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Plant micropropagation research in Ethiopia requires concerted efforts to meet desired levels of application for sustainable utilization of the country's diverse plant genetic resources. The purpose of the present review is to provide an update on the results of plant micropropagation conducted so far in Ethiopia. It assessed their strengths and identified gaps in order to standardize research methods and indicate future research directions. Two cereals, three oil crops, three spices, five medicinal plants, two high-value crops, six fruit plants, nine root crops, and one endangered multipurpose shrub were reviewed. The assessment of previously published research was carried out in terms of methods used in the selection of ex plants and their disinfestations, culture vessels, and media used with a variety of combinations and concentrations of plant growth regulators, macro- and micronutrient requirements, culture environments, and genetic stability of regenerated plantlets. Further assessments include the utilization of plant growth-promoting microbes and applications of “omics” research in order to establish standardized, efficient, and cost-effective micropropagation techniques. The findings of the assessments are summarized and current advances are highlighted, along with recommendations for future plant micropropagation studies in the country.

Coffee quality is a complex trait involving sensory and bean characteristics as well as biochemical contents. The objective of this study was to assess the major factors influencing the quality of wild Arabica coffee (Coffea arabica L.) in the natural coffee forests of southwest and southeast Ethiopia. Results revealed that both natural (soil, aspect, elevation, climate, geographic location) and human factors (cherry harvesting/ handing, theft, forest management) considerably influenced the quality of wild Arabica coffee. The soil factor affected every component of coffee quality (cup quality, bean characteristics and biochemical contents). The cup quality of coffee varied with soil properties, especially with available P and soil texture. The bean size distribution was also affected by soil properties; there was significant positive relationship between soil pH, sand or Mn and the proportion of bold beans (retained on screen 17). Soil organic matter, total N and sand content were inversely correlated with caffeine content, but available P and clay content were positively correlated with caffeine. Increase in elevation led to increase in bean size up to the elevation of about 1600 m above sea level, but thereafter no more increase in bean size (hump-shaped relationship, not monotonic). Bean size increased with increase in longitude, but it decreased with increase in latitude. Cup quality was also significantly influenced by coffee harvesting and handling, but its influence was not noticed on bean size and biochemical contents. Coffee quality is therefore the resultant of an interaction of different natural and human factors prevailing in the respective area. Key words: Arabica coffee, bean size, biochemical content, cup quality, environment, management/handling.

Yam plant has a major role in Ethiopia particularly in densely populated areas of south, southwestern, and western parts of the country. It grows in a wide range of soils with an altitude range of 1140 to 2200 masl. This study was done to identify yam species collected from major producing areas of the country. The total of sixty yam accessions from ten different geographic origins of South and Oromiya region of Ethiopia were used. The collected samples were planted in complete randomized block design at two research sites of South Agricultural Research Institute. Forty-five qualitative morphological characterizations were used to characterize and identify Dioscorea species. Among these qualitative characters observed in the study presence and absence of spines on stems and roots, number of male and female inflorescence, stem length, twining direction, and flesh color were the major traits considered for species identification. The organoleptic properties evaluation was carried out using fifteen selected local farmers. Statistical analysis was done using Numerical Taxonomy and Multivariate Analysis System Version 2.02 NTSYpc software program and the data reduction function of SPSS for windows. Based on this study, sixty yam germplams of ten major growing areas of the country were identified into six Dioscorea species. These identified Dioscorea species were again subjected to qualitative morphological characterization and 33 morphological traits revealed variability. This implies presence of high diversity in yam (Dioscorea species) of Ethiopia. Most of the morphological variations among the yam genotypes were contributed by young petiole color, tendency of tuber to branch, and tuber flesh color. Hence, these morphological traits could be taken as useful traits for identification of yam cultivars.

The rich linguistic, ethnic and cultural diversity of Ethiopia provides an unprecedented opportunity to understand the level to which cultural factors correlate with–and shape–genetic structure in human populations. Using primarily new genetic variation data covering 1,214 Ethiopians representing 68 different ethnic groups, together with information on individuals’ birthplaces, linguistic/religious practices and 31 cultural practices, we disentangle the effects of geographic distance, elevation, and social factors on the genetic structure of Ethiopians today. We provide evidence of associations between social behaviours and genetic differences among present-day peoples. We show that genetic similarity is broadly associated with linguistic affiliation, but also identify pronounced genetic similarity among groups from disparate language classifications that may in part be attributable to recent intermixing. We also illustrate how groups reporting the same culture traits are more genetically similar on average and show evidence of recent intermixing, suggesting that shared cultural traits may promote admixture. In addition to providing insights into the genetic structure and history of Ethiopia, we identify the most important cultural and geographic predictors of genetic differentiation and provide a resource for designing sampling protocols for future genetic studies involving Ethiopians., Ethiopia is one of the most ethnically and culturally diverse countries. Here, the authors look at genetic and cultural variation in 1,214 Ethiopians to unravel the relationship between genetic admixture and cultural factors.

