Breed-specific divergence in boar sperm regulatory profiles involves piRNA and mitochondrial small RNAs

Small non-coding RNAs (sRNAs) act as post-transcriptional regulators and protectors of genomic integrity. Environmental stress and genomic variation can both alter the sRNA composition in sperm, leading to altered offspring phenotypes. Commercial pig breeds, which have undergone years of selective breeding, vary in purpose: some are optimized for meat production, others for high reproductive capacity - traits that are often antagonistic. This study aims to characterize and compare the sperm sRNA composition in four commercial pig breeds, two used for meat production (sire lines) and two for reproductive purposes (dam lines). We find that the two breeds propagated for reproduction traits (Landrace, Yorkshire) show high variability in PIWI-interacting RNA (piRNA) which target transposable elements. In contrast, the two meat production breeds (Duroc, Hampshire) were enriched in mitochondrial ribosomal RNA-derived sRNA (mt rsRNA). These trends may reflect an emphasis on genome protection among reproductive breeds, and on mitochondrial function and metabolic output in meat production breeds. Other notable differences included amongst the miRNAs, which were associated with numerous developmental and metabolic processes. Our study investigates the unique sRNA profiles in boar sperm associated with different breeding objectives, highlighting possible epigenetic mechanisms that could be leveraged in selective breeding programs to optimize fertility, growth and offspring health.