Mohamed Habib Yahyaoui’s research while affiliated with Arid Regions Institute and other places

North Africa counts several sheep breeds that can be categorized as fat‐ and thin‐tailed. The former are well adapted to dryland environments. In this study, we used 50K genome‐wide single nucleotide polymorphism profiles from 462 animals representing nine fat‐tailed and 13 thin‐tailed sheep breeds across North Africa to localize genomic regions putatively under differential selective pressures between the two types of breeds. We observed genetic clines from east to west and from north to south. The east–west cline separates the fat‐ and thin‐tailed breeds, with the exception of the fat‐tailed Algerian Barbarine, which is closely related to a genetically homogeneous cluster of Moroccan and Algerian thin‐tailed breeds. Using a combination of three extended haplotype homozygosity tests, we detected seven candidate regions under divergent selection between fat‐ and thin‐tailed sheep. The strongest selection signals reside on chromosomes 1 and 13, with the latter spanning the BMP2 gene, known to be associated with the fat‐tail phenotype. Overall, the candidate regions under selection in fat‐tailed sheep overlap with genes associated with adaptation to desert‐like environments including adipogenesis, as well as heat and drought tolerance. Our results confirm previously reported candidate genes known to be a target of fat‐tail selection in sheep but also reveal novel candidate genes specifically under selection in North African populations.

In sheep, the woolly or hairy fleece type shows variation within and between breeds and populations. Recently, the woolly allele was shown to result from the insertion of an antisens retrogene into the 3’UTR of the ovine IRF2BP2 gene. The purpose of this study was to examine this InDel polymorphism within the IRF2BP2 gene using a specific PCR genotyping in 17 North African (Algeria and Tunisia) and Iranian sheep breeds showing various fleece types. The genotyping of the overall animals (n=908) showed the seg-regation of the two alleles insertion (I) and deletion (D), and the three genotypes (II, ID and DD) with vari-ous frequencies. Ouled Djellal, Rembi and Tâadmit known as woolly breeds had 100%, 94% and 94% of II homozygous animals, respectively. In contrast, Ifilène and Sidaou known as hairy breeds had 100% and 99% of DD homozygous animals. Other breeds showed the segregation of the I allele with a frequency from 3% to 91%. An association analysis, carried out only for the Algerian sheep breeds, revealed that this polymorphism was significantly associated with the fleece type trait (P<0.05). Thus, the current work meets previous results to further confirm the genetic effect of the insertion occurring into the 3′ UTR of the IRF2BP2 gene on the fleece type trait of sheep breeds.

North Africa has a wide range of great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics but also to certain historical events that took place in the region. Knowledge of population structure and identification of genomic regions that have been targets of selection are key steps for genetic resource conservation and breeding strategies designing. This work explores the population structure of two Tunisian and four Algerian sheep breeds and identifies genomic regions under selection in four of them. Leveraging high-throughput genomic data from Illumina Ovine SNP50K array from 59 animals belonging to the six breeds, we conducted a comprehensive analysis to unravel their population structure. Our results indicate a clear genomic admixture between the fat-tailed Tunisian and Algerian Barbarine with thin-tailed breeds raised in each of the two countries. Additionally, through the detection of genomic regions under selection and candidate gene identification, we provide insights into some putative genetic mechanisms that would have contributed to the adaptation and evolution of these breeds in response to local environmental pressures. We also highlight several genes related to economical traits. This study provides valuable information for the conservation and sustainable management of the studied Tunisian and Algerian sheep breeds and offers opportunities for future breeding and genomic improvement programs.

