Morphological diversity of northeastern fat-tailed and northwestern thin-tailed indigenous sheep breeds of Ethiopia.

Characterization of indigenous sheep breeds using morphological traits is essential for designing rational conservation and improvement strategies. This study was conducted to check the morphological diversity of three fat-tailed and three thin-tailed indigenous sheep breeds of Ethiopia. The phenotypic traits such as live body weight and linear body measurements (body length, wither height, chest girth, chest depth, rump height, rump length, ear length, tail length, and pelvic width) were measured and used for analysis. The statistical analysis was done using different procedures of SAS 9.4. Analysis of variance showed significant variation between breeds. Multivariate analyses clearly assigned the studied sheep breeds into distinct populations. Mahalanobis distance showed significant (p < 0.01) difference between breeds. The present morphometric information obtained could support future decision-making on the management, conservation, and improvement of the studied sheep genetic resources.

Genetic diversity, population structure, and gene flow analysis of lowland bamboo [Oxytenanthera abyssinica (A. Rich.) Munro] in Ethiopia.

Bamboo, a member of subfamily Bambusoideae in the grass family (Poaceae), is one of the most important nontimber forest resources and a potential alternative to wood and wood products. Ethiopian lowland bamboo (Oxytenanthera abyssinica) is an economically and ecologically important species which accounts about 85% of total bamboo coverage in the country. This species is experiencing population decline due to a number of anthropogenic factors. As a foundation step, genetic diversity, population structure, and gene flow analysis of various O. abyssinica populations found in Ethiopia are studied using inter-simple sequence repeat markers. One hundred and thirty isolates of bamboo belonging to 13 geographically diverse populations were collected for DNA extraction and analysis. Heterozygosity, level of polymorphism, marker efficiency, Nei's gene diversity (H), and Shannon's information index (I) analysis, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA), and admixture analyses were performed based on the markers banding pattern. The results indicated high genetic variation (84.48%) at species level. The H, I, observed and effective number of alleles at the species level were 0.2702, 0.4061, 1.8448, and 1.4744, respectively, suggesting a relatively high level of genetic diversity. However, genetic differentiation at the population level was relatively low. Using grouped populations, AMOVA revealed that most (61.05%) of the diversity was distributed within the populations with F ST = 0.38949, F SC = 0.10486, and F CT = 0.31797. Cluster analysis grouped the populations into markedly distinct clusters, suggesting confined propagation in distinct geographic regions. STRUCTURE analyses showed K = 2 for all populations and K = 11 excluding Gambella population. Using these markers, we found strong evidence that the genetic diversity of the lowland bamboo is associated with distinct geographic regions and that isolates of Gambella Region, with their unique genetic origin, are quite different from other bamboos found in the country.

Low Prevalence of Mycobacterium bovis in Tuberculosis Patients, Ethiopia.

An estimated 17% of all tuberculosis cases in Ethiopia are caused by Mycobacterium bovis. We used M. tuberculosis complex isolates to identify the prevalence of M. bovis as the cause of pulmonary tuberculosis. Our findings indicate that the proportion of pulmonary tuberculosis due to M. bovis is small (0.12%).

Line-probe assay and molecular typing reveal a potential drug resistant clone of Mycobacterium tuberculosis in Ethiopia.

BACKGROUND: Antimicrobial resistance is a global concern of increasing significance. Multidrug resistant tuberculosis (MDR-TB) is spreading worldwide. It is important to monitor trends of antimycobacterial resistance. This is particularly true for high TB burden countries such as Ethiopia where disproportionally less drug sensitivity data are reported from. METHODS: The prevalence of drug resistance was assessed with the line probe assay GenoType MTBDRplus in a set of 161 M. tuberculosis strains that were selected from four common lineages and sub-lineages previously identified in Ethiopia. Most of the tested M. tuberculosis isolates had been genotyped by established Spoligotyping and MIRU-VNTR typing methods. RESULTS: The proportion of MDR-TB among the isolates was 3.1%. Mono-resistance was 1.2% to rifampicin and 4.3% to isoniazid, and resistance to either of the two first line drugs was 8.7%. Strains of Lineage 4 had the highest resistance rate (13.6%) followed by Lineage 3 (4.9%). None of the isolates representing Lineages 1 and Lineage 7 were drug resistant. Multidrug resistance among pulmonary TB and TB lymphadenitis clinical isolates was 2.8 and 3.7%, respectively. Drug resistance of strains carrying the most prevalent spoligotype in Ethiopia - SIT149 - was further explored. Stratification by MIRU-VNTR identified one genotype with a high rate of drug resistance against Rifampicin and Isoniazid and circulation of a potential MDR-TB clone is proposed. CONCLUSION: Although the strain selection was not fully randomized, the overall M. tuberculosis drug resistance rate in this strain set was 8.7% while the rate of MDR was 3.1%. In parallel, we identified a sub-lineage that showed a high rate of resistance to both rifampicin and isoniazid. These resistant strains may belong to a clone of M. tuberculosis that is circulating in the highlands of Ethiopia.

Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system.

BACKGROUND: Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia. RESULTS: Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop. CONCLUSIONS: These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.

Molecular genetic diversity and population structure of Ethiopian white lupin landraces: Implications for breeding and conservation.

