Browsing by Author "Tesfaye, Kassahun (PhD)"

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    Agro-Morphological and Molecular Characterization of Enset (Ensete Ventricosum (Welw.) Cheesman) Landraces from Ethiopia
    (Addis Ababa University, 2018-06-01) Yemataw, Zerihun; Tesfaye, Kassahun (PhD)
    The study was conducted with the objective of assessing and documenting indigenous knowledge and perception associated with the distribution, diversity, Enset Xanthomonas Wil, its etiology and mode of transmission, and management of enset in the country, and the genetic diversity of enset landraces that were obtained from different geograpHical locations in Ethiopia, using Phenotypic traits and to develop a genome sequence data, identify and develop single nucleotide polymorpHism (SNPs) and genotyping of landraces that serve as molecular markers for future marker assisted breeding. Enset genetic resource utilization and management study was conducted in eight ethnic groups in the Southern Nations, Nationalities and Peoples’ Regional State. The data was collected mainly through individual interviews and direct on-farm participatory monitoring and observation, key informant interviews. Relevant secondary data, literature and inter-personal data were collected from unpublished progress report from National Enset Research Project, elderly people and senior experts. Enset-based farming system is one of major agricultural systems in Ethiopia that serves as a backbone for at least one-forth of country’s population. Farmers used three morphological characters, two growth attributes, disease resistance and five use values traits in folk classification and characterization of enset. A total of 312 folk landraces have been identified. The number of landraces cultivated on individual farms ranged from one to twenty eight (mean of 8.08 ± 0.93). All ethnic groups in the study area use five use categories in order of importance: kocho yield and quality, bulla quality, amicho use, fiber quality and medicinal/ritual value. Of the 312 landraces 245 landraces having more than two use types. Management and maintenance of on-farm enset diversity is influenced by systematic propagation of the landraces, exchange of planting material and selective pressure. Farmers’ knowledge and perception of enset Xanthomonas wilt showed that a significant number of farmers are aware of EXW, its symptoms, etiology and transmission and spread, but they are not able to readily relate modes of spread to control methods. Since 2002, EXW became prominent in Hadiya, with the highest EXW incidence and severity, followed by Wolaita, and Kembata-Tembaro. Farmers identified EXW as the major cause for declining production and productivity of enset in the region. EXW has spread widely and rapidly in southern Ethiopia, with significant socioeconomic impacts in smallholders’ livelihoods. There is a need for developing knowledge-based strategies and awareness-raising campaign for EXW management. In general, the existing farmers’ knowledge on naming, classification and diversity should be complemented with maintenance of the creative dynamics of traditional knowledge and transmission of the knowledge are crucial for constructing sustainable management. Assessment of genetic diversity in enset using Phenotypic markers were subjected to ANOVA and the variations among the landraces and regions were significant (p ≤ 0.01) for all the 15 traits studied. Mean for plant height, central shoot weight before grating, and fermented squeezed kocho yield per hectare per year showed regional variation along an altitude gradient and xxiii across cultural differences related to the origin of the collection. Furthermore, there were significant correlations among most of the characters. This included the correlation among agronomic characteristics of primary interest in enset breeding such as plant height, pseudostem height, and fermented squeezed kocho yield per hectare per year. Altitude of the collection sites also significantly impacted the various characteristics studied. Cluster analysis grouped the landraces into five distinct groups, with two outlying landraces. Landraces originating from regions with similar agro-climatic conditions grouped together. Principal component analysis showed that the first four principal components accounted for ~74% of the total variance of the 387 enset landraces for the 15 quantitative traits studied. The linear discriminant analyses depicted about 40.8% (160 of the 387) and 45.2% (175 of 387) correct origin-based classification of the germplasm in terms of altitude zones and