Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data.

The local cattle populations belonging to the 'Brune de l'Atlas' cattle in Algeria and Morocco are potential resources in terms of genetic diversity and socioeconomic prevalence and their characterization is an essential step in any program designed to conserve genetic diversity. Our objectives were to assess the genetic diversity, the population structure and relationships among four Algerian cattle breeds, the Biskra, Cheurfa, Chelifienne and Guelmoise and of two Moroccan, the Oulmès-Zaër and Tidili by genotyping 50 309 single nucleotide polymorphism in 203 unrelated animals. A low population structure was observed across breeds with pairwise F ST values ranging from 0.008 to 0.043, suggesting a high level of gene flow. These data were combined with the available data on cattle populations representative of Europe (EUT), West African taurine (WAT) and zebu (ZEB). Principle Components Analysis was carried out which revealed that the Maghrebin populations are closer to the EUT/ZEB population than to the WAT. Structure analysis confirmed this mixed origin of the Maghrebin cattle populations. We also detected the influence of zebu breeds in Cheurfa and Guelmoise populations. This study provides the first information about genetic diversity within and between Algerian and Moroccan cattle populations and gives a detailed description of their genetic structure and relationships according to their historical origins. This study revealed that several combined effects contributed to shape the genetic diversity of the six Maghrebin populations studied: (i) gene flow among local breeds, (ii) the recent introgression of European breeds in local Algerian breeds and (iii) the traditional management systems. The results of this study will primarily assist policy makers and livestock keepers to make useful decisions for improvement of genetic resources while ensuring the preservation and conservation of local breeds in Algeria and Morocco.

A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls.

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity.

Effects of established blood pressure loci on blood pressure values and hypertension risk in an Algerian population sample.

Genome-wide association studies and subsequent replication studies have pinpointed 29 genetic variants associated with blood pressure (BP). None of these studies included North African populations. We therefore looked at whether or not these genetic variants modulated BP and hypertension (HTN) risk in an Algerian population sample. Twenty-nine single-nucleotide polymorphisms (SNPs) were genotyped in a representative sample of 787 subjects from the InSulino-résistance à ORan (ISOR) study (378 men and 409 women aged between 30 and 64 years and recruited from within the city of Oran, Algeria). Genetic variants were considered both individually and when combined as genetic predisposition scores (GPSs) for systolic BP (SBP), diastolic BP (DBP) and HTN risk. The SNPs in CYP1A1-ULK3, HFE and SH2B3 were significantly associated with BP and/or HTN. The SBP-GPS, DBP-GPS and HTN-GPS were associated with higher levels of DBP (+0.24 mm Hg P=0.05, +0.23 mm Hg P = 0.05 and +0.26 mm Hg P = 0.03, respectively). Moreover, the three GPSs tended to be associated with a 6% higher risk of HTN. Our study is the first to show that some of the BP loci validated in subjects of European descent were associated (either individually or when combined as GPSs) with BP traits and/or the HTN risk in an Algerian population, but to a lesser extent than in European populations. Although larger studies and meta-analyses of North African populations are needed to confirm the present results, our data contribute to a better understanding of genetic susceptibility to HTN.

Association of PTPN22 (rs2476601) and STAT4 (rs7574865) polymorphisms with Rheumatoid Arthritis in the Western Algerian population.