Background Emerging wheat stem rust races have become a major threat to global wheat production. Finding additional loci responsible for resistance to these races and incorporating them into currently cultivated varieties is the most economic and environmentally sound strategy to combat this problem. Thus, this study was aimed at characterizing the genetic diversity and identifying the genetic loci conferring resistance to the stem rust of wheat. To accomplish this, 245 elite lines introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA) were evaluated under natural stem rust pressure in the field at the Debre Zeit Agricultural Research Center, Ethiopia. The single nucleotide polymorphisms (SNP) marker data was retrieved from a 15 K SNP wheat array. A mixed linear model was used to investigate the association between SNP markers and the best linear unbiased prediction (BLUP) values of the stem rust coefficient of infection (CI). Results Phenotypic analysis revealed that 46% of the lines had a coefficient of infection (CI) in a range of 0 to 19. Genome-wide average values of 0.38, 0.20, and 0.71 were recorded for Nei’s gene diversity, polymorphism information content, and major allele frequency, respectively. A total of 46 marker-trait associations (MTAs) encompassed within eleven quantitative trait loci (QTL) were detected on chromosomes 1B, 3A, 3B, 4A, 4B, and 5A for CI. Two major QTLs with –log10 (p) ≥ 4 (EWYP1B.1 and EWYP1B.2) were discovered on chromosome 1B. Conclusions This study identified several novel markers associated with stem rust resistance in wheat with the potential to facilitate durable rust resistance development through marker-assisted selection. It is recommended that the resistant wheat genotypes identified in this study be used in the national wheat breeding programs to improve stem rust resistance.

Objective: To analyze haptoglobin polymorphism, plasma haptoglobin concentration, and ABO blood groups associated with leprosy. Methods: Blood groups were determined using monoclonal anti-A and anti-B. Haptoglobin was genotyped by PCR; plasma haptoglobin concentration was measured by ELISA. Data were analyzed by SPSS version 21 and P-values ≤ 0.05 were considered as statistically significant. Results: ABO blood groups in leprosy patients were found to have no significant difference compared to controls and the general population (P > 0.05). The data showed a lower frequency of Hp1-1 (14.6%) and higher frequency of Hp2-2 (25.6%) in leprosy patients compared to healthy controls (23.1% and 19.8%, respectively), without significant association (P = 0.315). The mean of haptoglobin concentration was higher in leprosy patients [(1.32 ± 0.70) mg/ mL] than in healthy controls [(1.17 ± 0.67) mg/mL] (P = 0.160). The mean (1.44 mg/mL) and median (1.37 mg/mL) values of haptoglobin concentration were significantly higher in male leprosy patients than in male healthy controls (1.11 mg/mL and 1.11 mg/mL, respectively) (P = 0.018). Independent sample t-test and One-way ANOVA analysis also indicated significant mean elevation of Hp along leprosy spectrum and bacterial index (P < 0.05). Conclusions: In conclusion, the study revealed absence of influence of Hp polymorphism and ABO blood groups on leprosy occurrence; however, plasma haptoglobin concentration elevates in leprosy patients and is significantly associated with leprosy spectrum and bacterial loads in patients.

Background Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia. Results We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools. Conclusion The 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0540-4) contains supplementary material, which is available to authorized users.

A study was carried out between 2008 and 2011 to investigate the potential risks of gene flow and its consequences in the crop–wild–weedS. bicolorcomplex in Ethiopia to aid efforts to conserve genetic diversity. Morphological measurements and genomic DNA samples were takenin situfrom 30 wild and eight cultivated populations representing a total of 760 samples from five regions. Genetic diversity, gene flow, population structure and outcrossing rates of wild populations were computed using phenotypic measurements and/or polymorphic simple sequence repeat (SSR) markers. Moreover, morphological analyses of fitness of crop–wild hybrids were studied. High diversity was observed among the wild/weedy sorghum populations for phenotypic traits and SSRs. SSR diversity was high in both wild and cultivated populations, but the magnitude was greater in the former. Gene flow between the wild and the cultivated sorghum was observed to be higher than that within either pool. Wild sorghums exhibited variation in the multilocus outcrossing rate (range = 0.31–0.65) and fitness was not compromised in most wild × crop hybrids. The study indicated that crop-to-wild gene flow is possible in Ethiopia. Thus, genes from transgenic sorghum are expected to enter into the wild and non-transgenic cultivated populations and may spread and persist, if transgenic sorghum is deployed in Ethiopia and in other countries of Africa, which may pose risk of introduction of unwanted effects, which in turn may lead to loss of genetic diversity.

Yam (Dioscorea spp L.) is one of root and tuber crops grown in Ethiopia as source of food and income. It is cultivated mainly in south, southwest, and western part of the country. Two hundred ten yam accessions from ten different geographic origins of major growing areas of the country were used in this study. The sprouted tubers of some accessions were received from research centers where others were directly collected from farmers’ fields during early March, 2010. The collected yam genotypes were planted in complete randomized block design at two research sites (namely at Hawasa and Wonago) which are found under South Agricultural Research Institute in the end of April 2010. All important cultural practices such as staking, weeding and irrigation were done starting from planting till harvesting. Yam leaf samples with of different origin were observed separately using twenty SSR markers. A similarity matrix derived UPGMA cluster analysis based on geographical sites showed nine distinct clustering groups which indicated presence of relationship between genetic distances to that of geographical distance in most of clustering groups. These cluster grouping is supported by Analysis of Molecular Variance (AMOVA) that indicated presence of significance genetic variation of 210 yam accessions within and among ten collection sites.

According to Food and Agriculture Organization (FAO), droughts have significant economic, environmental, and social impacts, both direct and indirect. All field crops are affected by drought. Global warming and climate change are expected to exacerbate this phenomenon. Barley (Hordeum vulgare L.) ranks fourth among cereals after wheat (Triticum aestivum L.), maize (Zea mays L.), and rice (Oryza sativa L.). Drought is a significant issue in barley breeding programs. The purpose of this chapter is to review pertinent literature on general drought-tolerance mechanisms in important field crops and provide the latest state-of-the-art information on drought-coping mechanisms in barley, including molecular basis of crop response in moisture-limited environments. We highlight research insights, existing gaps, and future research directions regarding drought tolerance in barley. Known quantitative trait loci (QTL) and genes, such as Dhn and DREB, and their use in marker-assisted selection for drought tolerance are summarized. Traits associated with improved performance (early vigor, plant height, spike waxiness, and thousand-grain weight) under low-moisture stress environments have been identified as useful criteria in breeding for drought-tolerant barley. Low stomatal density cultivars of barley should be developed to combat drought and climate change. Latest innovations in genome-editing technology, such as clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9), clustered regularly interspaced short palindromic repeats from Prevotella and Francisella 1 (CRISPR-Cpf1), and multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC), should be useful for plant breeders in modifying the barley genome, as needed, to develop drought-tolerant cultivars.