regions, respectively. Six qualitative morphological traits were also analyzed using the Shannon Weaver diversity index (H’).The Shannon-Weaver Diversity Index (H') for all sampled germplasm ranged from 0.50 to 0.89, with a mean of 0.73. Analysis of variance for H' revealed highly significant (p<0.01) differences among regions for all traits. Cluster analysis grouped the landraces into four clusters. A high proportion of landraces sourced from similar altitude classes and similar regions were grouped together. This indicated that there was wide variability among landraces studied. The Phenotypic differences in these 15 traits suggest significant degrees of genetic variation and that these traits can be exploited to identify potential donors for future enset improvement efforts. The implication of the current results for plant breeding, germplasm collection, and in situ and ex situ genetic resource conservation are discussed. Seventeen (for genome sequence analysis) and four hundred eighty (for SNP catalogue development) different enset landraces used were obtained from Areka Agricultural Research Center field germplasm. We present raw sequence reads and genome assemblies resulting from the sequencing of 17 landraces of the crop plant enset. Landraces having the same names but different origin showed different reads. For SNP detection, we considered only sites either homozygous or heterozygous for all 17 data sets. We were able to identify 33,200 singlenucleotide variant sites. We generated a series of phylogenetic trees and there was no sequence variation at this locus among the 17 genomes presented here. By examining the pattern of bands in agarose electrophoresis of the product after restriction digestion, it is possible to assess the genotype at that SNP location. We applied the 22 PCR-RFLP assays to single accession of E.ventricosum. Further, we then went on to apply 5 of these assays to several hundred E. ventricosum landraces. This findings will facilitate high-resolution studies to determine the genetic architecture of traits of economic and ecological importance, to study the structure of enset populations and to apply genomic selection in breeding programs. In general, farmers cognitive, morphological, sequence and SNP output clearly distinguished between all landraces, even though they were genetically similar.
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    Agro-Morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian Potato [Plectranthus Edulis (Vatke) Agnew] From Ethiopia
    (Addis Ababa University, 2018-06-03) Gadissa, Fekadu; Tesfaye, Kassahun (PhD); Geleta, Mulatu (PhD)
    Agro-morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian Potato [Plectranthus edulis (Vatke) Agnew] from Ethiopia Fekadu Gadissa Addis Ababa University, 2018 Ethiopian potato syno. Ethiopian dinich [Plectranthus edulis (Vatke) Agnew] (Lamiaceae) is one of the ancient annual edible tuber crops, originating in Ethiopia. The crop is commonly cultivated by smallholder farmers around homesteads in the highland and semi-highland areas, usually for household consumption and rarely for marketing. In spite of its’ wide economic importances, the crop is neglected by research and development community and currently it is at risk of total extinction. Hence, this study was conducted with the main aims of assessing agro-morphological and molecular (EST-SSRs) markers-based extents of genetic diversity analysis as well as chromosome number and ploidy level determination using 174 accessions from diverse agro-ecologies in Ethiopia. For agro-morphological diversity analysis, the experimental samples were tested at Ambo and Holeta agricultural research centres, using an alpha lattice design at the locations and three blocks/replication followed by appropriate management practices. Agronomic and morphological traits-based data were collected on twenty-eight (12 qualitative and 16 quantitative) traits at the right growth stage and analysed using SAS v9.0, MINITAB® v14.13 and FigTree v1.4.3. Cytogenetic characterization was also carried out using very young root tips generated from soil covered stem rings, followed by appropriate pre-treatment, fixation and maceration. For molecular genetic diversity analysis, genomic DNA was extracted form silcagel dried young leaves collected from 287 plants (1-3 plants per accessions) following CTAB protocol. EST-SSRs marker were designed from Plectranthus barbatus cDNA sequences deposited in the GenBank, followed by PCR amplification, capillary electrophoresis, peak identification, and scoring. The scored allele size data were