Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis

Abstract

This study analyzed the genetic variability, inbreeding and population structure of the Tunisian–North African dairy sheep breed, the Sicilo-Sarde (SS), created by crossing the Sarda and Comisana dairy breeds. The level of variability in the SS, considered as an endangered breed after a dramatic decrease, was assessed using 17 microsatellite markers by analyzing the two breed populations sampled from their respective cradles: SS of Beja (SSB, n = 27) and SS of Mateur (SSM, n = 25). High levels of genetic diversity in SS were revealed, with a total of 212 alleles, a high mean number of alleles (12.47 ± 4.17) and a high average polymorphism information content (PIC) (0.81 ± 0.10). The observed heterozygosity was considerable in SSB and SSM (0.795 and 0.785, respectively). The inbreeding level measured by the population inbreeding coefficient FIS is higher in the SSM population (0.121) than in the SSB population (0.090). The higher genetic diversity level detected in SSB reflected the effect of new Italian Sarda genes introduced by intra-uterine artificial insemination recently practiced in this population. The Wilcoxon test and the mode-shift distribution indicated that the SS breed is a non-bottlenecked population. The structural analysis reflected the historical miscegenation practiced during breed creation and highlighted further ancient miscegenation, which could date back to the introduction of the first sheep wave introduction to the western Mediterranean. Microsatellite markers were successfully applied in the assessment of the genetic variability of SS and should be used in monitoring this variability during the application of conservation strategies.

Genetic Characterization and Alternative Preservation Ways of Locally Adapted Sheep Breeds: Cases of Private and Public Sheep Sectors in Tunisia and Italy

“…Consequently, because of this moderate variation among breeds, a large part of the total genetic variability (82%) can be explained by the between-individual variability. The high number of alleles for each locus (16 to 38), as well as the PIC values (higher than 0.5), confirmed that all microsatellite markers used in this study were appropriate to evaluate the biodiversity of the Tunisian-Italian local sheep breeds, as well as proved by previous studies on native sheep breeds [ 17 , 21 , 23 , 25 ]. Microsatellites are the most frequently used markers for genotyping local farm animal breeds between 2005 and 2020 [ 39 ].…”

“…The SS is a unique North African dairy breed created early in the last century from a crossbreeding schema between the Italian Sarda and Comisana dairy breeds in the northern region of Tunisia [ 25 ]. Counting about 38,000 ewes, the SS represents 1% of the total Tunisian sheep resources [ 78 ].…”

“…Counting about 38,000 ewes, the SS represents 1% of the total Tunisian sheep resources [ 78 ]. This breed, reared to produce high-quality milk and typical traditional cheese, is mostly found in the sub-humid Beja and Mateur regions due to its lesser adaptability to the harsh conditions of semi-arid production systems [ 15 , 25 ]. It is raised under two different production systems: a semi-extensive system in private or cooperative farms with large flocks (up to 200 breeding ewes) based on flock integration with cereal and forage production, and an extensive system in the mountains and foothills with small flocks less than 20 head [ 58 ].…”

“…Genomic DNA extraction was carried out from 200 µL whole blood using the Wizard Genomic DNA Extraction Kit (Promega, Madison, WI, USA) following the manufacturer’s protocol. The total of samples were genotyped at 17 microsatellite loci panel ( Table 2 ) established from the ISAG-recommended microsatellite markers [ 22 ] and from previous sheep genetic diversity studies in the Mediterranean region [ 21 , 23 , 24 , 25 ]. Genotypes for all 17 microsatellite markers were determined by means of three multiplex PCR reactions using fluorescence-labeled primers in a total volume of 12.5 µL.…”

Historical Westward Migration Phases of Ovis aries Inferred from the Population Structure and the Phylogeography of Occidental Mediterranean Native Sheep Breeds

“…Genomic DNA extraction was carried out from 300 µL whole blood using the Wizard Genomic DNA Extraction Kit (Promega, Madison, WI, USA) following the manufacturer’s protocol. The entire number of samples was genotyped at 17 microsatellites loci panel ( Table 2 ) established from the ISAG recommended microsatellites markers [ 38 ] and from previous sheep genetic diversity studies [ 39 , 40 , 41 ]. Genotypes for all 17 microsatellite markers were determined by means of three multiplex PCR reactions using fluorescence-labeled primers in a total volume of 12.5 µL.…”