Emil Ibragimov

Background: Understanding the genetic regulation of metabolism is essential for improving animal health and productivity and for strengthening the use of pigs as translational models for human metabolic diseases. Metabolomics, when integrated with genomic data, provides a powerful framework for identifying genetic factors that influence intermediate molecular phenotypes closely linked to physiology. While large-scale metabolomics genome‑wide association studies (GWAS) have been extensively performed in humans, comparable studies in pigs remain limited. Among omics disciplines, metabolomics, the systematic study of metabolites central to physiology, represents the omics layer most closely linked to end-point phenotypes in mammals, such as health and production traits (e.g. growth rate). Metabolite levels are influenced by genetics, diet, and microbiome composition, with human studies showing high heritability and identifying numerous metabolite quantitative trait loci (mQTLs). While such findings have advanced our understanding of disease biology in humans, comparable studies in pigs remain limited. Results: We performed GWAS of the serum metabolome in 213 three‑way crossbred pigs [(Landrace × Yorkshire) × Duroc], analyzing 248 metabolites and 30,628 metabolite ratios. We identified 41 significant metabolite–variant associations, which were consolidated into 18 mQTLs based on linkage disequilibrium (LD). Several regions were associated with multiple, biochemically related metabolites, while others showed highly specific effects. Cross-species comparison with the human GWAS catalog revealed candidate genes within seven mQTLs. Through an integrative prioritization strategy, putative causal genes—predominantly enzymes and transporters—were identified for 14 of 18 mQTLs. Conclusions: Our results expand the catalog of genetic loci influencing serum metabolite variation in pigs and highlight both conserved and pig specific components of metabolic regulation. These findings provide a foundation for incorporating metabolomics into pig breeding programs and reinforce the value of pigs as a translational model for studying metabolite-associated traits and diseases in humans.

Complete blood count with differential is a critical diagnostic tool for evaluating the physiological and health status of individuals by analyzing white blood cells, red blood cells, and platelets. While extensively used in human medicine, the application of complete blood count biomarkers in pigs remain limited. This review focuses on the genetic architecture of hematological traits in pigs (Sus scrofa) using data from genetic association studies. By compiling data from multiple porcine studies, we identified 509 SNPs within 53 high‐confidence QTL supported by more than one study. Among these, 37 QTL were homologous to human loci, with 19 containing plausible candidate genes likely to be influencing hematological traits. These genes are often linked to cytoskeletal formation, hematopoiesis, and immune function, highlighting conserved biological mechanisms across species. Our findings provide a foundation for further investigations into the genetic regulation of blood cell parameters in pigs and their implications for health, welfare, and production traits, offering potential translational insights for both veterinary and human medicine.

Feed efficiency (FE) in pigs is an important factor in the profitability of pig farming operations. It refers to the ability of a pig to convert the feed it consumes into body weight. We used two metrics to measure FE: feed conversion ratio and average daily residual feed intake. A previous genome‐wide association study and transcriptome study in crossbred pigs identified two QTL regions on SSC9 associated with residual feed intake and pointed out two candidate genes of interest: (a) the gene encoding the Aryl Hydrocarbon Receptor gene (AHR) transcription factor; and (b) the Dynein, Axonemal, Heavy Polypeptide 11 gene (DNAH11). The previous study identified missense mutations in both genes leading to a conservative substitution of glycine to cysteine in AHR (AHR_rs339939442) and two non‐conservative substitutions in DNAH11, where arginine is replaced by threonine (DNAH11_rs325475644) and alanine is replaced by threonine (DNAH11_rs346074031). We have now genotyped the missense mutations in independent cohorts of 107 Duroc, 155 Landrace and 160 Yorkshire pigs to substantiate further if these variants directly impact FE‐related phenotypes. We verified that allele T of AHR_rs339939442 in AHR improves FE in Yorkshire pigs. Genotype GG of AHR_rs339939442 was fixed in Duroc pigs. We also confirmed that the variants rs325475644 and rs346074031 in DNAH11 did not affect FE. The findings contribute valuable insights into the genetic mechanisms governing FE in pigs, potentially offering contributions for future enhancements of FE.

Lean meat percentage is a critical production trait in pig breeding systems with direct implications for the sustainability of the industry. In this study, we conducted a genome‐wide association study for lean meat percentage using a cohort of 850 Duroc × (Landrace × Yorkshire) crossbred pigs and we identified QTL on SSC3 and SSC18. Based on the predicted effect of imputed variants and using the PigGTEx database of molecular QTL, we prioritized candidate genes and SNPs located within the QTL regions, which may be involved in the regulation of porcine leanness. Our results indicate that a nonsense mutation in ZC3HAV1L on SSC18 has a direct effect on lean meat percentage.

Post-weaning diarrhea in pigs is a considerable challenge in the pig farming industry due to its effect on animal welfare and production costs, as well as the large volume of antibiotics, which are used to treat diarrhea in pigs after weaning. Previous studies have revealed loci on SSC6 and SSC13 associated with susceptibility to specific diarrhea causing pathogens. This study aimed to identify new genetic loci for resistance to diarrhea based on phenotypic data. In depth clinical characterization of diarrhea was performed in 257 pigs belonging to two herds during the first 14 days post weaning. The daily diarrhea assessments were used for the classification of pigs into case and control groups. Pigs were assigned to case and control groups based only on the incidence of diarrhea in the second week of the study in order to differentiate between differences in etiology. Genome-wide association studies and metabolomics association analysis were performed in order to identify new biological determinants for diarrhea susceptibility. With the present work, we revealed a new locus for diarrhea resistance on SSC16. Furthermore, studies of metabolomics in the same pigs revealed one metabolite associated with diarrhea.