analysed for polymorphism, diversity indices and genetic relationship and structure using windows compatible applications. The agro-morphological traits considered showed varied morphotypes in all of the leaf (four in leaf color, three in leaf arrangement, three in leaf shape), stem (three in stem color, two in each of stem spot and stem spot colors) and tuber (four in tuber skin color, three in each of tuber texture, tuber shape and tuber hair) characterstics. Similarly, the traits revealed a wide range of variability in mean performance (minimum range of 1.39 – 2.13 cm observed in tuber diameter and maximum range of 112.90 – 165.10 xvii days observed in days to 50% flower initiation) and variance components among and within the accessions. Similarly, the mean square of all the traits showed a highly significant (P< 0.001) variation among the tested accessions. Such wide variation suggests the presence of variability which can be exploited through selection. Several of the traits showed a slightly greater or nearly equal phenotypic coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV), suggesting larger contribution of the genotypic effect for phenotypic expression of such characters and hence, phenotypic values-based selection for the traits may be effective. High estimates of GCV (>23%) coupled with high estimate of heritability (Hb%) (>94%) and high genetic advance as a percent of mean (GAM) (>46) were revealed in tuber weight per hill, number of primary branches per plant, number of tubers per hill, and number of plants per hill indicating the importance of such traits for selection in Ethiopian potato improvement programs. The significantly positive phenotypic, and genotypic correlation in tuber weight per hill and number of tubers per hill with each other and several other traits as well as their negative phenotypic correlation with some other traits indicates the direction of selection. Moreover, the significantly higher absolute magnitudes in genotypic correlation compared to their corresponding phenotypic correlation suggest the genetic base of those traits. Cytogenetic characterization revealed a very smaller sized metaphase chromosome with a count of 2n = c.56 and hepta- or octa-ploidy was speculated on the bases of basic chromosome number reports (x = 8 or 7) for the species of genus Plectranthus and other members of the Lamiaceae family. Such chromosome count and ploidy level report could serve as a baseline information in selection and crosshybridization of Ethiopian potato with other closely related species. In total, twenty new polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers have successfully been developed and used in genetic diversity analyses. The marker detected a total of 128 alleles (6.4 alleles per locus) over the entire loci and populations with effective number of alleles ranging from 1.06 - 3.17 (an average of 1.67). The marker showed an overall highest (94.17%) percent polymorphism, and extents of PIC in the range of slightly informative to highly informative suggesting the potential of those developed markers as a valuable genetic tool and resource to evaluate the extent of genetic diversity and population structure of not only Ethiopian potato but also various other species within the Lamiaceae family. The ranges and levels of mean observed heterozygosity (0.33 – 0.429), Shanon’s information index (0.523 – 0.663), and Nei’s gene diversity (0.307 – 0.384) across loci showed a medium degree of variation among the populations which is a direct reflection of sharing of most of the alleles among the populations that partly resulted from high overall gene flow (Nm=18.29). Comparatively, Wenbera (Wen), Wolaita Sodo (WSo), Hadiya and Kambata-Tembaro (HKT) and Southwest Shewa (SwSh) populations could be considered as Ethiopian potato diversification and in-situ conservation sites. xviii Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with at most 3% of the total variation in each of the groupings, such as among the populations, among geographic regions, and among regions of accessions. Likewise, cluster analysis in all the cases and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and/or the reproductive biology of the crop. In conclusion, this study has wider implications in bringing such a ‘super-neglected’ crop to the scientific agenda and thus, opens up the door to its improvement and conservation. However, it is important to exhaust all areas and regions in the country and more number of SSRs or other up-to-date molecular marker systems to come up with more accurate level of genetic diversity estimates.
