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Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Gene Technology.
KTH, School of Biotechnology (BIO), Gene Technology.ORCID iD: 0000-0003-4313-1601
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2006 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 7Article in journal (Refereed) Published
Abstract [en]

Background: Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results: The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion: We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.

Place, publisher, year, edition, pages
2006. Vol. 7
Keyword [en]
genome sequence, domestic dog, origin
National Category
Medical Biotechnology
Identifiers
URN: urn:nbn:se:kth:diva-16107DOI: 10.1186/1471-2156-7-45ISI: 000241743700001Scopus ID: 2-s2.0-33750703200OAI: oai:DiVA.org:kth-16107DiVA: diva2:334149
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved
In thesis
1. Analysis of the origin and spread of the domestic dog using Y-chromosome DNA and mtDNA sequence data
Open this publication in new window or tab >>Analysis of the origin and spread of the domestic dog using Y-chromosome DNA and mtDNA sequence data
2012 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The domestic dog was probably the first domesticated animal, and the only one to spread to all continents in ancient times. The dog is one of the most phenotypically diverse animals, a result of human selection throughout dog history. Studies of the genetic origins and early spread of domestic dogs is important to gather information about biological and cultural mechanisms behind domestication but also to investigate early human history. The step from a hunter and gatherer lifestyle to farming is one of the most important steps in human history. In this thesis I will present work aimed at understanding both domestic dog origins and dispersal. In order to be able to investigate dog origins based on a second haploid chromosome we identified 14,437 bp of Y-chromosomal DNA sequence. Based on this we show that dogs in Asia south of Yangtze River (ASY) has the highest genetic diversity and was founded from a large number of wolf founders confirming earlier mtDNA results. Early dog dispersal is tightly coupled to human history with the dog brought along as a cultural item. We have for the first time investigated the dog dispersal into Polynesia and Australia and our data can be used as evidence for a more complex settlement of Polynesia than earlier indicated from archaeological and linguistic studies. Analysis of Y-chromosome SNPs in Australian dingoes confirms earlier mtDNA genetic studies that the dingo is part of the domestic dog phylogeny and was founded from a small population of domestic dogs. We have also for the first time investigated the dog population on Madagascar and our data strongly indicates a mainland African origin for the Madagascan dogs. Finally, we have investigated the American dog population sampled from throughout the continent and also for the first time included putative indigenous breed dogs such as Chihuahua and Pero Sín Pelo del Peru, and the free-ranging Carolina dogs from southern USA. Our data clearly indicates a primarily Old World origin for the indigenous breed dogs and also for the free-ranging Carolina dogs in USA. We can also for the first time present evidence for continuity between the ancient and extant dog population with e.g. exclusive sharing of a haplotype between a modern sample of Chihuahua and an ancient Mexican sample.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2012. 66 p.
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2012:6
Keyword
mtDNA, domestication, Y-chromosome, SNP, ASY, dog, dingo
National Category
Other Industrial Biotechnology
Identifiers
urn:nbn:se:kth:diva-94145 (URN)978-91-7501-364-0 (ISBN)
Public defence
2012-05-25, Lennart Nilsson-salen, Nobels väg 15A, Solna, 13:00 (English)
Opponent
Supervisors
Funder
Swedish Research Council
Note
QC 20120510Available from: 2012-05-10 Created: 2012-05-08 Last updated: 2012-05-10Bibliographically approved

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