Novel Y‐chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations

Abstract

SummaryY-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 (H D = 0.904 AE 0.011 and H D = 0.491 AE 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 (F ST = 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.

Y‐chromosome haplotype analysis revealing multiple paternal origins in swamp buffaloes of China and Southeast Asia

“…The gross haplotype diversity of swamp buffalo was 0.308 ± 0.026. This value is close to that of domestic sheep (0 ~ 03849; Zhang et al, 2014), but lower than that of cattle (0.422 ± 0.3; Edwards et al, 2011) and pig (0.491 ± 0.077-0.711 ± 0.118; Iacolina et al, 2016). Our results suggest a low level of Y-chromosome genetic diversity in swamp buffalo.…”

Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East‐Caucasian and Central Italian populations

“…Throughout its history, the wild boar has been strongly influenced by human practices such as hunting, pig domestication, and animal translocation (Larson et al, 2005;Scandura, Iacolina, & Apollonio, 2011). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014).…”

“…Thus, analysis of the changes in the geographical range of S. scrofa could aid our understanding of not only the global patterns of evolution and ecosystem change (Anijalg et al, 2018). Previous studies revealed the complex genetic structure of wild boar populations in Eurasia, including multiple domestication events and gene flow between wild boar and domestic pig breeds (Iacolina et al, 2016;Larson et al, 2005;Ramíres et al, 2009;Ribani et al, 2019;Šprem et al, 2014).…”

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

“…The use of molecular genetic methods makes it possible to characterize animal populations and determine the degree of their genetic differentiation. Various types of DNA markers are used to characterize the wild boar populations from Russia: mitochondrial DNA [ 10 , 11 , 12 ], Y-chromosome [ 12 , 13 ], STR [ 14 , 15 , 16 , 17 ], SNP [ 18 , 19 , 20 ].…”