Genetic regulation and variation of foetal plasma metabolome in the context of sex, paternal breeds and variable foetal weight

We present data on 1,112 plasma metabolites using untargeted UHPLC-MS/MS methods, of 260 backcross (BC) foetuses from two sires’ breeds at 63 days post-conception (dpc). Eight chemical superclasses have been identified, with lipids accounting for the majority of metabolites. Genomic heritability (h²) was estimated for each metabolite, revealing that 50% had h² values below 0.2, with a higher average in the amino acid class compared to the lipid. We annotated 448 significant metabolite quantitative trait loci (mQTLs) associated with 10 metabolites, primarily lipids, indicating strong genetic regulation. Additionally, metabolite associations with sex, foetal weight, and sire's breed were explored, revealing significant associations for 354 metabolites.Foetal weight influenced the largest number of metabolites, particularly glycerophospholipids and sphingolipids, emphasizing the genetic and metabolic complexity underlying foetal development.