Novel Y-chromosome STRs in Sus scrofa and their variation in European wild boar and domestic pig populations

Y-chromosome markers are important tools for studying male-specific gene flow within and
between populations, hybridization patterns and kinship. However, their use in non-human
mammals is often hampered by the lack of Y-specific polymorphic markers. We identified
new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome
sequence. We selected four polymorphic loci (5–10 alleles per locus), falling in one
duplicated and two single-copy regions. A total of 32 haplotypes were found by screening
211 individuals from eight wild boar populations across Europe and five domestic pig
populations. European wild boar were characterized by significantly higher levels of
haplotype diversity compared to European domestic pigs (HD = 0.904+-0.011 and
HD = 0.491+-0.077 respectively). Relationships among STR haplotypes were investigated
by combining them with single nucleotide polymorphisms at two linked genes (AMELY and
UTY) in a network analysis. A differentiation between wild and domestic populations was
observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled
wild boar. Similarly, a certain degree of geographic differentiation was observed across
Europe, with a number of local private haplotypes and high diversity in northern
populations. The described Y-chromosome markers can be useful to track male inheritance
and gene flow in wild and domestic populations, promising to provide insights into
evolutionary and population genetics in Sus scrofa.