Differential distribution of Y-chromosome haplotypes in Swiss and Southern European goat breeds

Abstract

The analysis of Y-chromosome variation has provided valuable clues about the paternal history of domestic animal populations. The main goal of the current work was to characterize Y-chromosome diversity in 31 goat populations from Central Eastern (Switzerland and Romania) and Southern Europe (Spain and Italy) as well as in reference populations from Africa and the Near East. Towards this end, we have genotyped seven single nucleotide polymorphisms (SNPs), mapping to the SRY, ZFY, AMELY and DDX3Y Y-linked loci, in 275 bucks from 31 populations. We have observed a low level of variability in the goat Y-chromosome, with just five haplotypes segregating in the whole set of populations. We have also found that Swiss bucks carry exclusively Y1 haplotypes (Y1A: 24%, Y1B1: 15%, Y1B2: 43% and Y1C: 18%), while in Italian and Spanish bucks Y2A is the most abundant haplotype (77%). Interestingly, in Carpathian goats from Romania the Y2A haplotype is also frequent (42%). The high Y-chromosome differentiation between Swiss and Italian/Spanish breeds might be due to the post-domestication spread of two different Near Eastern genetic stocks through the Danubian and Mediterranean corridors. Historical gene flow between Southern European and Northern African goats might have also contributed to generate such pattern of genetic differentiation.

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

“…A preliminary analysis of the Y-chromosomal diversity in European and Turkish goats defined the three haplotypes Y1A, Y1B and Y2, showing strong geographic differentiation (Lenstra and Econogene Consortium, 2005). The same haplotypes were found in goats from Portugal and North-Africa (Pereira et al, 2009), Turkey (Cinar Kul et al, 2015), east and south Asia (Waki et al, 2015), Switzerland and Spain (Vidal et al, 2017) with additional haplotypes Y2B in east Asia, Y2C in Turkish Kilis goats, and Y1B2 as well Y1C mainly in Switzerland (Table 1). However, these haplotypes are based on a low number of SNPs in or near DBY-1, SRY and ZFY.…”

“…We differentiating the major Y-chromosomal haplogroups Y1AA, Y1AB, Y1B, Y2A and Y2B for 1720 domestic goats from 132 breeds by combining data from several sources as detailed per breed in Table 4: From the goat panel collected for the Econogene project, DNA samples of 353 male goats from 38 European or southwestern Asian breeds were analyzed by PCR amplification and dideoxy-sequencing of segments within the DBY, SRY and ZFY genes (Lenstra and Econogene Consortium, 2005) as described previously for bovine samples (Nijman et al, 2008; Edwards et al, 2011) and using the primers listed in Table 5. We used published data for 90 goats from 5 Portuguese breeds or from Morocco (Pereira et al, 2009), for 211 goats from 10 Asian breeds (Waki et al, 2015), for 181 goats from 8 Turkish breeds (Cinar Kul et al, 2015) and for 270 goats from 26 Spanish or Swiss breeds (Vidal et al, 2017). 362 DNA samples (57 breeds) from several sources, including the AdaptMap panel (Colli et al, 2018) were genotyped by the KASP assay (Table 4).…”

“…We used published data for 90 goats from 5 Portuguese breeds or from Morocco (Pereira et al, 2009), for 211 goats from 10 Asian breeds (Waki et al, 2015), for 181 goats from 8 Turkish breeds (Cinar Kul et al, 2015) and for 270 goats from 26 Spanish or Swiss breeds (Vidal et al, 2017).…”

“…For samples collected by Cinar-Kul (2015) and Vidal et al (2017) or analyzed by KASP before genomic data became available, Y1AA and Y1AB have been both scored as Y1A haplotype. Several of these samples did not contain Y1A or belonged to breeds for which additional data were available (Table 3).…”

“…However, for 31 breeds we only have the Y1A frequency. Likewise, Vidal et al (2017) and the Kasp assay did not differentiate Y2A and Y2B. Since sequence data indicate that Y2B does not occur in modern domestic goats from Europe, Anatolia and Iran, we assigned all Y2 scores in European and African goats to Y2A.…”