Noug (Guizotia abyssinica) is a semidomesticated oil-seed crop, which is primarily cultivated in Ethiopia. Unlike its closest crop relative, sunflower, noug has small seeds, small flowering heads, many branches, many flowering heads, and indeterminate flowering, and it shatters in the field. Here, we conducted common garden studies and microsatellite analyses of genetic variation to test whether high levels of crop–wild gene flow and/or unfavorable phenotypic correlations have hindered noug domestication. With the exception of one population, analyses of microsatellite variation failed to detect substantial recent admixture between noug and its wild progenitor. Likewise, only very weak correlations were found between seed mass and the number or size of flowering heads. Thus, noug's ‘atypical’ domestication syndrome does not seem to be a consequence of recent introgression or unfavorable phenotypic correlations. Nonetheless, our data do reveal evidence of local adaptation of noug cultivars to different precipitation regimes, as well as high levels of phenotypic plasticity, which may permit reasonable yields under diverse environmental conditions. Why noug has not been fully domesticated remains a mystery, but perhaps early farmers selected for resilience to episodic drought or untended environments rather than larger seeds. Domestication may also have been slowed by noug's outcrossing mating system.

Genetic diversity assessment of genetic resources maintained at Gene-Banks has important implication for future improvement, conservation and collection activities. However, such information is not available for sesame collected by IBC, Ethiopia. Inter simple sequence repeat (ISSR) marker was used to assess the level of genetic diversity, genetic structure and genetic distance, and to indirectly estimate the level of gene flow among populations of sesame in Ethiopia. A total of 120 (82 Ethiopian and 38 exotic) sesame accessions and six ISSR primers were used. DNA was extracted using a triple CTAB extraction method from silica gel dried bulked sample of five randomly selected individual plants per accession at the stage of three to four weeks after planting. The presence of higher polymorphism was revealed among accessions collected from Ethiopia (75.85) than the exotic accessions (65.52). The average gene diversity relative to the overall population was 0.24. Samples from Welega was the most diverse, with gene diversity value of 0.26 followed by samples from Tigray (0.20) and Shewa (0.20). Samples from Gojam (0.10) and Sudan (0.12) were the least diverse. Inter-population genetic distance (D) ranged from 0.031 to 0.165 for the overall population. From the exotic accession, samples of South East Asia are distantly related to most of the Ethiopian accessions. Unweighted pair group method with arithmetic mean analysis (UPGMA) of Ethiopian sesame populations revealed two major groups and three outliers (Cultivated, Welega and Illubabore). Key words: Bulk sampling, gene flow, genetic differentiation, genetic distance, inter simple sequence repeat (ISSR), genetic diversity and sesame landrace accessions.

Since the immediate wild relatives ofSorghum bicolor(L.) Moench are indigenous to Ethiopia, studying their population biology is timely for undertaking conservation measures. A study was conducted to investigate the occurrence of population bottlenecks and to estimate the long-term effective population size (Ne) in wild relatives of sorghum. For this, 40 samples of wild sorghum were collected from two remotely located populations that were allopatric to the cultivated sorghum. The presence of bottlenecks was investigated using heterozygosity excess/deficiency, mode shift and allelic diversity based on nine polymorphic simple sequence repeat (SSR) loci. We also estimated theNeof the studied populations using two different methods employing SSR mutation models. The expected heterozygosity was found to be 0.41 and 0.71 and allelic richness was 3.0 and 4.9, in Awash and Gibe populations, respectively. Neither the heterozygosity excess nor the mode-shift methods detected signatures of bottlenecks in the studied populations. The effective size of the two wild sorghum populations studied also showed no risk of population reduction in these regions of Ethiopia. Therefore, these allopatric wild sorghum populations can survive by occupying patches by the roadsides and fences, areas within abandoned farm lands, forests, etc., which shows that their wild characteristics of adaptation have been adequate for them to survive from extinction despite extensive deforestation of their habitat for modern agriculture and frequent grazing by livestock. However, this does not guarantee the survival of these species for the future andex situconservation measures or policies could help maintain their diversity.

Forests of SW Ethiopia constitute the native habitat of Coffea arabica and also the place where domestication of Arabica coffee started. Selection from wild populations has led to numerous landraces (farmer’s varieties) and cultivars. Inter-simple sequence repeats (ISSRs) were generated from a representative set of forest coffee populations and landraces across Ethiopia. For the broad diversity assessment, nine di- and tri-nucleotide ISSR primers were applied, as chosen from a total of 102 primers tested initially. Tetranucleotide ISSR primers differed in amplifying fingerprints that could hardly be analysed due to excessive variation. Tree building analysis (NJ, UPGMA) of 84 polymorphic loci amplified for 125 C. arabica individuals provided evidence for several groups of related genotypes occurring in certain geographical areas of Ethiopia and underscored the existence of wild coffee distinct from landraces. Landraces seem to have originated in different geographical areas of Ethiopia in a stepwise domestication process. While the overall geographical signal in the dataset was weak, analysis in a Bayesian framework using the admixture model with geographical priors in STRUCTURE recovered some genetic clustering. Based on Shannon’s diversity index, populations from Yayu (0.47) and Bonga (0.46) showed highest diversity, followed by individuals from Berhane Kontir (0.41). A likely scenario for the differentiation of C. arabica after an allopolyploidization event is that the hierarchical-geographical patterning of wild Coffea genotypes expected from stepwise range extension was obscured by recent or ancient gene flow. The diversity and geographical distribution of autochthonous C. arabica genotypes indicates the need for a multi-site in situ conservation approach.

