Capturing Genetic Diversity and Selection Signatures of the Endangered Kosovar Balusha Sheep Breed

Abstract

There is a growing concern about the loss of animal genetic resources. The aim of this study was to analyze the genetic diversity and potential peculiarity of the endangered Kosovar sheep breed Balusha. For this purpose, a dataset consisting of medium-density SNP chip genotypes (39,879 SNPs) from 45 Balusha sheep was generated and compared with SNP chip genotypes from 29 individuals of a second Kosovar breed, Bardhoka. Publicly available SNP genotypes from 39 individuals of the relatively closely located sheep breeds Istrian Pramenka and Ruda were additionally included in the analyses. Analysis of heterozygosity, allelic richness and effective population size was used to assess the genetic diversity. Inbreeding was evaluated using two different methods (FIS, FROH). The standardized FST (di) and cross-population extended haplotype homozygosity (XPEHH) methods were used to detect signatures of selection. We observed the lowest heterozygosity (HO = 0.351) and effective population size (Ne5 = 25, Ne50 = 228) for the Balusha breed. The mean allelic richness levels (1.780–1.876) across all analyzed breeds were similar and also comparable with those in worldwide breeds. FROH estimates (0.023–0.077) were highest for the Balusha population, although evidence of decreased inbreeding was observed in FIS results for the Balusha breed. Two Gene Ontology (GO) TERMs were strongly enriched for Balusha, and involved genes belonging to the melanogenesis and T cell receptor signaling pathways, respectively. This could result from selection for the special coat color pattern of Balusha (black head) and resistance to certain infectious diseases. The analyzed diversity parameters highlight the urgency to preserve the local Kosovar Balusha sheep as it is clearly distinguished from other sheep of Southeastern Europe, has the lowest diversity level and may harbor valuable genetic variants, e.g., for resistance to infectious diseases.

Genomic Diversity Analyses of Some Indigenous Montenegrin Sheep Populations

“…These breeds have higher Ne 5 values, similar to Australian breeds (Ne from 140 to 348) [24], Russian breeds (Ne 5 from 65 to 543) [27], and some breeds in Kyrgyzstan (Gissar Ne 5 = 660 and Aykol Ne 5 = 563) [28]. The Ne 5 reported in our study for BA in Montenegro are significantly higher than those reported for Bardhoka (Bardoka) in Kosovo [35]. This may depend on the structure of the sampling flocks, related individuals, breed mixing, or migration, but also on the software used [55].…”

“…The results for Montenegrin sheep for rarified allelic richness were higher than those reported by Deniskova et al (2018) [27] for Russian sheep breeds, Deniskova et al (2019) [28] for Kyrgyz sheep breeds, and Adeniyi et al (2022) [35] for Kosovar sheep breeds.…”

“…Montenegrin sheep populations have slightly higher genetic diversity than other Balkan Peninsula breeds: Croatian sheep breeds [34], Kosovar sheep breeds [35], and other Balkan breeds described in Ciani et al 2020 [42]. In addition, the BA sheep breed on the territory of Montenegro had higher observed and expected heterozygosity than Barloka (the same sheep population from Kosovo) [35].…”

“…Nowadays, the OvineSNP50 BeadChip (54,241 SNPs) and the high-density Ovine SNP600 BeadChip (606,006 SNPs) are predominantly used for the genetic analysis of sheep populations in different parts of the world. In the last decade, large amounts of SNP genotyping data have been obtained from worldwide sheep breeds: American sheep breeds [22,23]; Australian [24]; Chinese [25]; Ethiopian [26]; Russian [27]; Kyrgyz [28]; French [29]; Swedish [30]; Spanish [31]; Italian [32]; Welsh sheep breeds [33]; or regional studies including the Pramenka sheep group [1,34,35]. SNP BeadChips are an important tool for exploring genetic diversity and genetic relatedness, assessing population structure and admixture, detecting selection signatures, and in GWAS studies [22][23][24]26,28,[36][37][38][39].…”

Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds

“…Four methods developed to identify selection signatures in livestock populations, all based on within-population approaches: i) extremely high SNP incidence in ROH ("extreme ROH islands" or "eROHi"), ii) integrated haplotype score (iHS), iii) number of segregating sites by length (nSL), and iv) composite likelihood ratio test (CLR), are widely used to identify hard and soft selection signals [ 12 – 18 ]. For example, many previous studies on Mediterranean sheep used statistical methods with medium density genomic data and found candidate genes for coat color, morphology, milk, and wool [ 19 – 24 ].…”