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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #391443
Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Geographic contrasts of Y-chromosomal haplogroups from wild and domestic goats reveals ancient migrations and recent introgressions

Author
item NIJMAN, ISSAC - Utrecht University
item Rosen, Benjamin - Ben
item BARDOU, PHILIPPE - Inrae
item FARAUT, THOMAS - Collaborator
item CUMER, TRISTAN - Collaborator
item DALY, KEVIN - Trinity College Dublin
item ZHENG, ZHUQING - Northwest A&f University
item LE, CHUZHAO - Northwest A&f University
item CAI, YUDONG - Northwest A&f University
item ASADOLLAHPOUR, HAJJAT - Northwest A&f University
item KUL, BENGI - Ankara University Of Turkey
item ZHANG, WEI-YI - Southwest University
item E, GUANXIN - Southwest University
item AYIN, A - Kobe University
item BAKHTIN, MEIRAT - Collaborator
item BALTEANU, VALENTIN - Collaborator
item BARFIELD, DIANA - Collaborator
item BEARD, HAILEY - Agresearch
item BERGER, BEATE - University Of Natural Resources & Applied Life Sciences - Austria
item BLICHFELDT, THOR - Collaborator
item BOINK, GEERT - Wageningen University
item BUGIWATI, SRI - Collaborator
item CAI, ZEXI - Aarhus University
item CAROLAN, SEAN - Collaborator
item CUBRIC-CURIK, VLATKA - University Of Zagreb
item DAGONG, IHSAN - Collaborator
item DORJI, TASHI - International Centre For Integrated Mountain Development
item DREW, LOUISE - Collaborator
item GUO, JIAZONG - Sichuan Agricultural University
item HALLSSON, JON - Collaborator
item KANTANEN, JUHA - Natural Resources Institute Finland (LUKE)
item KAWAGUCHI, FUKI - Kobe University
item KAZYMBET, POLAT - Collaborator
item KHAYATZADEH, NEGAR - University Of Natural Resources & Applied Life Sciences - Austria
item KIM, NAMSHIN - Collaborator
item KUMAR, SHAH MANOJ - Collaborator
item LIAO, YUYING - Collaborator
item MARTINEZ, AMPARO - University Of Cordova (UCO), Spain
item MASANGKAY, JOSEPH - University Of The Philippines
item MASAOKA, MAHO - Kobe University
item MAZZA, RAFFAELE - Laboratorio Di Genetica E Servizi (LGS)
item MCEWAN, JOHN - Agresearch
item MILANESI, MARCO - University Of Tuscia
item OMAR, FARUQUE - Bangladesh Agricultural University
item NOMURA, YUTO - Kobe University
item OUCHENE-KHELIFI, NADJET-AMINA - Collaborator
item PEREIRA, FILIPE - Collaborator
item SAHANA, GOUTAM - Aarhus University
item SASAZAKI, SHINJI - Kobe University
item DA SILVA, ANNE - Inrae
item SIMCIC, MOJCA - University Of Ljubljana
item SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria
item SUTHERLAND, ALISON - Collaborator
item TIGCHELAAR, JOHANNE - Wageningen University
item ZHANG, HONGPIN - International Centre For Integrated Mountain Development
item AJMONE-MARSAN, PAOLO - Università Cattolica Del Sacro Cuore
item BRADLEY, DANIEL - Trinity College Dublin
item COLLI, LICIA - Università Cattolica Del Sacro Cuore
item DROGEMULLER, CORD - University Of Bern
item MANNEN, HIDEYUKI - Kobe University
item POMPANON, FRANÇOIS - Collaborator
item TOSSER-KLOPP, GWENOLA - Inrae
item YU, JIANG - Northwest A&f University
item LENSTRA, JOHANNES - Utrecht University
item VARGOATS CONSORTIUM - Collaborator

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/20/2022
Publication Date: 6/25/2022
Citation: Vargoats Consortium, Nijman, I.J., Rosen, B.D., Bardou, P., Faraut, T., Cumer, T., Daly, K., Zheng, Z., Le, C., Cai, Y., Asadollahpour, H., Kul, B.C., Zhang, W., E, G., Ayin, A., Bakhtin, M., Balteanu, V.A., Barfield, D., Beard, H., Berger, B., Blichfeldt, T., Boink, G., Bugiwati, S.R., Cai, Z., Carolan, S., Cubric-Curik, V., Dagong, I.A., Dorji, T., Drew, L., Guo, J., Hallsson, J., Kantanen, J., Kawaguchi, F., Kazymbet, P., Khayatzadeh, N., Kim, N., Kumar, S., Liao, Y., Martinez, A., Masangkay, J.S., Masaoka, M., Mazza, R., Mcewan, J., Milanesi, M., Omar, F., Nomura, Y., Ouchene-Khelifi, N., Pereira, F., Sahana, G., Sasazaki, S., Da Silva, A., Simcic, M., Solkner, J., Sutherland, A., Tigchelaar, J., Zhang, H., Ajmone-Marsan, P., Bradley, D.G., Colli, L., Drogemuller, C., Mannen, H., Pompanon, F., Tosser-Klopp, G., Yu, J., Lenstra, J.A. 2022. Geographic contrasts of Y-chromosomal haplogroups from wild and domestic goats reveals ancient migrations and recent introgressions. Molecular Ecology. https://doi.org/10.1111/mec.16579.
DOI: https://doi.org/10.1111/mec.16579

Interpretive Summary: The VarGoats project is an international collaboration. The goal of this group is to sequence at least 1,000 genomes to better understand the consequences of domestication and selective breeding on the genetic diversity of domestic goats. An additional goal is to understand how the process of spcies formation and crossing have affected the genomes of a set of species representative of the genus Capra (goats). Because the Y chromosome is paternally inherited, it is a sensitive marker of population history and male-mediated crossing. Previous studies identified 4 major Y chromosome groups in domestic goats. This study was able to expand that to 5 major groups. The distribution of these groups indicate ancient population bottlenecks during the migration into northern Europe, eastern and southern Asia and Africa. It also reveals an early introduction of Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and AngloNubian breeds. More recent crosses are those of European goats into the native Korean goat population and of Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study demonstrates the power of Y chromosomal variation for understanding the history of globally distributed domestic species.

Technical Abstract: By its paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified SNPs in the SRY, ZFY, DBY genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, whole-genome sequences (WGSs) of 386 domestic goats from 75 modern breeds and 7 wild goat species generated by the Vargoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, but Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 170 domestic breeds indicate ancient paternal population bottlenecks during the migration into northern Europe, eastern and southern Asia and Africa. In addition, sharing of haplogroups reveals male-mediated introgressions, most notably an early gene flow of Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and AngloNubian breeds. More recent introgressions are those of European goats into the native Korean goat population and of Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variation for reconstructing the history of domestic species with a wide geographic range.