The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009TG (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep.

Natural hybridization between wild/weedy and crop species often results in rare hybrids, which can be more weedy and difficult to control. Moreover, the advent of transgenic crop plants raises questions of biosafety risk assessment on the consequences of rare hybrids with possible fitness enhancing genes on the environment. This study aimed at measuring the fitness components of wild–crop sorghum hybrids for various juvenile survival and adult morphological and fertility characters as part of the risk assessment of transgenic sorghum in Africa where the crop was believed to have first domesticated and serves as the major staple. Out of a pool of hybrids made in 2010 from 23 wild sorghum accessions and two released cultivated sorghum varieties using hand emasculation techniques, seven were selected for the field study of their fitness components in 2011. The study confirmed that crop–wild hybrids of sorghum are fertile. Two approaches were followed (relative fitness and mid-parent heterosis) which showed that most of the hybrids were as fit as their wild parents, and in some cases they showed mid-parent heterosis for the measured traits. The results of this study highlighted a potential risk that hybrids carrying crop genes (including herbicide resistance transgenes) could pose because they could be more weedy than their wild/weedy parents if transgenic sorghum is deployed in regions where the wild and cultivated sorghum populations coexist, such as in Ethiopia and in other parts of Africa.

Because transgenic sorghum (Sorghum bicolor L.) is being developed for Africa, we investigated the potential for transgenes to spread to conspecific wild/weedy sorghum populations in Ethiopia, which is considered the centre of origin of cultivated sorghum. In the current study, the extent of outcrossing, and uniparental and biparental inbreeding were investigated in seven wild/weedy sorghum populations collected at elevations ranging from 631 to 1709 m. Based on allele frequency data of 1120 progenies and 140 maternal plants from five polymorphic microsatellite markers, outcrossing rates were estimated using standard procedures. The average multilocus outcrossing rate was 0.51, with a range of 0.31-0.65 among populations, and the family outcrossing rate was in the extreme range of 0 to 100%. The highest outcrossing (t(m) = 0.65) was recorded in a weedy population that was intermixed with an improved crop variety in Abuare (Wello region). It was also observed that the inbreeding coefficient of the progenies (F(p)) tend to be more than the inbreeding coefficient of both their maternal parents (F(m)) and the level of inbreeding expected at equilibrium (F(eq)), which is a characteristic of predominantly outbreeding species. Biparental inbreeding was evident in all populations and averaged 0.24 (range = 0.10-0.33). The high outcrossing rates of wild/weedy sorghum populations in Ethiopia indicate a high potential for crop genes (including transgenes) to spread within the wild pool. Therefore, effective risk management strategies may be needed if the introgression of transgenes or other crop genes from improved cultivars into wild or weedy populations is deemed to be undesirable.

Background Korarima (Aframomum corrorima) is a perennial and aromatic herb native and widely distributed in southwestern Ethiopia. It is known for its fine flavor as a spice in various Ethiopian traditional dishes. Few molecular studies have been performed on this species so far. In the present paper, the ISSR technique was employed to study the genetic diversity in populations of cultivated A. corrorima. Results Seven ISSR primers produced a total of 86 clearly scorable DNA bands. High levels of genetic diversity were detected in cultivated A. corrorima (percentage of polymorphic bands = 97.67%, gene diversity = 0.35, Shannon’s information index = 0.52). Analysis of molecular variance (AMOVA) showed that 27.47% of the variation is attributed to the variation among populations and 72.53% to the variation within populations. The Fst (0.28) value showed a significant (p

Passport data of A. corrorima samples collected from different sites in Ethiopia. (DOCX 17Â kb)

UPGMA dendrogram based on pair wise simple matching dissimilarity index showing the genetic relationships among Ethiopian cultivated and wild korarima populations using SSR markers. The analysis resulted in two major clusters shown as “I” and “II”. (DOCX 27 kb)

Characteristics of 23 microsatellite primers developed for Aframomum corrorima (The bold one are used for genetic diversity analysis) (DOCX 16Â kb)

A biplot detected the maximum peak at KÂ =Â 2 (the optimum number of clusters) based on Evanno et al. 2005 [35] prediction. (PDF 10Â kb)

Objective CYP3A4 expression varies up to 100-fold among individuals, and, to date, genetic causes remain elusive. As a major drug-metabolizing enzyme, elucidation of such genetic causes would increase the potential for introducing personalized dose adjustment of therapies involving CYP3A4 drug substrates. The foetal CYP3A isoform, CYP3A7, is reported to be expressed in ∼10% of European adults and may thus contribute towards the metabolism of endogenous substances and CYP3A drug substrates. However, little is known about the distribution of the variant expressed in the adult. Methods We resequenced the exons, flanking introns, regulatory elements and 3'UTR of CYP3A4 in five Ethiopian populations and incorporated data from the 1000 Genomes Project. Using bioinformatic analysis, we assessed likely consequences of observed CYP3A4 genomic variation. We also conducted the first extensive geographic survey of alleles associated with adult expression of CYP3A7 - that is, CYP3A7*1B and CYP3A7*1C. Results and conclusion Ethiopia contained 60 CYP3A4 variants (26 novel) and more variants (>1%) than all non-African populations combined. No nonsynonymous mutation was found in the homozygous form or at more than 2.8% in any population. Seventy-nine per cent of haplotypes contained 3'UTR and/or regulatory region variation with striking pairwise population differentiation, highlighting the potential for interethnic variation in CYP3A4 expression. Conversely, coding region variation showed that significant interethnic variation is unlikely at the protein level. CYP3A7*1C was found at up to 17.5% in North African populations and in significant linkage disequilibrium with CYP3A5*3, indicating that adult expression of the foetal isoform is likely to be accompanied by reduced or null expression of CYP3A5.

