DOI: 10.5281/zenodo.14046985
title: Description of metabolic differences between castrated males and intact gilts obtained from high-throughput metabolomics of porcine plasma

description: Content





Dataset of the study: Description of metabolic differences between castrated males and intact gilts obtained from high-throughput metabolomics of porcine plasma.

 
description: Surgically castrated male pigs, which are commonly produced in pork production systems, have slightly lower production efficiency, compared to intact female pigs (gilts). This is mainly due to an unfavorable feed conversion rate and fatter carcasses. These differences influenced by physiological and genetic factors, can be identified through metabolomics, which describes metabolic profiles. In this study, we used untargeted metabolomics to analyze the plasma of 694 Italian Large White pigs (228 castrated males and 466 intact gilts), sampled at slaughter. The metabolomic profiles included 731 metabolites (82% and 9% of endogenous or unknown origin),  covering 98 sub-pathways. The raw metabolomic data were cleaned and imputed using Multivariate Imputation by Chained Equations. The Boruta algorithm was then employed to identify metabolites that had different concentrations between castrated males and intact gilts. To address the random nature of feature selection, multiple Boruta runs were generated, nested within a 10-fold cross validation, resulting in 1,250 Boruta datasets. These datasets helped identify 40 informative metabolites, with a reduced core of 15 metabolites consistently confirmed across all runs. Their calculated random forest Out-Of-Bag (OOB ) error was 0.25 and 0.27,  respectively. The relevance, ranking and predictive ability of each selected metabolite were determined based on the Mean Decrease Gini (MDG) and the area under the curve (AUC) of the Receiver Operating Characteristic (ROC) curve analysis, with values of 0.024±0.007 and 0.030±0.009, and 0.62±0.04 and 0.65±0.03 for the two metabolite sets, respectively. Of the 40 selected metabolites, 60% had higher concentrations in castrated males than in intact gilts, while in the 15 metabolites set, this percentage was 80%. Network and biological pathways analyses conducted with MetaboAnalyst indicated that the selected metabolites were primarily amino acids and lipids, many of which belonged to their respective sub-pathways, suggesting minimal biological differences between castrated males and intact gilts. These findings support previous results obtained using a targeted metabolomic platform. This study represents the largest investigation to date on the pig sex metabolome, providing essential biological insights that could inform precise husbandry and feeding strategies in pigs, taking into consideration the castration status of the males.
description: Financial support statement

This study was supported by: (1) PRIN2017 PigPhenomics that has received funding from the Italian MUR (for the production metabolomic data); (2) the Horizon Europe Re-Livestock project that has received funding from the European Union's Horizon Europe research and innovation programme under the grant agreement No. 01059609 (for the elaboration and analysis of the data); (3) the Italian PRIN2022 project FEEDTHEPIG, Funded by the European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice PRIN 2022 PNRR (DD N. 1409 del 14/09/2022), proposal code P2022FZMJ9 - CUP J53D23018310001 for the analysis of part of the data; (4) the Italian PRIN2022 HamCapture, funded by the European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice Prin 2022 - DD N. 104 del 2/2/2022, proposal code 202238NP9N – CUP J53D23009570001 (for the analysis of part of the data); (5) and was carried out within the Agritech National Research Center (Agritech Spoke 1) and received funding from the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032 17/06/2022, CN00000022) - This manuscript reflects only the authors’ views and opinions, neither the European Union nor the European Commission can be considered responsible for them.