AIM: The aim of the present study was to replicate the association of five risk gene polymorphisms (PTPN22-rs2476601, STAT4-rs7574865, 6q23-rs6927172, IRF5-rs2004640 and TRAF1/C5-rs10818488) with RA in a specific population of the Western Algeria. MATERIAL AND METHODS: The study group comprised 110 patients with RA and 197 ethnically matched healthy control subjects. All polymorphisms were genotyped using predesigned TaqMan® assays. Allele and genotype frequencies in patients and control subjects were compared by chi-square test and odds ratios with 95% confidence intervals. Correction for multiple testing was carried out using the Bonferroni adjustment. RESULTS: Statistically significant associations with RA were detected. The strongest signal was obtained for PTPN22-rs2476601 with an allelic Pvalue 3.32 x 10(-11) (OR = 9.83, 95% CI [4.28 - 22.56]). A second significant association was obtained with STAT4-rs7574865 (allelic Pvalue = 4 x 10(-3); OR = 1.75, 95% CI [1.16 - 2.63]). The third SNP, 6q23-rs6927172, showed a significant result of association with RA, but missed our criteria for significance at allelic level after Bonferroni's correction (allelic Pvalue = 0.027; OR = 0.64, 95% CI [0.42 - 0.97]). Finally, IRF5-rs2004640 and TRAF1/C5-rs10818488 showed a significant association only at genotypic level (Pvalues: 3 x 10(-4) and 2.9 x 10(-3) respectively) but did not reach statistical significance when comparing allele frequencies (Pvalues: 0.96 and 0.21 respectively). CONCLUSIONS: From this initial study, we can conclude that PTPN22-rs2476601 and STAT4-rs7574865 polymorphisms are clearly associated with the risk of RA in the Western Algerian population.

Molecular characterization and differentiation of five horse breeds raised in Algeria using polymorphic microsatellite markers.

In this study, genetic analyses of diversity and differentiation were performed on five horse breeds raised in Algeria (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). All microsatellite markers were highly polymorphic in all the breeds. A total of 123 alleles from 14 microsatellite loci were detected in 201 horses. The average number of alleles per locus was the highest in the Arab-Barb horses (7.86) and lowest in the thoroughbred breed (5.71), whereas the observed and expected heterozygosities per breed ranged from 0.71 (Thoroughbred) to 0.752 (Barb) and 0.71 (Thoroughbred) to 0.77 (Arab-Barb), respectively. The genetic differentiation between the breeds was significant (p < 0.01) based on the infinitesimal model (FST ). Three different approaches for evaluating the genetic relationships were applied. Genetic distances, the factorial correspondence analysis and structure analysis showed that a significant amount of genetic variation is maintained in the native horse populations and the other breeds. The Barb and Arab-Barb breeds seem to be the most genetically related and support the decision to consider the breeds as same population.

Characterization, genetic variation and chromosomal assignment to sheep chromosome 2 of the ovine heart fatty acid-binding protein gene (FABP3).

The purpose of this study was to locate and detect genetic variation in the sheep FABP3 gene, a candidate gene for milk and meat quality traits in sheep. We have obtained an almost complete sequence (4,689 bp, excluding a part of intron 1) of the sheep FABP3 gene using PCR-based comparative genome walking. Sheep FABP3 has been located to chromosome 2 by sheep sequence-specific PCR on DNA from a sheep/rodent cell hybrid panel, and confirmed by linkage mapping using the International Mapping Flock. Direct sequencing of PCR products amplified from different DNA samples of Manchega breed sheep over the complete sheep FABP3 gene revealed 13 SNPs, one CTC insertion/deletion and a variable polyA tract. This poly A tract was found in association with a SINE/artiodactyls repeat. In addition, two SNPs were screened in different sheep breeds.

Cytogenetical anchoring of sheep linkage map and syntenic groups using a sheep BAC library.

In order to simultaneously integrate linkage and syntenic groups to the ovine chromosomal map, a sheep bacterial artificial chromosome (BAC) library was screened with previously assigned microsatellites using a sheep-hamster hybrid panel and genetic linkage. Thirty-three BACs were obtained, fluorescently labelled and hybridised on sheep-goat hybrid metaphases (2n = 57). This study allowed us, (i), to anchor all linkage groups on sheep chromosomes, (ii), to give information on the probable position of the centromere on the linkage map for the centromeric chromosomes, (iii), to contradict the previous orientation of the ovine X linkage group by the mapping of BMS1008 on OARXq38. Concerning our somatic cell hybrid panel, this study resulted in the assignment of all the previously unassigned groups to ovine chromosomes and a complete characterisation of the hybrid panel. In addition, since hybridisations were performed on a sheep-goat hybrid, new marker/anchoring points were added to the caprine cytogenetic map.

Regional characterization of a hamster-sheep somatic cell hybrid panel.