Extensive studies of genetic diversity and population structure important for conservation of wild sorghum are yet lacking in Ethiopia, the centre of origin for cultivated sorghum. To assess both genetic diversity and the probability of gene flow between wild and cultivated types, collections of wildSorghum bicolorwere made from regions in Ethiopia where wild and cultivated sorghum coexist. Morphological data were recordedin situfor both quantitative and qualitative characters from 30 populations in five diverse geographical regions and eight agroecologies. High phenotypic diversity was observed among the wild and weedy sorghum populations. The overall standardized Shannon–Weaver diversity index (H′), computed from the frequencies of all qualitative traits, ranged from 0.47 to 0.98 with an average value of 0.76. Moreover, warm semi-arid lowland (SA2) agroecologies, which contain Tigray populations, supported the highest diversity for these traits. Subspeciesverticilliflorumanddrummondii(the two major subspecies of wildS. bicolor) were observed in diverse habitats throughout northern and central Ethiopia. In some areas, weedy types showed domestication traits including the absence of awns and reduced seed shattering. The existence of morphologically intermediate forms indicates that gene flow between cultivated and wild forms has likely occurred. Deployment of transgenic crop sorghum, therefore, would pose a distinct risk for transgene movement into wild Ethiopian populations.

In situ population studies of wild relatives of crops are crucial for the conservation of plant genetic resources, especially in regions with high genetic diversity and a risk of local extinction. Ethiopia is the center of origin for sorghum, yet little is known about the genetic structure of extant wild populations. Using 9 Simple Sequence Repeat loci, we characterized 19 wild populations from five regions, 8 local cultivar populations from three regions, and 10 wild sorghum accessions from several African countries. To our knowledge, this is the most comprehensive study to date of in situ wild sorghum populations in Africa. Genetic diversity corrected for sample size was significantly greater in the wild populations in situ than in local cultivars or the accessions. Approximately 41 % of the genetic variation in the wild plants was partitioned among populations, indicating a high degree of differentiation and potential value for germplasm conservation, and the average number of migrants (Nm) per generation was 0.43. Cluster analyses showed that some wild populations were grouped by geographic region, whereas others were not, presumably due to long-distance seed movement. Four wild populations from disjunct regions formed a unique cluster with an Ethiopian accession of subsp. drummondii and probably represent a weedy race. STRUCTURE and other analyses detected evidence for crop-wild hybridization, consistent with previous molecular marker studies in Kenya, Mali, and Cameroon. In summary, in situ wild sorghum populations in Ethiopia harbor substantial genetic diversity and differentiation, despite their close proximity to conspecific cultivars in this crop/wild/weedy complex.

Chickpea (Cicer arietinum L.) is an economically and ecologically important food legume crop. Ethiopia has a large collection of chickpea germplasm accessions; but, it has not been extensively characterized for desirable sources of agronomic and symbiotic significance for use in breeding programs. A study was conducted at two locations (Ambo and Ginchi) in 2009/2010 to characterize and evaluate Ethiopian chickpea germplasm accessions for symbiotic and agronomic performance. One hundred and thirty-nine germplasm accessions were evaluated with 16 other genotypes including non-nodulating reference checks. Differences among genotypes, locations and genotype by location interaction effects were significant for a number of characters. A number of accessions better performing over the improved genotypes were identified for both symbiotic and agronomic characters. The amount of fixed nitrogen ranged from 13 to 49% in foliage, 30 to 44% in grain and 28 to 40% in total above-ground biomass. Grain yield performance varied from 31 to 70 g per 5 plants and seed size ranged from 82 to 288 g per 1000 seeds. For both symbiotic and agronomic characters, landraces were found to be overwhelmingly superior to introduced genotypes, except for seed size, where the best genotypes were all from exotic sources. The result indicated that Ethiopian chickpea landraces have better genetic potential for improving a number of symbiotic and agronomic characters over the varieties currently in use. Selection of best individuals within and among the accessions would be expected to be effective.

Humans and their ancestors have traversed the Ethiopian landscape for millions of years, and present-day Ethiopians show great cultural, linguistic, and historical diversity, which makes them essential for understanding African variability and human origins. We genotyped 235 individuals from ten Ethiopian and two neighboring (South Sudanese and Somali) populations on an Illumina Omni 1M chip. Genotypes were compared with published data from several African and non-African populations. Principal-component and STRUCTURE-like analyses confirmed substantial genetic diversity both within and between populations, and revealed a match between genetic data and linguistic affiliation. Using comparisons with African and non-African reference samples in 40-SNP genomic windows, we identified "African" and "non-African" haplotypic components for each Ethiopian individual. The non-African component, which includes the SLC24A5 allele associated with light skin pigmentation in Europeans, may represent gene flow into Africa, which we estimate to have occurred ∼3 thousand years ago (kya). The non-African component was found to be more similar to populations inhabiting the Levant rather than the Arabian Peninsula, but the principal route for the expansion out of Africa ∼60 kya remains unresolved. Linkage-disequilibrium decay with genomic distance was less rapid in both the whole genome and the African component than in southern African samples, suggesting a less ancient history for Ethiopian populations.