White lupin is one of the four economically important species of the Lupinus genus and is an important grain legume in the Ethiopian farming system. However, there has been limited research effort to characterize the Ethiopian white lupin landraces. Fifteen polymorphic simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 212 Ethiopian white lupin (Lupinus albus) landraces and two genotypes from different species (Lupinus angustifolius and Lupinus mutabilis) were used as out-group. The SSR markers revealed 108 different alleles, 98 of them from 212 landraces and 10 from out-group genotypes, with an average of 6.5 alleles per locus. The average gene diversity was 0.31. Twenty eight landraces harbored one or more private alleles from the total of 28 private alleles identified in the 212 white lupin accessions. Seventy-seven rare alleles with a frequency of less than 5% were identified and accounted for 78.6% of the total alleles detected. Analysis of molecular variance (AMOVA) showed that 92% of allelic diversity was attributed to individual accessions within populations while only 8% was distributed among populations. At 70% similarity level, the UPGMA dendrogram resulted in the formation of 13 clusters comprised of 2 to 136 landraces, with the out-group genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and Ethiopian white lupin populations collected by Australians. A model-based population structure analysis divided the white lupin landraces into two populations. All Ethiopian white lupin landrace populations, except most of the landraces collected by Australians (77%) and about 44% from Awi, were grouped together with significant admixtures. The study also suggested that 34 accessions, as core collections, were sufficient to retain 100% of SSR diversity. These accessions (core G-34) represent 16% of the whole 212 Ethiopian white lupin accessions and populations from West Gojam, Awi and Australian collections contributed more accessions to the core collection.

Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers.

BACKGROUND: Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum. RESULTS: In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency. CONCLUSION: These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.

A 24-well plate assay for simultaneous testing of first and second line drugs against Mycobacterium tuberculosis in a high endemic setting.

BACKGROUND: Early detection of drug resistance is one of the priorities of tuberculosis (TB) control programs as drug resistance is increasing. New molecular assays are only accessible for a minority of the second line drugs and their availability in high endemic settings is also hampered by high cost and logistic challenges. Therefore, we evaluated a previously developed method for drug susceptibility testing (DST) including both first- and second line anti-TB drugs for use in high endemic areas. RESULTS: Baseline mycobacterial isolates from 78 consecutive pulmonary TB patients from Addis Ababa, Ethiopia who were culture positive for Mycobacterium tuberculosis at the end of a two-month directly observed treatment short course (DOTS) were included. The isolates were simultaneously tested for isoniazid, rifampicin, ethambutol, streptomycin, amikacin, kanamycin, capreomycin, ofloxacin, moxifloxacin, ethionamide and para-aminosalicylic acid susceptibility using the indirect proportion method adopted for 24-well agar plates containing Middlebrook 7H10 medium. Applying the 24-well plate assay, 43 (55.1%) isolates were resistant to one or more of the first line drugs tested (isoniazid, rifampicin and ethambutol). MDR-TB was identified in 20.5% of this selected group and there was a perfect correlation for rifampicin resistance with the results from the genotype MTBDRplus assay. All isolates were susceptible to aminoglycosides and fluoroquinolones in agreement with the genotype MTBDRsl assay. The only tested second line drug associated to resistance was ethionamide (14.1% resistant). The method was reproducible with stable results for internal controls (one multi-drug resistant (MDR) and one pan-susceptible strain (H37Rv) and DST results could be reported at two weeks. CONCLUSIONS: The 24-well plate method for simultaneous DST for first- and second line drugs was found to be reproducible and correlated well to molecular drug susceptibility tests. It is likely to be useful in high-endemic areas for surveillance as well as for the detection of second line drug resistance in targeted groups such as in those who fail empirical MDR treatment.

AFLP and RAPD analyses of genetic diversity of wild and/or weedy Guizotia (Asteraceae) from Ethiopia.

Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers were used to provide estimates of the comparative genetic variation within and among populations of various Guizotia taxa with the goal of conserving and utilizing their genetic diversity. The percentage of polymorphic loci (P(S)) ranged from 28.5%-90% (AFLP) and 85.6%-99.6% (RAPD). The overall gene diversity estimate () has shown slight variation among taxa ranging from 0.32-0.37 (AFLP) and from 0.22 to 0.28 (RAPD). The within population diversity of "Chelelu" and "Ketcha" was found to be unexpectedly high. Both parameters used to estimate population differentiation (G(ST) and F(ST)) revealed the highest population differentiation G. zavattarii in followed by G. arborescens. Genetic variation among populations within a taxon was highly significant for all the five taxa as revealed by AMOVA (P<0.0001). The need for immediate conservation activities for G. arborescens and G. zavattarii, and factors that contribute to the existing genetic variability and population genetic structures are discussed.

Evidence of genetic variability of human immunodeficiency virus type 1 in plasma and cervicovaginal lavage in ethiopian women seeking care for sexually transmitted infections.

Most human immunodeficiency virus type 1 (HIV-1) transmission in developing countries occurs through heterosexual intercourse or during birth from mother to child. It is critical to characterize the virus of the genital tract variants as a target for the development of an HIV-1 vaccine and microbicidal therapies. We compared the C2V3 env domain genetic diversity of HIV-1 in female genital secretions and in plasma from Ethiopian women seeking care for sexually transmitted infections (STIs). Sequences within an individual differed between the plasma and cervicovaginal lavage (CLV) compartments with nucleotide and amino acid median difference values of 8.3 and 4.8%, respectively. Sequence diversity in CVL was greater than in plasma. And the V3 loop positive charge was often more elevated in CVL. These are markers of the differential evolution of the viruses in CVL and peripheral blood indicating that limited evolution at the site of contact is not the limiting factor determining the preferential transmission of macrophage tropic viruses.