High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

Abstract

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Genomic diversity of the locally developed Latvian Darkheaded sheep breed

“…Previously estimated heterozygosity levels for different native breeds from Southern Europe ranged between 0.30 and 0.398. Ho ranged from 0.30 to 0.42 for those from Central Europe, and Ho estimates derived from other studies on sheep breeds originating from northern regions ranged between 0.30 and 0.39 [ 11 , [36] , [37] , [38] , [39] , [40] , [41] ]. For example, the Lithuanian Blackface sheep, considered a modern improved breed with a population of approximately 9000 sheep, has been shown to harbor high genetic diversity, with an average H o of 0.41 [ 40 ].…”

“…This exacerbates the demand for livestock breeds with improved productivity [ [6] , [7] , [8] , [9] , [10] ]. Without careful management of breed improvement, numerous indigenous breeds may be lost [ [5] , [6] , [7] , [11] , [12] , [13] ]. Thus, there is a risk of losing genotypes formed in the natural environment that have adapted to local conditions over a long period and are resistant to specific environmental conditions [ 3 , 4 , 14 ].…”

Insight into the current genomic diversity, conservation status and population structure of Tunisian Barbarine sheep breed

“…Actively observing and preserving this genetic diversity is essential to ensure the sustained viability of traditional breeding methods in the future, as emphasized by Asmare et al (2023). The investigation provided valuable insights into the genetic diversity of the Tunisian Barbarine breed and its relationships with other sheep breeds.…”