Plant breeding is one way to confront the challenge of bridging the widening gap between the demand and supply of food. Despite the importance, however, plant breeding has its own negative side effects. The replacement of landraces with a few genetically uniform varieties depletes genetic diversity and provides ideal conditions for diseases and insect pests that called genetic vulnerability. The increasingly growing human population and the subsequently rising de- mands for more food, on the one hand, and the success of such efforts like the "Green Revolution" from adoption of ge- netically uniform varieties in many parts of the world, on the other, are the main driving force towards this narrow genetic base. It is, therefore, important to understand the phenomena and plan to minimize the risks from genetic vulnerability. Under marginal conditions where resource-poor farmers dominate, the current plant breeding strategies, variety release, registration and certification procedures leading to genetic uniformity should be reconsidered and some level of genetic diversity should deliberately be maintained in variety development programs. Genetic diversity can be introduced at different levels and in different ways which may include intra-varietal, inter-varietal, inter-parental and inter-specific diversities. Breeding for specific adaptation instead of wide adaptation, systematic spatial and temporal gene deployment, use of inter-specific varietal mixtures and integration of horizontal and vertical resistances have been suggested as solutions.

Continuous breeding efforts in Ethiopia resulted in the release of 15 improved chickpea (Cicer arietinum L.) varieties with improved yield, seed quality, disease resistance and better adaptation to different production zones within Ethiopia. This study was conducted to examine whether breeding for increased yield and other important agronomic traits without direct selection for resistance to the adzuki bean beetle (Callosobruchus chinensis L.) has inadvertently resulted in a significant level of susceptibility to this seed pest within the new cultivars. Field and laboratory studies were conducted to see whether breeding for better seed quality has increased susceptibility to infestation by the adzuki bean beetle. Seeds of 130 accessions/genotypes were infested with the beetle in 2009 under ambient temperature and relative humidity at Holetta, Ambo and Debre Zeit, Ethiopia. Data were recorded on attributes of infestation level and seed damage. Data on seed size, proportion of seed coat and grain yield were collected from a replicated field trial conducted with the same accessions/genotypes grown under the same conditions in 2009/10 at Ginchi and Ambo, Ethiopia. Differences among the genotypes were significant for most traits with the exception of the number of uninfested seeds. Accessions with partial resistance include 41320, 41289, 41291, 41134, 41315, 207658, 41103, 41168, 41142, 41174, 41029, 41207, 209087, 231327, 41161 and 41008. The improved varieties were more susceptible than germplasm accessions. The results indicate that genetic progress was achieved both in grain yield and seed size, but breeding efforts for these traits had also inadvertently increased seed susceptibility to C. chinensis. Improvements in seed size resulted in higher infestation levels and seed damage. Future breeding to improve seed quality should simultaneously consider corrective measures to incorporate resistance to the adzuki bean beetle.

Genetic diversity and population structure were studied in 155 chickpea (Cicer arietinum L.) entries using 33 polymorphic microsatellite (SSR) markers. Molecular analysis of variance showed variations of 73% within and 27% among populations. Introduced genotypes exhibited highest polymorphism (70.27%) than the landraces (36–57%). Collections from Shewa, Harerge, W. Gojam and S. Gonder regions also showed higher polymorphism (50–57%) than the rest of the local accessions (36–45%). Analyses of pairwise population Nei genetic distance and PhiPT coefficients, expected heterozygosity (He) and unbiased expected heterozygosity (UHe), Shannon’s information index (I) and percent polymorphism (% P) showed existence of high genetic variation between geographical regions. Accessions from adjoining geographical regions mostly showed more genetic similarities than those from origins far isolated apart. This could be associated with the ease and likelihood of inter-regional gene flow and seed movement particularly during times of drought. The 155 entries were grouped into five clusters following analysis of population structure. The first cluster (C1) constituted accessions from Arsi; the second (C2) from Gojam and Gonder; the third (C3) from Harerge and E. and N. Shewa; and the fourth (C4) from W. Shewa, Tigray, and Wello regions. The fifth cluster (C5) was entirely consisted of improved genotypes. Improved genotypes of both Kabuli and Desi types distinctly fell into cluster five (C5) regardless of their difference in seed types. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. Further implications of the findings as regards to chickpea germplasm management and its utilization in breeding program are also discussed.

Variation of a short (TA)(n) repeat sequence (rs8175347) covering the TATA box of UGT1A1 (UDP-glucuronosyltransferase1A1) is associated with hyperbilirubinaemia (Gilbert's syndrome) and adverse drug reactions, and is used for dosage advice for irinotecan. Several reports indicate that the low-activity (risk) alleles ((TA)(7) and (TA)(8))) are very frequent in Africans but the patterns of association with other variants in the UGT1A gene complex that may modulate these responses are not well known. rs8175347 and two other clinically relevant UGT1A variants (rs11692021 and rs10929302) were assayed in 2616 people from Europe and Africa. Low-activity (TA)(n) alleles frequencies were highest in equatorial Africa, (TA)(7,) being the most common in Cameroon, Ghana, southern Sudan, and in Ethiopian Anuak. Haplotypic diversity was also greatest in equatorial Africa, but in Ethiopia was very variable across ethnic groups. Resequencing of the promoter of a sample subset revealed no novel variations, but rs34547608 and rs887829 were typed and shown to be tightly associated with (TA)(n). Our results illustrate the need for investigation of the effect of UGT1A variants other than (TA)(n) on the risk of irinotecan toxicity, as well as hyperbilirubinaemia due to hemolytic anaemia or human immunodeficiency virus protease inhibitors, so that appropriate pharmacogenetic advice can be given.

Storage insect pests cause significant losses of food legumes particularly in the Tropics and the Sub-tropics. The most important species of storage insect pests of food legumes include Callosobruchus chinensis , C. maculatus , C. analis , Acanthoscelides obtectus , Bruchus incarnatus , B. rufimanus , B. dentipes , B. quinqueguttatus , B. emarginatus , B. ervi , B. lentis and B. pisorum . Effective post-harvest insect pest control measures should constitute part of the overall crop husbandry practices for preserving the quality of produce. Storage insect pests are commonly controlled using chemical insecticides which, however, bear many drawbacks related to high cost, environmental pollution and food safety risks. Breeding legume crops to improve their resistance against storage insect pests, although having technical limitations, is the best way of overcoming these disadvantages in an environment-friendly manner. In this paper, we present the findings of our extensive reviews on the potential of breeding resistant varieties of food legumes against storage insect pests along with the major technical limitations one would likely encounter and the prospective ways of tackling them.