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    Agro-morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian Potato [Plectranthus edulis (Vatke) Agnew] from Ethiopia
    (Addis Ababa University, 2018-06-03) Gadissa, Fekadu; Tesfaye, Kassahun (PhD)
    Agro-morphological and Molecular Genetic Diversity, and Cytogenetic Analysis of Ethiopian Potato [Plectranthus edulis (Vatke) Agnew] from Ethiopia Fekadu Gadissa Addis Ababa University, 2018 Ethiopian potato syno. Ethiopian dinich [Plectranthus edulis (Vatke) Agnew] (Lamiaceae) is one of the ancient annual edible tuber crops, originating in Ethiopia. The crop is commonly cultivated by smallholder farmers around homesteads in the highland and semi-highland areas, usually for household consumption and rarely for marketing. In spite of its’ wide economic importances, the crop is neglected by research and development community and currently it is at risk of total extinction. Hence, this study was conducted with the main aims of assessing agro-morphological and molecular (EST-SSRs) markers-based extents of genetic diversity analysis as well as chromosome number and ploidy level determination using 174 accessions from diverse agro-ecologies in Ethiopia. For agro-morphological diversity analysis, the experimental samples were tested at Ambo and Holeta agricultural research centres, using an alpha lattice design at the locations and three blocks/replication followed by appropriate management practices. Agronomic and morphological traits-based data were collected on twenty-eight (12 qualitative and 16 quantitative) traits at the right growth stage and analysed using SAS v9.0, MINITAB® v14.13 and FigTree v1.4.3. Cytogenetic characterization was also carried out using very young root tips generated from soil covered stem rings, followed by appropriate pre-treatment, fixation and maceration. For molecular genetic diversity analysis, genomic DNA was extracted form silcagel dried young leaves collected from 287 plants (1-3 plants per accessions) following CTAB protocol. EST-SSRs marker were designed from Plectranthus barbatus cDNA sequences deposited in the GenBank, followed by PCR amplification, capillary electrophoresis, peak identification, and scoring. The scored allele size data were analysed for polymorphism, diversity indices and genetic relationship and structure using windows compatible applications. The agro-morphological traits considered showed varied morphotypes in all of the leaf (four in leaf color, three in leaf arrangement, three in leaf shape), stem (three in stem color, two in each of stem spot and stem spot colors) and tuber (four in tuber skin color, three in each of tuber texture, tuber shape and tuber hair) characterstics. Similarly, the traits revealed a wide range of variability in mean performance (minimum range of 1.39 – 2.13 cm observed in tuber diameter and maximum range of 112.90 – 165.10 xvii days observed in days to 50% flower initiation) and variance components among and within the accessions. Similarly, the mean square of all the traits showed a highly significant (P< 0.001) variation among the tested accessions. Such wide variation suggests the presence of variability which can be exploited through selection. Several of the traits showed a slightly greater or nearly equal phenotypic coefficient of variation (PCV) to that of genotypic coefficients of variation (GCV), suggesting larger contribution of the genotypic effect for phenotypic expression of such characters and hence, phenotypic values-based selection for the traits may be effective. High estimates of GCV (>23%) coupled with high estimate of heritability (Hb%) (>94%) and high genetic advance as a percent of mean (GAM) (>46) were revealed in tuber weight per hill, number of primary branches per plant, number of tubers per hill, and number of plants per hill indicating the importance of such traits for selection in Ethiopian potato improvement programs. The significantly positive phenotypic, and genotypic correlation in tuber weight per hill and number of tubers per hill with each other and several other traits as well as their negative phenotypic correlation with some other traits indicates the direction of selection. Moreover, the significantly higher absolute magnitudes in genotypic correlation compared to their corresponding phenotypic correlation suggest the genetic base of those traits. Cytogenetic characterization revealed a very smaller sized metaphase chromosome with a count of 2n = c.56 and hepta- or octa-ploidy was speculated on the bases of basic chromosome number reports (x = 8 or 7) for the species of genus Plectranthus and other members of the Lamiaceae family. Such chromosome count and ploidy level report could serve as a baseline information in selection and crosshybridization of Ethiopian potato with other closely related species. In total, twenty new polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers have successfully been developed and used in genetic diversity analyses. The marker detected a total of 128 alleles (6.4 alleles per locus) over the entire loci and populations with effective number of alleles ranging from 1.06 - 3.17 (an average of 1.67). The marker showed an overall highest (94.17%) percent polymorphism, and extents of PIC in the range of slightly informative to highly informative suggesting the potential of those developed markers as a valuable genetic tool and resource to evaluate the extent of genetic diversity and population structure of not only Ethiopian potato but also various other species within the Lamiaceae family. The ranges and levels of mean observed heterozygosity (0.33 – 0.429), Shanon’s information index (0.523 – 0.663), and Nei’s gene diversity (0.307 – 0.384) across loci showed a medium degree of variation among the populations which is a direct reflection of sharing of most of the alleles among the populations that partly resulted from high overall gene flow (Nm=18.29). Comparatively, Wenbera (Wen), Wolaita Sodo (WSo), Hadiya and Kambata-Tembaro (HKT) and Southwest Shewa (SwSh) populations could be considered as Ethiopian potato diversification and in-situ conservation sites. xviii Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with at most 3% of the total variation in each of the groupings, such as among the populations, among geographic regions, and among regions of accessions. Likewise, cluster analysis in all the cases and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and/or the reproductive biology of the crop. In conclusion, this study has wider implications in bringing such a ‘super-neglected’ crop to the scientific agenda and thus, opens up the door to its improvement and conservation. However, it is important to exhaust all areas and regions in the country and more number of SSRs or other up-to-date molecular marker systems to come up with more accurate level of genetic diversity estimates.
