Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data.

Introduction: The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. Methods: In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. Results and discussion: We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

Sequencing and Characterization of αs2-Casein Gene (CSN1S2) in the Old-World Camels Have Proven Genetic Variations Useful for the Understanding of Species Diversification.

The CSN1S2 gene encodes αs2-casein, the third most abundant protein in camel milk. Despite its importance in foals, human nutrition, and dairy processing, the CSN1S2 gene in camels has received little attention. This study presents the first complete characterization of the CSN1S2 gene sequence in Old-World camels (Camelus bactrianus and Camelus dromedarius). Additionally, the gene promoter, consisting of 752 bp upstream of exon 1, was analyzed. The entire gene comprises 17 exons, ranging in length from 24 bp (exons 4, 8, 11, and 13) to 280 bp (exon 17). Interesting was the identification of the exon 12 in both species. The promoter analysis revealed 24 putative binding sites in the Bactrian camel and 22 in dromedary camel. Most of these sites were typical elements associated with milk protein, such as C/EBP-α, C/EBP-ß, Oct-1, and AP1. The SNP discovery showed relatively high genetic diversity compared to other camel casein genes (CSN1S1, CSN2, and CSN3), with a total of 34 polymorphic sites across the two species. Particularly noteworthy is the transition g.311G>A in the CSN1S2 promoter, creating a new putative consensus binding site for a C/EBP-ß in the Bactrian camel. At the exon level, two novel variants were found. One was detected in exon 6 of the Bactrian camel (g.3639C>G), resulting in an amino acid replacement, p.36Ile>Met. The second variant was found in noncoding exon 17 of dromedary CSN1S2 (g.1511G>T). Although this mutation occurs in the 3'-UnTranslated Region, it represents the first example of exonic polymorphism in the CSN1S2 for this species. This SNP also affects the binding sites of different microRNAs, including the seed sequence of the miRNA 4662a-3p, highlighting its role as a regulatory factor for CSN1S2 gene. A PCR-RFLP was set up for genotyping a dromedary Tunisian population (n = 157), and the minor allele frequency was found to be 0.27 for the G allele, indicating a potential yield improvement margin. The interspersed elements (INEs) analysis revealed 10 INEs covering 7.34% and 8.14% of the CSN1S2 sequence in the Bactrian and dromedary camels, respectively. Furthermore, six elements (A, B, F, H, I, and L) are shared among cattle and camels and are partially found in other ruminants, suggesting a common ancestral origin of these retrotransposons. Conversely, elements C, D, E, and G are specific to camels.

Marker-assisted introgression of fecundity mutation into Barbarine sheep breed under low input production system.

Fecundity gene introgression has become an economical method to improve sheep prolificacy in developing countries. The FecXBar and FecGH mutations are variants of the BMP15 and GDF9 sheep genes, respectively, identified in Tunisian Barbarine sheep prolific line "W-INRAT," created through a prolificacy-based selection program. The first mutation caused increased prolificacy in heterozygous state and sterility in homozygous ewes. The aim of this work was to increase the number of effective carriers by the introgression of fecundity mutation into non-carrier conventional flocks based on a marker-assisted breeding program. The genotyping was carried out to follow up on the segregation of prolificacy mutation. The conventional ewes, raised in state farms of Tunisia and inseminated by "W-INRAT" rams, yielded 100% carriers females at heterozygous state. These females were selected to be inseminated with conventional rams and produced carriers' lambs with 66.7% males and 33.3% females. The prolific males will be kept in breeding centers to disseminate the fecundity mutation in commercial flocks. This approach facilitates the dissemination of fecundity genes and contributes to livelihood improvement in communities raising Barbarine sheep.

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

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.

Haplotype structure of MSTN, IGF1, and BMP2 genes in Tunisian goats (Capra hircus) and their association with morphometric traits.

The aim of the present study was to evaluate variability and haplotype structure of twenty-eight single nucleotide polymorphisms (SNPs) at myostatin (MSTN), insulin-like growth factor 1 (IGF1), and bone morphogenetic protein 2 (BMP2) genes. Association between the polymorphic SNPs and morphometric traits was performed on a population of 263 Tunisian goats. The SNPs analyzed were all polymorphic (except one), and the three genes had different haplotype structures. Significant association of SNPs at MSTN with head length was highlighted in the Tunisian goats. The variability at IGF1 gene was associated with body length, ear length, tail length, and chest depth. For BMP2, significant association was revealed with chest depth. Significant association was also detected between linkage disequilibrium (LD) block 2 at IGF1 with body length. These findings might play a potential role in gene-assisted programs.

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds.

The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker FST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.

FecX Bar a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine Sheep.

BACKGROUND: Naturally occurring mutations in growth and differentiation factor 9 (GDF9) or bone morphogenetic protein 15 (BMP15) genes are associated with increased ovulation rate (OR) and litter size (LS) but also sterility. Observing the Tunisian Barbarine ewes of the "W" flock selected for improved prolificacy, we found prolific and infertile ewes with streaky ovaries. Blood genomic DNA was extracted from a subset of low-ovulating, prolific and infertile ewes of the "W" flock, and the entire coding sequences of GDF9 and BMP15 were sequenced. RESULTS: We evidenced a novel polymorphism in the exon 1 of the BMP15 gene associated with increased prolificacy and sterility. This novel mutation called FecX Bar is a composite polymorphism associating a single nucleotide substitution (c.301G > T), a 3 bp deletion (c.302_304delCTA) and a C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101. Calculated in the "W" flock, the FecX Bar allele increased OR by 0.7 ova and LS by 0.3 lambs (p = 0.08). As for already identified mutations, homozygous females carrying FecX Bar exhibited streaky ovaries with a blockade at the primary stage of folliculogenesis as shown by histochemistry. CONCLUSIONS: Our investigation demonstrates a new mutation in the BMP15 gene providing a valuable genetic tool to control fecundity in Tunisian Barbarine, usable for diffusion program into conventional flocks looking for prolificacy improvement.