Reverter-Gomez, A. | Search bioRxiv

bioRxiv2021

Leveraging host-genetics and gut microbiota to determine immunocompetence in pigs

The aim of the present work was to identify microbial biomarkers linked to immunity traits and to characterize the contribution of host-genome and gut microbiota to the immunocompetence in healthy pigs. To achieve this goal, we undertook a combination of network, mixed model and microbial-wide association studies (MWAS) for 21 immunity traits and the relative abundance of gut bacterial communities in 389 pigs genotyped for 70K SNPs. The heritability (h2; proportion of phenotypic variance explained by the host genetics) and microbiability (m2; proportion of variance explained by the microbial composition) showed similar values for most of the analyzed immunity traits, except for both IgM and IgG in plasma that were dominated by the host genetics, and the haptoglobin in serum which was the trait with larger m2 (0.275) compared to h2 (0.138). Results from the MWAS suggested a polymicrobial nature of the immunocompetence in pigs and revealed associations between pigs gut microbiota composition and 15 of the analyzed traits. The lymphocytes phagocytic capacity (quantified as mean fluorescence) and the total number of monocytes in blood were the traits associated with the largest number of taxa (6 taxa). Among the associations identified by MWAS, 30% were confirmed by an information theory network approach. The strongest confirmed associations were between Fibrobacter and phagocytic capacity of lymphocytes (r=0.37), followed by correlations between Streptococcus and the percentage of phagocytic lymphocytes (r=-0.34) and between Megasphaera and serum concentration of haptoglobin (r=0.26). In the interaction network, Streptococcus and percentage of phagocytic lymphocytes were the keystone bacterial and immune-trait, respectively. Overall, our findings reveal an important connection between immunity traits and gut microbiota in pigs and highlight the need to consider both sources of information, host genome and microbial levels, to accurately characterize immunocompetence in pigs.

microbiology↗

bioRxiv2019

Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach

Mineral amount in bovine muscle affect meat quality, growth, health and reproductive traits in beef cattle. To better understand the genetic basis of this phenotype, we implemented new applications of use for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), by including GEBVs as part of the input. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and mineral amount. Then, RIF was used to determine the regulatory impact of genes and miRNA expression over mineral amount. We also investigated over-represented pathways, as well as evidences from previous studies carried in the same population, to determine regulatory genes for mineral amount e.g. NOX1, whose expression was positively correlated to Zn and was described as regulated by this mineral in humans. With this methodology, we were able to identify genes, miRNAs and pathways not yet described as important for mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the molecular relationships between gene expression and minerals.

genomics↗