title: Analysis of the non-recombining Y chromosome defines polymorphisms in domestic pig breeds: ancestral bases identified by comparative sequencing.
abstract: Sequences from 20 amplicons representing nine different loci and 11369bp from the short arm of the pig Y chromosome were compared using pools of DNA from different European and Chinese breeds. A total of 33 polymorphic sites were identified, including five indels and 28 single nucleotide polymorphisms (SNPs). Three high frequency SNPs within the coding regions of SRY were further analysed across 889 males representing 25 European and 25 Asian breeds or Lines, plus a European Line of Meishan. Two haplotypes seen to be associated with 'European' or 'Chinese' origin in the initial SNP discovery phase were found to be the most common in their respective groups of breeds in a more detailed genotyping study. Two further SRY haplotypes are relatively rare. One was found exclusively within Tamworth, at low frequency in Retinto, and in three Chinese breeds (Huai, Sahwutou and Xiaomeishan). The other uncommon haplotype is found exclusively in Bamajiang, two further Chinese breeds (Hangjiang Black and Longling) and two European rare breeds (Mangalica and Linderödssvin), but appears based on comparison with other suids to represent an ancestral sequence.
authors.affiliation: PIC Research Laboratory, Department of Pathology, Tennis Court Road, Cambridge, UK.
authors.forename: K M
authors.initials: KM
authors.lastname: Cliffe
authors.forename: A E
authors.initials: AE
authors.lastname: Day
authors.forename: M
authors.initials: M
authors.lastname: Bagga
authors.forename: K
authors.initials: K
authors.lastname: Siggens
authors.forename: C R
authors.initials: CR
authors.lastname: Quilter
authors.forename: S
authors.initials: S
authors.lastname: Lowden
authors.forename: H A
authors.initials: HA
authors.lastname: Finlayson
authors.forename: C J
authors.initials: CJ
authors.lastname: Palgrave
authors.forename: N
authors.initials: N
authors.lastname: Li
authors.forename: L
authors.initials: L
authors.lastname: Huang
authors.forename: S C
authors.initials: SC
authors.lastname: Blott
authors.forename: C A
authors.initials: CA
authors.lastname: Sargent
mesh_terms: D000818:Animals; D001947:Breeding; D002681:China; D017931:DNA Primers / Q000235:genetics; D005060:Europe; D006239:Haplotypes; D008297:Male; D021141:Nucleic Acid Amplification Techniques; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D051876:Sex-Determining Region Y Protein / Q000235:genetics; D034421:Sus scrofa / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics*
chemical_list: D017931:DNA Primers; D051876:Sex-Determining Region Y Protein