title: Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations.
abstract: 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.
authors: Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy. liacolina@uniss.it.|Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, 9000, Denmark. liacolina@uniss.it.
authors: L
authors: L
authors: Iacolina
authors: Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia.
authors: V
authors: V
authors: Brajković
authors: Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy.
authors: A
authors: A
authors: Canu
authors: Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia.
authors: N
authors: N
authors: Šprem
authors: Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia.
authors: V
authors: V
authors: Cubric-Curik
authors: Division of Animal Science, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, I-40127, Italy.
authors: L
authors: L
authors: Fontanesi
authors: Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia.
authors: U
authors: U
authors: Saarma
authors: Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy.
authors: M
authors: M
authors: Apollonio
authors: Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy.
authors: M
authors: M
authors: Scandura
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D005060:Europe; D051456:Gene Flow; D014644:Genetic Variation; D005828:Genetics, Population; D006239:Haplotypes; D008297:Male; D018895:Microsatellite Repeats; D034421:Sus scrofa / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*
keywords: Y haplotype; genetic diversity; microsatellite; paternal DNA markers