Background and objectives CYP1A2 metabolizes various drugs, endogenous compounds and procarcinogens. As human genetic diversity has been reported to decrease with distance from Ethiopia, we resequenced CYP1A2 in five Ethiopian ethnic groups representing a rough northeast to southwest transect across Ethiopia to establish: (i) what variation exists in comparison with what is already known globally and (ii) what CYP1A2 pharmacogenetic profiles may be present as several CYP1A2-metabolized drugs are administered to Ethiopians. Results and conclusions We found 49 different variable sites (30 of which are novel), nine nonsynonymous changes (seven of which are novel), one synonymous change and 55 different haplotypes, only three of which are previously reported. When haplotypes were constructed using only nonsynonymous polymorphisms to restrict haplotypes to those most likely to affect enzyme structure/function, 10 haplotypes were identified (seven contain previously unidentified nonsynonymous variants and four are predicted to alter the enzyme structure/function). Most individuals have at least one copy of the ancestral haplotype. Comparing these data with those from publically available databases, Ethiopian groups display twice the variation seen in all other populations combined (gene diversity using nonsynonymous variants): Ethiopia = 0.17 +/- 0.02, other populations = 0.08 +/- 0.03. Across the entire gene, Ethiopia also evidences all common variation found on a global scale. We provide evidence of weak purifying selection acting on CYP1A2 and show that the time to most recent common ancestor, calculated using variation in a nearby microsatellite, places several variants into a period predating the expansion of modern humans out of Africa less than 100 000 years ago. Pharmacogenetics and Genomics 20:647-664 (C) 2010 Wolters Kluwer Health vertical bar Lippincott Williams & Wilkins.

Parsimony-based phylogenetic analyses of the genus Guizotia were undertaken based on DNA sequence data from the following chloroplast DNA (cpDNA) regions: trnT-trnL, trnL-trnF, trnY-rpoB, trnC-petN, psbM-trnD and rps16-trnQ intergenic spacers, trnL, rps16 and matK-5′trnK introns and matK gene. Out of the 26 primers used in this study, 14 were newly designed. The study was conducted to determine (1) the closest relative of Guizotia abyssinica, (2) the taxonomic status of some Guizotia taxa and (3) the subtribal placement of Guizotia in the tribe Heliantheae. The analyses of the sequence data showed that G. abyssinica, G. scabra ssp. scabra, G. scabra ssp. schimperi and G. villosa are phylogenetically closely related. However, G. scabra ssp. schimperi appeared as the most closely related taxon to G. abyssinica. Based on this phylogenetic analysis, we suggest that the two subspecies of G. scabra are better treated as separate species. The analysis also clearly demonstrated that “Chelelu” and “Ketcha” are distinct Guizotia species. The trnT-trnL and trnL-trnF intergenic spacer-based phylogenetic analysis of various subtribes of the tribe Heliantheae strongly supports the placement of the genus Guizotia within the subtribe Milleriinae.

MYH9 has been proposed as a major genetic risk locus for a spectrum of nondiabetic end stage kidney disease (ESKD). We use recently released sequences from the 1000 Genomes Project to identify two western African-specific missense mutations (S342G and I384M) in the neighboring APOL1 gene, and demonstrate that these are more strongly associated with ESKD than previously reported MYH9 variants. The APOL1 gene product, apolipoprotein L-1, has been studied for its roles in trypanosomal lysis, autophagic cell death, lipid metabolism, as well as vascular and other biological activities. We also show that the distribution of these newly identified APOL1 risk variants in African populations is consistent with the pattern of African ancestry ESKD risk previously attributed to MYH9. Mapping by admixture linkage disequilibrium (MALD) localized an interval on chromosome 22, in a region that includes the MYH9 gene, which was shown to contain African ancestry risk variants associated with certain forms of ESKD (Kao et al. 2008; Kopp et al. 2008). MYH9 encodes nonmuscle myosin heavy chain IIa, a major cytoskeletal nanomotor protein expressed in many cell types, including podocyte cells of the renal glomerulus. Moreover, 39 different coding region mutations in MYH9 have been identified in patients with a group of rare syndromes, collectively termed the Giant Platelet Syndromes, with clear autosomal dominant inheritance, and various clinical manifestations, sometimes also including glomerular pathology and chronic kidney disease (Kopp 2010; Sekine et al. 2010). Accordingly, MYH9 was further explored in these studies as the leading candidate gene responsible for the MALD signal. Dense mapping of MYH9 identified individual single nucleotide polymorphisms (SNPs) and sets of such SNPs grouped as haplotypes that were found to be highly associated with a large and important group of ESKD risk phenotypes, which as a consequence were designated as MYH9-associated nephropathies (Bostrom and Freedman 2010). These included HIV-associated nephropathy (HIVAN), primary nonmonogenic forms of focal segmental glomerulosclerosis, and hypertension affiliated chronic kidney disease not attributed to other etiologies (Bostrom and Freedman 2010). The MYH9 SNP and haplotype associations observed with these forms of ESKD yielded the largest odds ratios (OR) reported to date for the association of common variants with common disease risk (Winkler et al. 2010). Two specific MYH9 variants (rs5750250 of S-haplotype and rs11912763 of F-haplotype) were designated as most strongly predictive on the basis of Receiver Operating Characteristic analysis (Nelson et al. 2010). These MYH9 association studies were then also extended to earlier stage and related kidney disease phenotypes and to population groups with varying degrees of recent African ancestry admixture (Behar et al. 2010; Freedman et al. 2009a, b; Nelson et al. 2010), and led to the expectation of finding a functional African ancestry causative variant within MYH9. However, despite intensive efforts including re-sequencing of the MYH9 gene no suggested functional mutation has been identified (Nelson et al. 2010; Winkler et al. 2010). This led us to re-examine the interval surrounding MYH9 and to the detection of novel missense mutations with predicted functional effects in the neighboring APOL1 gene, which are significantly more associated with ESKD than all previously reported SNPs in MYH9. Electronic supplementary material The online version of this article (doi:10.1007/s00439-010-0861-0) contains supplementary material, which is available to authorized users.