Background Prion diseases, also known as transmissible spongiform encephalopathies (TSEs) remain one of the deleterious disorders, which have affected several animal species. Polymorphism of the prion protein (PRNP) gene majorly determines the susceptibility of animals to TSEs. However, only limited studies have examined the variation in PRNP gene in different Nigerian livestock species. Thus, this study aimed to identify the polymorphism of PRNP gene in Nigerian livestock species (including camel, dog, horse, goat, and sheep). We sequenced the open reading frame (ORF) of 65 camels, 31 village dogs and 12 horses from Nigeria and compared with PRNP sequences of 886 individuals retrieved from public databases. Results All the 994 individuals were assigned into 162 haplotypes. The sheep had the highest number of haplotypes (n = 54), and the camel had the lowest (n = 7). Phylogenetic tree further confirmed clustering of Nigerian individuals into their various species. We detected five non-synonymous SNPs of PRNP comprising of G9A, G10A, C11G, G12C, and T669C shared by all Nigerian livestock species and were in Hardy-Weinberg Equilibrium (HWE). The amino acid changes in these five non-synonymous SNP were all “benign” via Polyphen-2 program. Three SNPs G34C, T699C, and C738G occurred only in Nigerian dogs while C16G, G502A, G503A, and C681A in Nigerian horse. In addition, C50T was detected only in goats and sheep. Conclusion Our study serves as the first to simultaneously investigate the polymorphism of PRNP gene in Nigerian livestock species and provides relevant information that could be adopted in programs targeted at breeding for prion diseases resistance.

This study investigated the MHC DRB genes in the Arabian camel (Camelus dromedarius). The results revealed the presence of — at least — two transcribed DRB-like genes in chromosome 20, designated MhcCadr-DRB1 and MhcCadr-DRB2. These genes are 155 Kb apart, have similar gene structure, and are transcribed in opposite directions. Compared to DRB1, the DRB2 locus contains a deletion of 12 nucleotides in the second exon (270 bp), exhibits lower transcript abundance, and is expressed as two splice variants differing by exon 2 skipping. This gene seems to be of minor functional relevance in the dromedary camel. Conversely, the DRB1 is thought to be the main gene in this species showing higher transcript abundance and polymorphism levels. A total of seven DRB1 exon 2 alleles were identified in the Tunisian dromedary camel resulting from 18 amino acid substitutions. Six full length alleles were characterized at the mRNA level. Although there is no clear evidence for balancing selection (i.e., heterozygote advantage), signals of weak historical positive selection acting on the DRB1 gene were detected, as indicated by the limited number of the sites being positively selected. This trend might be related to the low exposure to pathogens and to the demographic history of the species. Comparative analysis with Bactrian and wild camel genomes suggested occurrence of trans species polymorphism (TSP) in the Camelus genus. The results lay the foundation for the MHC DRB1 genetic diversity analysis in this genus since the developed genotyping protocols are fully applicable in the three Camelus species.

Polymorphism of the prion protein gene (PRNP) gene determines an animal’s susceptibility to scrapie. Three polymorphisms at codons 136, 154, and 171 have been linked to classical scrapie susceptibility, although many variants of PRNP have been reported. However, no study has investigated scrapie susceptibility in Nigerian sheep from the drier agro-climate zones. In this study, we aimed to identify PRNP polymorphism in nucleotide sequences of 126 Nigerian sheep by comparing them with public available studies on scrapie-affected sheep. Further, we deployed Polyphen-2, PROVEAN, and AMYCO analyses to determine the structure changes produced by the non-synonymous SNPs. Nineteen (19) SNPs were found in Nigerian sheep with 14 being non-synonymous. Interestingly, one novel SNP (T718C) was identified. There was a significant difference (P < 0.05) in the allele frequencies of PRNP codon 154 between sheep in Italy and Nigeria. Based on the prediction by Polyphen-2, R154H was probably damaging while H171Q was benign. Contrarily, all SNPs were neutral via PROVEAN analysis while two haplotypes (HYKK and HDKK) had similar amyloid propensity of PRNP with resistance haplotype in Nigerian sheep. Our study provides valuable information that could be possibly adopted in programs targeted at breeding for scrapie resistance in sheep from tropical regions.

