing pigs

Cited by 5 publications

References 71 publications

A first characterization of the Microbiota-Resilience Link in Swine

A first characterization of the Microbiota-Resilience Link in Swine

Genome-wide Association Studies of Novel Resilience Traits Identify Important Immune QTL Regions and Candidate Genes in Duroc Pigs

Sequence variants associated with resilient responses in growing pigs

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