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.

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

“…Considering the frequencies of haplotypes with SNPs, pairwise nucleotide diversity [38] is π = 3.71×10 −6 , an extremely low value compared to those observed in domestic pigs (π = 1.38×10 −3 ) [11], [12] and dogs (π = 2.91×10 −4 ) [46].…”

“…Depending on the genetic regions analysed, uniparentally inherited markers can be used to trace individual founder lines or families [7]. In livestock, Y-chromosomal and mtDNA variation has been used to study the domestication and population structure of the domestic dog [8]–[10], pig [11], [12], sheep [13] and cattle [14].…”

Contacts in the last 90,000 years over the Strait of Gibraltar evidenced by genetic analysis of wild boar (Sus scrofa)

“…For the Y-chromosome analysis, we sequenced the partial AMELY, USP9Y and UTY (UTYin1 and UTYin9) regions in one male from Morocco (WBMoroc2) in order to compare them with the published sequences of previous studies [21,48,49] and to identify their haplotype. There were three defined haplotypes, and our results showed that, according to Ramírez et al [21], our sample belonged to the HY2 haplotype.…”

“…Obviously, we cannot rule out previous contacts to the Late Pleistocene during former glacial periods. The absence of a genetic footprint could be due to the genetic flow not being enough to have endured [49]. The CR182 haplotype found in Tunisia should be the result of either genetic introgression with the Near East wild boar or a trace from the past.…”

“…As for the causes of movements, if they took place approximately from 90,000 onward, it is difficult to know if contacts were made by natural colonisations, by human action, or by a combination of both without having further data [48,49]. This is due to several events occurring at the same time.…”