Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers

Bedhiaf-Romdhani, Sonia; Baazaoui, Imen; Ciani, Elena; Mastrangelo, Salvatore; Sassi, M. Ben

doi:10.1016/j.smallrumres.2020.106192

Cited by 14 publications

(16 citation statements)

References 35 publications

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“…Past and recent human-mediated translocations and dispersal of the two breeds across Tunisia has brought the two breeds in close geographic proximity [57] and is resulting in cross-mating that is homogenizing their genomes. A similar nding was reported by [52]. The fact that the genomes of the B and Q breeds could not be differentiated by ADMIXTURE in each cluster provides evidence at the genome level that supports past and on-going uncontrolled mating of the fat-tailed Barbarine with thin-tailed breeds to reduce the fat content, especially of the tail, in the Barbarine carcass [58].…”

Section: Discussionsupporting

confidence: 71%

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Genome Variation in Tick Infestation and Cryptic Divergence in Tunisian Indigenous Sheep

Ahbara¹,

Khbou²,

Rhomdhane³

et al. 2021

Preprint

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Background: Ticks are obligate haematophagous ectoparasites considered second to mosquitos as vectors and reservoirs of multiple pathogens of global concern. Individual variation in tick infestation has been reported in indigenous sheep, but the genes regulating the trait are poorly understood.Results: Here, we report 397 genome-wide signatures of selection overlapping 991 genes from the analysis, using four methods (ROH, LR-GWAS, XP-EHH, FST), of 600K SNP genotype data from 170 Tunisian sheep exhibiting high and low resistance to ticks. We considered 45 signatures detected by consensus results of at least two methods as high-confidence selection sweep regions. These spanned 104 genes which included immune system function genes, solute carriers and chemokine receptor. One region spanned STX5, that has been associated with tick resistance in cattle, implicating it as a prime candidate in sheep. We also observed RAB6B and TF in a high confidence candidate region that has been associated with growth traits suggesting natural selection is enhancing growth and developmental stability under tick challenge. The analysis also reveals fine-scale genome structure suggesting the existence of cryptic divergence in the Tunisian sheep.Conclusion: Our findings provide genomic reference that could enhance our understanding of the genetic architecture of tick resistance and cryptic divergence in indigenous sheep.

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Section: Discussionsupporting

confidence: 71%

“…The variability in the four genetic groups revealed by PCA and ADMIXTURE was of the same magnitude as that of the two cohorts. Comparable levels of genetic variability have been reported in Egyptian [50], Algerian [51], Tunisian [52] and Russian [53] breeds of sheep.…”

Section: Discussionmentioning

confidence: 84%

Genome Variation in Tick Infestation and Cryptic Divergence in Tunisian Indigenous Sheep

Ahbara¹,

Khbou²,

Rhomdhane³

et al. 2021

Preprint

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“…Gaouar et al [ 23 ] reported an F ST value of 0.036 for the five major sheep breeds of Morocco, and of 0.038 for six Algerian breeds [ 41 ]. Concerning the Tunisian breeds, the genetic differentiation was even lower, with F ST values of about 1.7% for a set of four breeds [ 39 , 42 ], and 0.021 for a set of six breeds, including one crossed population [ 43 ]. In contrast, higher values were reported for Central and South African [ 44 , 45 ], European [ 46 – 51 ], and Oriental breeds [ 52 , 53 ].…”