Scrapie is a fatal prion protein disease stiffly associated with single nucleotide polymorphism (SNPs) of the prion protein gene (PRNP). The prevalence of this deadly disease has been reported in small ruminants, including goats. The Nigerian goats are hardy, trypano-tolerant, and contribute to the protein intake of the increasing population. Although scrapie has been reported in Nigerian goats, there is no study on the polymorphism of the PRNP gene. Herein, we evaluated the genetic and allele distributions of PRNP polymorphism in 132 Nigerian goats and compared them with publicly available studies on scrapie-affected goats. We utilized Polyphen-2, PROVEAN and AMYCO programs to examine structural variations produced by the non-synonymous SNPs. Our study revealed 29 SNPs in Nigerian goats, of which 14 were non-synonymous, and 23 were novel. There were significant differences (P <0.001) in the allele frequencies of PRNP codons 139, 146, 154 and 193 in Nigerian goats compared with scrapie-affected goats, except for Northern Italian goats at codon 154. Based on the prediction by Polyphen-2, R139S and N146S were 'benign', R154H was 'probably damaging', and T193I was 'possibly damaging'. In contrast, PROVEAN predicted 'neutral' for all non-synonymous SNPs, while AMYCO showed a similar amyloid propensity of PRNP for resistant haplotype and two haplotypes of Nigerian goats. Our study is the first to investigate the polymorphism of scrapie-related genes in Nigerian goats.

The goal of this study is to characterize the diversity of the Algerian south donkey population, characterize its biometric variability, and determine the evolutionary relationships of this animal with its congeners at various latitudes. A total of sixty-six adult asses, distributed on the level of three wilayas from where eleven body measurements, six body indexes developed in horses and adapted to donkeys were calculated, and seven phenotypical characters were retained for this study. Measurements Lsi, HG, TP, LH, LE, Pc, LT, LO, LQ, LaT, Tm, Pv1, Pv2 are respectively: 98.05±10..62. Those information are used to compute 6 body indexes. According to body and profile indexes we deduce that our animals were medial linear and small (PI ≈ 1,08 and BI ≈ 0,82), they could not even bear their own weight loads (CI > 1), their heads were long (HI ≈ 0,45< 1) with a square body shape (LI ≈ 0,93< 1,10). Donkeys' thoracic development was average according to (CD≈ 1,13). All parameters except the LE, PC, TM for the regions showed a significant difference on examined body measurements (p>0,05). On the phenotypical characteristics, a factorial analysis of the multiple correspondences revealed two main components that account for 48,90 and 44,26 % of total inertia, or 93,2 %. These percentages are related to the dress color, the head, the members, the hairs, the muzzle, and the belly. This research revealed significant phenotypic differences that should be included in the specie's characterization and conservation efforts.

Scrapie is a fatal prion disease. It belongs to transmissible spongiform encephalopathies (TSEs), and occurs in sheep and goats. Similarly, to ovine species, the prion protein gene (PRNP) plays a major role in conferring resistance or susceptibility to TSE in goats. This study assesses the variability of PRNP in native and crossed-breed goat populations raised in the Southeast of Tunisia and provides information on the distribution of PRNP haplotypes and genotypes in these goat populations. A total of 116 unrelated goats including 82 native and 34 crossed-breed goats were screened for PRNP polymorphisms using Sanger sequencing. Sequence analysis revealed 10 non-synonymous polymorphisms (G37V, M137I, R139S, I142M, H143R, N146D, R154H, R211Q, Q222K, and S240P), giving rise to 12 haplotypes and 23 genotypes. Moreover, four silent mutations were detected at codons 30, 42, 138, and 179; the former was reported for the first time in goat (nucleotide 60 c→t). Interestingly, the PrP variants associated with resistance (D146 and K222) or with a prolonged incubation time of goat to scrapie (M142, R143, H154, Q211) were absent or detected with low frequencies except for H154 variant, which is present with high frequency (1%, 1%, 4%, 0%, 88%, and 6%, respectively, for native goats, and 0%, 1%, 0%, 1%, 78%, and 1%, respectively, for crossed goats). The analysis of PRNP polymorphisms of goats raised in other regions of the country will be useful in getting a global view of PRNP genetic variability and the feasibility of goat breeding programs in Tunisia.