Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

Christian Natanaelsson,Helen Angleby,Joakim Lundeberg,Peter Savolainen,Ewen Kirkness,Mattias Cr Oskarsson

doi:10.1186/1471-2156-7-45

Abstract

BackgroundPopulation 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.ResultsThe 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.ConclusionWe 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.

Highlights

Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs
For a sequence to be accepted as Y specific three criteria had to be fulfilled: (i) it should, in a Blast search against the human genome, have a best hit or be linked to a read with a best hit, to the human Y chromosome, (ii) it should in a Blast search against the reference female dog genome sequence have a negative result and (iii) it should in a PCR against samples from five male and five female dogs yield PCR product only for the male samples
Identification of candidate Y-chromosome sequences by Blast analysis The Blast analysis was performed in two steps; to reject the thousands of male sequences that lack identity with the female genome sequence owing to gaps in the female genome assembly or polymorphisms between the two genomes, a screen of the male dog genome sequence against the human Y chromosome sequence was done before comparing with the female dog genome sequence

Summary

Introduction

Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. Population genetic studies of the earliest history of the domestic dog have so far mainly been based on the analysis of mitochondrial DNA (mtDNA), which represents a single genetic marker and, since it is maternally inherited, can only describe the history of females [1,2,3,4]. It has been shown for humans that individuals may have Ychromosomal haplotypes that are identical based on a large number of microsatellite markers even though the haplotypes as defined by biallelic markers are different, a contradiction which is due to recurrent mutations of the microsatellites [7] This shows that Y-chromosomal biallelic markers are imperative for phylogenetic studies where they can serve as a backbone for the Y-chromosome phylogeny upon which the more detailed microsatellite variation can be imposed. There is a need for DNA sequence information for the dog Y chromosome

Methods

Results

Conclusion