Complete sequences of transcribed spacers and introns from the trnT trnF region of chloroplast DNA (cp DNA) were generated from Musaceae species to establish the phylogenetic relationships among 3 species of Ensete including the economically important Ensete ventricosum (Welw.) Cheesman and 13 species of Musa. Parsimony analysis and pair wise distance data produced a single tree, with Ensete and Musa as clearly distinguished clades. Six Musa and three Ensete clades were generated. The topology of these clades did not change when the data were split into spacers and introns, although the split resulted in poor bootstrap support. Removing a hotspot from the entire data set improved clade support. The clades produced are discussed with reference to existing taxonomic and phylogenetic treatments. In contrast to previous suggestions, most of the Rhodochlamys species that we investigated clustered together with strong support establishing their distinctiveness from the Musa species studied. Ensete glaucum (Roxb.) Cheesman and Musa beccartii Simmonds appear to represent ancestral forms of Ensete and Musa, respectively for the presently studied species, and both genera have a common ancestor that is yet to be established. Our data also show that E. ventricosum cannot be reduced to E. glaucum, nor can E. gilleti (De Wild.) Cheesman be reduced to E. ventricosum, as some authorities have suggested. Ensete gilleti or a species very close to it appears to be the ancestral species of E. ventricosum.

Persistence of intestinal lactase into adulthood allows humans to use milk from other mammals as a source of food and water. This genetic trait has arisen by convergent evolution and the derived alleles of at least three different single nucleotide polymorphisms (-13910C>T, -13915T>G, -14010G>C) are associated with lactase persistence in different populations. Each allele occurs on an extended haplotype, consistent with positive directional selection. The SNPs are located in an 'enhancer' sequence in an intron of a neighboring gene (MCM6) and modulate lactase transcription in vitro. However, a number of lactase persistent individuals carry none of these alleles, but other low-frequency single nucleotide polymorphisms have been observed in the same region. Here we examine a cohort of 107 milk-drinking Somali camel-herders from Ethiopia. Eight polymorphic sites are identified in the enhancer. -13915*G and -13907*G (a previously reported candidate) are each significantly associated with lactase persistence. A new allele, -14009*G, has borderline association with lactase persistence, but loses significance after correction for multiple testing. Sequence diversity of the enhancer is significantly higher in the lactase persistent members of this and a second cohort compared with non-persistent members of the two groups (P = 7.7 x 10(-9) and 1.0 x 10(-3)). By comparing other loci, we show that this difference is not due to population sub-structure, demonstrating that increased diversity can accompany selection. This contrasts with the well-documented observation that positive selection decreases diversity by driving up the frequency of a single advantageous allele, and has implications for association studies.

Seventeen populations of niger (Guizotia abyssinica), representing all regions in Ethiopia where this crop is grown, were investigated using the amplified fragment length polymorphism (AFLP) technique, in order to determine the extent and distribution of its genetic diversity. A total of 539 AFLP loci were scored using seven primer combinations applied to 170 individual plants. Of these, 90% were polymorphic and all the individuals investigated were genetically unique. Despite the fact that most of the variation was within populations, populations were differentiated at a significant level (analysis of molecular variance;P

Bekele, E. 1984. Relationships between morphological variance. gene diversity and flavonoid patterns in the land race populations of Ethiopian barley. —Hereditas 100: 271–294. Lund, Sweden. ISSN 0018–0661. Received February 7, 1984 An argument is forwarded that in addition to multiple genetic factors, single gene mutation with major effect could be very important in the evolution of natural populations and domesticates. The effect of null alleles and correlations between traits determined by major and minor genes are suggested to show different strategies of adaptation among different kinds of organisms. Sturtevant's hybrid dysgenesis could be the genetic reasons for Vavilov's emancipation of recessives. The three linked esterase loci are assumed to be the results of some form of gene duplication. The genetic backgrounds of the gene are reasons for unspecific polytype correlations between all states of genes and ecological variables. The rank correlation of the percentage of the contribution to the total variation by the differences between individuals in each population between enzymatic and morphological variation was not significant except for row number and Est-A locus. Diversity indices of morphological variables and enzymes are differently correlated in different regions. Enzyme variation and quantitative characters are positively correlated in some regions and negatively in others. But negative correlations are mainly concentrated into three regions. This, together with the result of kurtosis and skewness of quantitative characters are taken to be the results of multidirectional selection schemes. Correlations of quantitative characters showed an overall higher occurrence of negative correlations between plant height and number of sterile florets. Regional cluster differences based on genetic distance measures of enzymatic data and morphological data are perhaps due to differences in the fitness potential that can be related to particular allelic combinations at one level and more directly, to phenotypic properties at another. Enzyme variations and frequencies of flavonoid patterns are negatively correlated. The eleven frequent alleles that were correlated with means of six quantitative characters showed both negative and positive correlations with uneven distribution over regions. Flavonoid C pattern is negatively correlated with a number of sterile florets and positively correlated with a number of seeds.