The regional characterization of a previously obtained hamster-sheep hybrid panel is reported. Using data available from ruminant maps (sheep, cattle, and goat), we have selected a set of 300 markers and have analyzed them by PCR in this hybrid panel. Results obtained for 204 markers show the presence of all sheep chromosomes (including gonosomes) in entire or fragmented form. Analysis of syntenies has given 130 types of answer defining segments of variable sizes. This study has led to the regional characterization of this panel and provides comparative data on a set of bovine and caprine markers. With the level of characterization now achieved for this hybrid panel, the regional assignment of new genes or markers to sheep chromosomes can be rapidly obtained. Finally, this panel will help to collect new data for comparative mapping of domestic animals and to highlight the conservation of syntenic groups between closely related species, that is, sheep, cattle, and goat.

Synteny conservation between parts of human chromosome 4q and bovine and ovine chromosomes 6.

Booroola Merino sheep are characterized by a high ovulation rate attributable to the presence of the FecB allele of the FEC gene. This gene, which has been assigned to sheep chromosome 6, is linked to the gene for EGF, which in man is located on the long arm of chromosome 4 (HSA 4q). To increase the number of known markers on sheep chromosome 6, we used comparative mapping data from sheep, man, and cattle. In our study, we show a synteny between EGF and the genes PDHA2 and FGF5 (from HSA 4q) and microsatellites ILSTS018, ILSTS090, and ILSTS093 (from bovine chromosome 6) in sheep. We also show that the conservation between HSA 4q and sheep chromosome 6 is disrupted between EGF and FGF2.

Sheep gene mapping: assignment of ALDOB, CYP19, WT and SOX2 by somatic cell hybrid analysis.

Twenty-four hamster-sheep hybrid cell lines representing eleven ovine synteny groups were used to make syntenic assignments for seven loci ALDOB (aldolase B, fructose biophosphate); AMH (anti-Müllerian hormone); CYP19 [cytochrome P450 aromatase, subfamily XIX (aromatization of androgens)]; WT (Wilms' tumour gene); SOX2 (SRY-related HMG-box gene 2); FSHB (follicle-stimulating hormone, beta polypeptide); and SRY (sex region of Y chromosome). These loci were assigned to synteny groups U11(chr2) (ALDOB); U19 (AMH); U3(chr7) (CYP19); and to chromosome 15 (WT) and 1 (SOX2). SRY defines the hybrids containing the Y chromosome.

Evolutionary conservation of a microsatellite in the Wilms tumour (WT) gene: mapping in sheep and cattle.

A microsatellite in the WT (Wilms tumour) gene is shown to be evolutionarily conserved in a range of mammals. The microsatellite was monomorphic in pig and two alleles have been found in goat. In cattle, a one-base size polymorphism has been discovered outside the microsatellite. WT was genetically mapped to bovine chromosome 15 and to sheep chromosome 15 by synteny mapping. Conservation of chromosome segments of HSA11 and BTA15 is discussed.

Isolation and characterisation of five new anonymous X-specific probes. One of them detecting a TaqI RFLP.

The authors isolated five single-copy X-specific probes from an X-enriched library. These probes were regionally localized on the X chromosome by using somatic hybrid cell lines obtained from patients carrying different X-autosome translocations. Three clones were located between Xq23 and Xq26, the two others were mapped between Xp21 and Xp11.2. Analyses with different restriction enzymes indicated that one of them detects a TaqI polymorphism with a polymorphism information content (PIC) of 0.28.

Sheep gene mapping: synteny between COL2A1 and the LDHB-PEPB-TPI-GAPD-LALBA-IGF1 group.

DNA extracted from 21 hamster-sheep hybrid cell lines was subjected, after Southern blotting, to hybridization with a type-II alpha 1 collagen genomic probe (COL2A1). The corresponding locus was found to be syntenic with the LDHB-PEPB-TPI-GAPD-LALBA-IGF1 group in sheep.

Sheep gene mapping: additional DNA markers included (CASB, CASK, LALBA, IGF-1 and AMH).

