A Genetic Window on Sardinian Native Horse Breeds through Uniparental Molecular Systems

Abstract

Sardinia, an island located to the west of Italy in the Mediterranean Sea, boasts three native horse breeds: Giara, Sarcidano, and Sardinian Anglo-Arab. Here, we have investigated for the first time three loci of the non-recombining region of the Y chromosome (NRY) in 34 stallions from these breeds and performed a phylogenetic analysis of the maternal relationships among 178 previously published mitochondrial control regions. We found that the current NRY diversity of Sardinian horse breeds is linked to three haplotypes (HT), all identified within Sarcidano. Each breed showed a typical HT: HT1 (ancestral) was the most represented in Sarcidano, HT2 (Neapolitan/Oriental wave) in Giara, and HT3 (Thoroughbred wave) in Sardinian Anglo-Arab. The specificity of each haplotype suggests the influence of independent breeding strategies and the effect of genetic drift in each Sardinian population. The female counterpart, extended to 178 horses, showed a low genetic variability and a common maternal origin for Giara and Sarcidano. The higher variability of the Sardinian Anglo-Arab indicates multiple mare lineages in its current population. Further genetic analyses will be crucial to understand the paternal history of male horses, preserve the endangered mares’ and stallions’ lineages, and improve the enhancement of autochthonous genetic resources on this island.

Unlocking Horse Y Chromosome Diversity

“…In particular, differently from the European and North American breeds [ 92 , 136 ], almost half of Chinese horses did not show a direct link between the SNP T/A and the deletion in np 10,594 for the HT3 [ 138 ]. The same low variability in the other modern European breeds was observed in three local breeds from Sardinia (Italy), each showing one distinctive haplotype (HT1, HT2 and HT3) frequency: 50% of HT1 in the Sarcidano breed, 75% of HT2 in the Giara breed and 58% of HT3 in the Sardinian Anglo-Arab breed [ 139 ]. These haplotype distributions highlight the replacement of autochthonous Y chromosomes with the import of stallions belonging to three paternal lines (ancestral line, Neapolitan/Oriental and Thoroughbred wave) for the improvement of native breeds.…”

“…The widespread presence of HT1 and HT2 is probably due to the Oriental wave, as Arabian horses carrying these MSY haplotypes were imported into Central European studs, while the frequency of HT3 in modern horses is attributable to the intensive use of English Thoroughbred in the improvement of other horse breeds. The SNPs and indels identifying the different haplotypes were further investigated in 42 breeds from different areas of Europe, Asia and America [ 136 ] and in 13 Chinese indigenous [ 138 ], 3 Sardinian [ 139 ] and 1 Kazach [ 140 ] horse breeds ( Figure 2 and Table S3 ).…”

Characterization of the Sarcidano Horse Coat Color Genes

“…Sarcidano Horse frequently has supernumerary bilateral upper premolars, which have disappeared in modern horse breeds, placing this breed on an archaic model (similarly to the Przewalski’s Horse). Previous research confirmed the marginal impact of crossbreeding on the Sarcidano Horse mitochondrial gene pools and the lack of recent gene flow from outside [ 2 ], suggesting that this breed represents an important resource to be preserved, but also an important model to be studied.…”

The Revolution of Animal Genomics in Forensic Sciences

“…Within some species, populations may be isolated from others, and they could not be subject to gene flow. In this scenario, genetic differences are accumulated over evolutionary time until members of a population living in an isolated region will display similar types of genetic markers ( [119,120], as examples).…”