Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats
Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats
Abstract The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.
Lenstra Johannes A.、Nijman Isa?c J.、Rosen Benjamin D.、Balteanu Valentin A.、Berger Beate、Blichfeldt Thor、Carolan Sean、Sutherland Alison、Tigchelaar Johannes、Ajmone-Marsan Paolo、da Silva Anne、Bradley Daniel G.、Jiang Yu、Econogene Consortium、Cubric-Curik Vlatka、Ouchene-Khelifi Nadjet-Amina、Cumer Tristan、Colli Licia、Khayatzadeh Negar、Daly Kevin G.、Sim?i? Mojca、Kantanen Juha、Boink Geert、Mart¨anez Amparo、S?lkner Johann、Pereira Filipe、Zheng Zhuqing、Pompanon Fran?ois、Mazza Raffaele、Kim Namshin
Faculty of Veterinary Medicine, Utrecht UniversityFaculty of Veterinary Medicine, Utrecht University||Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht UniversityAnimal Genomics and Improvement Laboratory, Agriculture Research ServiceFaculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine of Cluj-NapocaUniversity of Natural Resources and Life Sciences Vienna (BOKU)Norwegian Association of Sheep and Goat BreedersOld Irish Goat SocietyNew Zealand Arapawa Goat AssociationStichting Zeldzame HuisdierrassenDip. di Scienze Animali, della Nutrizione e degli Alimenti, Univ. Cattolica del S. Cuore di PiacenzaUniv. Limoges, INRASmurfit Institute of Genetics, Trinity College DublinKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityDep. Animal Science, University of ZagrebLaboratory of Biotechnologies related to Animal Reproduction, Science Veterinary Institute, University of BlidaUniversit¨| Grenoble Alpes, Universit¨| Savoie Mont Blanc, CNRS, LECADip. di Scienze Animali, della Nutrizione e degli Alimenti, Univ. Cattolica del S. Cuore di PiacenzaUniversity of Natural Resources and Life Sciences Vienna (BOKU)Smurfit Institute of Genetics, Trinity College DublinUniv. Ljubljana, Biotechnical Faculty, Dep. Animal ScienceNatural Resources Institute Finland (Luke)Stichting Zeldzame HuisdierrassenDep. Gen¨|tica, Universidad de C¨?rdobaUniversity of Natural Resources and Life Sciences Vienna (BOKU)IDENTIFICA, UPTECKey Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F UniversityUniversit¨| Grenoble Alpes, Universit¨| Savoie Mont Blanc, CNRS, LECALaboratorio Genetica e ServiziKorea Research Institute of Bioscience and Biotechnology (KRIBB)
畜牧、动物医学遗传学动物学
goatgenomeY-chromosomehaplotypemigrationbottleneckintrogression
Lenstra Johannes A.,Nijman Isa?c J.,Rosen Benjamin D.,Balteanu Valentin A.,Berger Beate,Blichfeldt Thor,Carolan Sean,Sutherland Alison,Tigchelaar Johannes,Ajmone-Marsan Paolo,da Silva Anne,Bradley Daniel G.,Jiang Yu,Econogene Consortium,Cubric-Curik Vlatka,Ouchene-Khelifi Nadjet-Amina,Cumer Tristan,Colli Licia,Khayatzadeh Negar,Daly Kevin G.,Sim?i? Mojca,Kantanen Juha,Boink Geert,Mart¨anez Amparo,S?lkner Johann,Pereira Filipe,Zheng Zhuqing,Pompanon Fran?ois,Mazza Raffaele,Kim Namshin.Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats[EB/OL].(2025-03-28)[2025-06-19].https://www.biorxiv.org/content/10.1101/2020.02.17.952051.点此复制
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