Section: Discussionmentioning

confidence: 99%

How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns

et al. 2021

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Background Based on the relatively homogeneous origin of the sheep breeds in Morocco that originate mainly from Iberia, it is highly relevant to address the question of how these very diverse sheep populations differentiated from each other. The Mountains of the High Atlas and Middle Atlas are expected to constitute North–South and West–East geographical barriers, respectively, which could have shaped the history of the differentiation of sheep breeds. The aim of this study was to test this hypothesis by considering the genetic structure and the spatial distribution of five major breeds (Sardi, Timahdite, Beni Guil, Boujaad and D’man) and one minor breed (Blanche de Montagne), by analysing the mtDNA control region, using 30 individuals per breed. Results Phylogenetic and network analyses did not indicate any clear separation among the studied breeds and discriminant component principal analysis showed some overlap between them, which indicates a common genetic background. The calculated pairwise FST values and Nei’s genetic distances revealed that most breeds showed a moderate genetic differentiation. The lowest and highest degrees of differentiation were retrieved in the Beni Guil and Boujaad breeds, respectively. Analysis of molecular variance (AMOVA) indicated that more than 95% of the genetic diversity occurs within individuals, while between- and within-population variabilities represent only 1.332% and 2.881%, respectively. Isolation-by-distance, spatial Principal Component Analysis (sPCA), and spatial AMOVA analyses evidenced clear examples of geographical structuration among the breeds, both between and within breeds. However, several enigmatic relationships remain, which suggest the occurrence of complex events leading to breed differentiation. Conclusions The approaches used here resulted in a convergent view on the hypothetic events that could have led to the progressive differentiation between the Moroccan breeds. The major split seems to be linked to the West–East barrier of the Middle Atlas, whereas the influence of the High Atlas is less obvious and incompletely resolved. The study of additional breeds that have settled near the High Atlas should clarify the relationships between the breeds of the West part of the country, in spite of their small population size.

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“…The population differentiation analysis showed a relatively weak population structure between BARB and QFO breeds and their crossed population (CROSS) with the exception of the subpopulation of the BARB group that originated from a prolificacy-based selected flock with significant levels of inbreeding (Lassoued et al, 2017). Moreover, the PCA and admixture results revealed clear differentiation of breeds originating from Europe (THIB and SS) from the remaining populations previously evidenced in genome-wide studies using medium density ovine array (Baazaoui et al, 2021;Bedhiaf-Romdhani et al, 2020). Indeed, this structure was expected because THIB has shown substantial Merino introgression via Merino ancestry to acquire tolerance against white-colored skin photosensitization (Baazaoui et al, 2020), whereas the SS breed is a small population imported into Tunisia by Italians in the early twentieth century to be the only dairy breed in North Africa (Saadoun et al, 2004).…”

Section: Population Stratificationmentioning

confidence: 70%

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

et al. 2023

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In developing countries, the use of simple and cost‐efficient molecular technology is crucial for genetic characterization of local animal resources and better development of conservation strategies. The genotyping by sequencing (GBS) technique, also called restriction enzyme‐ reduced representational sequencing, is an efficient, cost‐effective method for simultaneous discovery and genotyping of many markers. In the present study, we applied a two‐enzyme GBS protocol (PstI/MspI) to discover and genotype SNP markers among 197 Tunisian sheep samples. A total of 100 333 bi‐allelic SNPs were discovered and genotyped with an SNP call rate of 0.69 and mean sample depth 3.33. The genomic relatedness between 183 samples grouped the samples perfectly to their populations and pointed out a high genetic relatedness of inbred subpopulation reflecting the current adopted reproductive strategies. The genome‐wide association study contrasting fat vs. thin‐tailed breeds detected 41 significant variants including a peak positioned on OAR20. We identified FOXC1, GMDS, VEGFA, OXCT1, VRTN and BMP2 as the most promising for sheep tail‐type trait. The GBS data have been useful to assess the population structure and improve our understanding of the genomic architecture of distinctive characteristics shaped by selection pressure in local sheep breeds. This study successfully investigates a cost‐efficient method to discover genotypes, assign populations and understand insights into sheep adaptation to arid area. GBS could be of potential utility in livestock species in developing/emerging countries.

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Genetic structure of Tunisian sheep breeds as inferred from genome-wide SNP markers

Cited by 14 publications

References 35 publications

Genome Variation in Tick Infestation and Cryptic Divergence in Tunisian Indigenous Sheep

Genome Variation in Tick Infestation and Cryptic Divergence in Tunisian Indigenous Sheep

How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns

Efficiency of genotyping by sequencing in inferring genomic relatedness and molecular insights into fat tail selection in Tunisian sheep

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