DNA extracted from 25 hamster-sheep hybrid cell lines was subjected, after Southern blotting, to hybridization with CASB, CASK, LALBA, IGF-1 and AMH cDNA probes. CASB and CASK segregated together and IGF-1 and LALBA were found syntenic with the LDHB-PEPB-TPI-GAPD-SHMT-KRTB group. No other synteny was observed with any of the previously described groups using the same hybrid cell panel. Gene nomenclature: ACO 1: aconitase 1 (soluble); ADA: adenosine deaminase; AMH: antiMüllerian hormone; ARA 1: murine sarcoma 3611 viral (v-raf) oncogene homologue 1; CASB: beta-casein; CASK: kappa-casein; ENO 1: enolase 1 (alpha); G6PD: glucose-6-phosphate dehydrogenase; GALA (or GLA): glactosidase (alpha); GAPD: glyceraldehyde -3- phosphate dehydrogenase; GPI: glucose phosphate isomerase; GSR: glutathione reductase; HBG: haemoglobin gamma; HPRT: hypoxanthine phosphoribosyl transferase; IDH 1: isocitrate dehydrogenase 1 (soluble); IGF-1: insulin growth factor 1; ITPA: inosine triphosphatase; KRTA: keratin (acid); KRTB: keratin (basic); LALBA: alpha-lactalbumin; LDHA: lactate dehydrogenase A; LDHB: lactate dehydrogenase B; MDH 2: malate dehydrogenase NAD (soluble); ME 1: malic enzyme (soluble); MPI: mannose phosphate isomerase; NP: nucleoside phosphorylase; OLA: ovine leucocyte antigen; OTC: ornitine carbamoyltransferase; PAIS: phosphoribosyl amino imidazole synthetase; PEPA, PEPB, PEPC: peptidase A, B, C; PGD: phospho gluconate dehydrogenase; PGK: phosphoglycerate kinase; PGM 3: phospho glucomutase 3; PKM 2: pyruvate kinase (muscle); PLP: proteolipid protein; PRGS: phosphoribosyl glycinamide synthetase; RCP: red cone pigment; SHMT: serine hydroxymethyl transferase; SOD 1: superoxide dismutase 1 (soluble); SYN 1: synapsin 1; TPI l: triose phosphate isomerase 1.

The anonymous PAS45 probe detects RFLPs in 13q31.

An anonymous DNA probe PAS45 was isolated. This probe detects an RFLP with two alleles 1 and 2 at the same locus, with the different restriction enzymes (Bg1II, EcoRI, HindIII, PstI, MspI, XbaI). The observed polymorphism is explained by a chromosome rearrangement involving these enzyme cleavage sites. The frequency of alleles 1 and 2 was 0.875 and 0.125, respectively, in a sample of 48 unrelated individuals in France. Codominant inheritance of alleles 1 and 2 was demonstrated in 13 families with 30 offspring. The PAS45 probe was localized on chromosome 13 by somatic cell hybrid analysis and on 13q31 by in situ hybridization. The rearrangement on 13q31 is present in one out of four healthy individuals in France.

Sheep gene mapping by somatic cell hybridization. III. Synteny between pyruvate kinase M2 (PKM2) and nucleoside phosphorylase (NP) in domestic sheep.

Twenty-five independent chinese hamster x sheep hybrids were analysed for ovine pyruvate kinase M2 (PKM2), nucleoside phosphorylase (NP) and mannosephosphate isomerase (MPI). An independent segregation is observed between PKM2 and MPI, whereas the results show a synteny between PKM2 and NP.

[Ovine histocompatibility complex OLA and enzymatic markers in hamster X sheep hybrids. I. Asynteny between PGM3-ME1 and OLA. (author's transl)]. / Complexe d'histocompatibilité ovin (ola) et marqueurs enzymatiques dans des hybrides hamster x mouton. I. Asynténie entre PGM3-ME1 et OLA.

Eighteen independent hamster X sheep fibroblast hybrids have been obtained. OLA typing of parental cells has shown that ovine fibroblasts carry the OLA A1, A8, B7, and B9 specificities. Analysis of the segregation of the OLA genes compared with the segregation of the 16 enzymatic markers studied previously indicated that, in contrast to the situation and man and certain other mammals, the genes of the histocompatibility complex of ovines (OLA) and those coding for the enzymes PGM3 and and ME1 are asyntenic. No synteny between OLA and any other enzymatic marker studied has been established.