Effect of environmental variance-based resilience selection on the gut metabolome of rabbits

Background Gut metabolites are key actors in host-microbiota crosstalk with efect on health. The study of the gut metabolome is an emerging topic in livestock, which can help understand its efect on key traits such as animal resilience and welfare. Animal resilience has now become a major trait of interest because of the high demand for more sustainable production. Composition of the gut microbiome can reveal mechanisms that underlie animal resil ience because of its infuence on host immunity. Environmental variance (VE), specifcally the residual variance, is one measure of resilience. The aim of this study was to identify gut metabolites that underlie diferences in the resilience potential of animals originating from a divergent selection for VE of litter size (LS). We performed an untargeted gut metabolome analysis in two divergent rabbit populations for low (n=13) and high (n=13) VE of LS. Partial least square-discriminant analysis was undertaken, and Bayesian statistics were computed to determine dissimilarities in the gut metabolites between these two rabbit populations. Results We identifed 15 metabolites that discriminate rabbits from the divergent populations with a prediction performance of 99.2% and 90.4% for the resilient and non-resilient populations, respectively. These metabolites were suggested to be biomarkers of animal resilience as they were the most reliable. Among these, fve that derived from the microbiota metabolism (3-(4-hydroxyphenyl)lactate, 5-aminovalerate, and equol, N6-acetyllysine, and serine), were suggested to be indicators of dissimilarities in the microbiome composition between the rabbit populations. The abundances of acylcarnitines and metabolites derived from the phenylalanine, tyrosine, and tryptophan metabo lism were low in the resilient population and these pathways can, therefore impact the infammatory response and health status of animals. Conclusions This is the frst study to identify gut metabolites that could act as potential resilience biomarkers. The results support diferences in resilience between the two studied rabbit populations that were generated by selec tion for VE of LS. Furthermore, selection for VE of LS modifed the gut metabolome, which could be another factor that modulates animal resilience. Further studies are needed to determine the causal role of these metabolites in health and diseas

Selection for environmental variance shifted the gut microbiome composition driving animal resilience

Background. Understanding how the host’s microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (VE), the withinindividual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced VE could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the VE of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) VE of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations. Results. We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the VE rabbit populations of over than 80%. Compared to the high VE population, the low VE (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience. Conclusions. This is the first study to show that selection for VE of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the VE rabbit population

Five genomic regions have a major impact on fat composition in Iberian pigs

Abstract The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content

Correlated genetic trend in the environmental variability of weight traits in mice

[EN] Genetic trends for weight traits and their environmental variability were analysed in an experimental mice population selected during 17 generations to increase weight gain by comparing three selection methods: classic selection with random mating (Method A), classic weighted selection with random mating (Method B) and classic selection with minimum coancestry mating (Method C). Males were selected based on their own phenotypic records for WG. The analysis involved three traits: weight at 21 days (W21), weight at 42 days (W42) and weight gain between 21 and 42 days (WG). Genetic trends were obtained by averaging, within generations, the breeding values obtained for the traits and their environmental variability under a classical animal model assuming that the environmental variance is homogeneous and an alternative model assuming the heterogeneous environmental variance is partly under genetic control. All the genetic trends were positive for the traits and negative for their environmental variability but the trend in phenotypic variances was steady showing that the model analysing the environmental variability failed to separate correctly the genetic from the systematic effects under an artificial selection scenario. The higher additive genetic variance estimated under the heterogeneity model led to higher genetic trends when this model was used, thus changing the order of the preferred methods of selection moving Method B form intermediate to be the worst. The results also showed that correlated changes in the variability of weight gain and related traits originated as a consequence of selection process in the trait, but these changes do not seem to be unfavourable for the animals since the scale effect tends to compensate the correlated reduction in variability of these traits.This paper was partially funded by a Grant from the Spanish Government (AGL2008-00794).Moreno, A.; Ibanez-Escriche, N.; García-Ballesteros, S.; Salgado, C.; Nieto, B.; Gutiérrez, JP. (2012). Correlated genetic trend in the environmental variability of weight traits in mice. Livestock Science. 148(1-2):189-195. https://doi.org/10.1016/j.livsci.2012.05.009S1891951481-