Genetic assignment of Tunisian meat sheep breeds and the effect of the reduction of microsatellites number on their structure assessment

Microsatellite markers succeeded to reveal different population genetic parameters. The present work aimed to investigate the genetic assignment and structure of the Tunisian meat sheep breeds. (Barbarin (BB), Western Thin Tail (WTT), and Black Thibar (BT)).The current study also opted for testing different methods of assignment implemented in several programs for genetic identification and traceability purposes of these breeds and for assessing whether these markers could be useful for an efficient genetic assignment of these ovine breeds. The genotypes of 90 animals (30 samples per breed) were typed for 22 microsatellite markers. All the loci displayed a high polymorphic content (between 0.561 and 0.884). The GENECLASS2 and the WHICHLOCI programs were used to choose the most powerful markers (17 microsatellites). The FLOCK program was more efficient with 22 markers. Genetic differentiation tests (FST = 0.0127) and assignment of individuals to populations revealed the highest level of misassignment in BB and WTT breeds, while the BT breed revealed the highest percentage of individuals assigned to itself. The reduction of the number of microsatellites (from 22 to 17) does not affect the assessment of the genetic structure of Tunisian sheep breeds. This result shed the light on the importance of the shift towards lambs with thin tails imposed by the butchers. It also revealed the unfitness of microsatellite markers in genetic identification analysis for studied sheep breeds.Publishe

Admixture and local breed marginalization threaten Algerian sheep diversity

Due to its geo-climatic conditions, Algeria represents a biodiversity hotspot, with sheep breeds well adapted to a patchwork of extremely heterogeneous harsh habitats. The importance of this peculiar genetic reservoir increases as climate change drives the demand for new adaptations. However, the expansion of a single breed (Ouled-Djellal) which occurred in the last decades has generated a critical situation for the other breeds; some of them are being subjected to uncontrolled cross-breeding with the favored breed and/or to marginalization (effective size contraction). This study investigated genetic diversity within and among six of the nine Algerian breeds, by use of 30 microsatellite markers. Our results showed that, in spite of the census contraction experienced by most of the considered breeds, genetic diversity is still substantial (average gene diversity ranging 0.68 to 0.76) and inbreeding was not identified as a problem. However, two breeds (Rembi and Taadmit) appeared to have lost most of their genetic originality because of intensive cross-breeding with Ouled-Djellal. Based on the above evidence, we suggest Hamra, Sidaoun, and D'man as breeds deserving the highest priority for conservation in Algeria

Analysis of differences in prion protein gene (PRNP) polymorphisms between Algerian and Southern Italy's goats

Goats are adapted to live in harsh areas of the world ensuring minimum levels of milk and meat production without much economic input. Scrapie is a fatal prion disease of small ruminants detected in different countries worldwide. Polymorphisms in the prion protein gene (PRNP) modify the degree of susceptibility/resistance to scrapie. PRNP polymorphisms were analysed in the four main Algerian goat breeds (Naine de Kabylie, Arbia, Mozabite, Mekatia), and in two native breeds of South Italy (Aspromontana from Calabria and Cilentana from Campania). The results were compared also with two previously described Sicilian native breeds (Girgentana and Rossa Mediterranea). Seven amino acid substitutions were detected in Naine de Kabylie goat which represents the original native Berber breed. All other breeds presented no more than six variants and common polymorphisms were present at codons, 154 and 240. Isoleucine at 137 was present in Algerian breeds only. The Italian Cilentana shared more variants with Algerian breeds whereas the Aspromontana breed was the only one to show a Serine at 127. Exclusive new variants were not detected since all polymorphisms were already described in other goats worldwide. The scrapie protective allele encoding lysine (K) at codon 222 was detected in the Naine de Kabylie and M’zabite breeds at low-frequency whereas is present with frequencies higher than 10% in all the Italian breeds reared in regions with elevated scrapie incidence. The overall results showed a substantial number of polymorphisms in PRNP, particularly in Naine de Kabylie breed, which carried also unique genotypes

Scatterplot of the first two principal components of DAPC using breeds as prior clusters.

<p>Breeds are labeled inside their 95% inertia ellipses and dots represent individuals. The inset indicates the eigenvalues of the first five principal components.</p

Pair-wise F_ST among Algerian breeds (a) and Italian breeds (b), calculated with a common set of 15 microsatellites^* (with confidence intervals at 95%).

<p>Ba, Bagnolese; Co, Comisana; Ge, Gentile Di Puglia; La, Laticauda; Le, Leccese; Sa, Sarda.</p><p>*the common set of microsatellites was: MAF65, MAF214, OARFCB304, ILST11, OARAE129, OARFCB193, MAF209, OARJMP58, ILST5, OARFCB128, INRA63, BM1824, MAF33, MCM140, BM8125.</p><p>Pair-wise F_ST among Algerian breeds (a) and Italian breeds (b), calculated with a common set of 15 microsatellites^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122667#t003fn002" target="_blank">*</a>} (with confidence intervals at 95%).</p

Pair-wise F_ST among Algerian breeds (with confidence intervals at 95%).

<p>Pair-wise F_ST among Algerian breeds (with confidence intervals at 95%).</p

Genetic diversity measured by breed.

<p>n, sample size; n Loc. Samp., number of Locales Sampling; GF*¹, governmental farms; RM*², Regional market; MNA, Mean Number of Alleles; R, allelic Richness; PR, Private allelic Richness; H_e, expected heterozygosity; H_o, observed heterozygosity; HWE, Hardy Weinberg Equilibrium; FDR*³, loci in HWD after False Discovery Rate correction [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122667#pone.0122667.ref021" target="_blank">21</a>] and F_IS, inbreeding coefficient (estimator of Weir and Cockerham [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122667#pone.0122667.ref023" target="_blank">23</a>]).</p><p>Genetic diversity measured by breed.</p

Genetic structure of Algerian sheep breeds by Bayesian analysis with 30 microsatellite loci (K = number of clusters).

<p>(a) Analysis on the entire data set with increasing number of inferred clusters (K = 2 to K = 6); (b) Graph showing ΔK calculated according to Evanno et al. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122667#pone.0122667.ref030" target="_blank">30</a>]; (c) further analysis in the group of “white breeds” (Ouled-Djellal, Rembi and Taâdmit) and the group of the three other breeds (D’man, Hamra and Sidaoun).</p

Single nucleotide polymorphisms (SNPs) in the open reading frame (ORF) of prion protein gene (PRNP) in Nigerian livestock species

Abstract 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

Polymorphism of prion protein gene (PRNP) in Nigerian sheep

ABSTRACTPolymorphism 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