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    Analyses of Phenotypic and Molecular Diversity, Genotype by Environment Interaction and Food-Feed Traits in Tef [Eragrostistef (Zucc.) Trotter]
    (Addis Ababa University, 2018-12-05) Jifar, Habte; Tesfaye, Kassahun (PhD); Dagne, Kifle (PhD)
    Tef [Eragrostis tef (Zucc.) Trotter] is an indigenous major cereal crop widely grown and utilized in Ethiopia. It is an excellent source of healthy and nutritious human food and livestock feed. However, its productivity is significantly lower than that of major cereals grown in Ethiopia. Although diverse constraints contribute for its inferior grain yield, the huge diversity present in tef germplasm has not been exploited. This study was, therefore, conducted to assess the phenotypic and molecular diversity, genotype by environment interactions and variation of food-feed traits in tef genotypes from various sources. The field experiments were conducted at Holetta, Debre Zeit, Alem Tena, Adet, Axum and Shambu using randomized complete block design with three replications whereas, the laboratory analyses were conducted at the University of Bern in Switzerland, Sci-Co in South Africa, International Livestock Research Institute (ILRI) in Ethiopia and International Crops Research Institute for Semi-Arid Tropics (ICRISAT) in India. Phenotypic diversity was assessed based on 12 quantitative and five qualitative traits of 188 tef genotypes while, the genotyping study was conducted using 189 genotypes with 16 SSR markers. Results from phenotypic study revealed the existence of huge variability in plant height (60.7 to 107.1 cm), panicle length (19.5 to 39.5 cm), number of fertile tillers per plant (2.1 to 5.5), number of spikelets per panicle (156.7 to 441.7), thousand kernel weight (20.7 to 33.0 mg), grain yield (3.7 to 7.3 t/ha) and lodging index (44.7 to 79.3%). Molecular diversity study generated a total of 260 alleles for the total studied loci. Cluster and STRUCTURE analyses showed four gene pools, but with high level of admixtures due to geographic proximity and/or trans human seed exchange. Analysis of molecular variance showed significant variation of 56.6% within individuals, 40.8% among individuals within population and 2.6% among populations. Based on SSR study, furthermore, a core collection composed of 64 genotypes (33.9%) is suffice to capture the entire alleles of studied genotypes. Significant variations were also detected for all traits due to genotypes, environments and their interaction. Based on AMMI, GGE and Eberhart Russell’s model, G6 (Melko) was identified as the highest yielding and moderately stable variety while, E5 (Debre Zeit-1) was the highest yielding and ideal environment. GGE biplot grouped the test environments into four mega environments and the studied genotypes into seven groups. Analysis of food-feed traits revealed significant (P<0.01) effect of genotypes, year, locations and their interactions. Based on this, the highest mean crude protein (CP), in vitro organic matter digestibility (IVOMD), metabolic energy (ME), total biomass (TBM) and straw yield (STY), and the lowest mean for neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL) were obtained from genotypes evaluated at Debre Zeit. Cluster analysis and PCA-biplot grouped the genotypes into four. These are, (i) those with improved feed quality traits such as Kena, Genet and Ambo Toke;(ii)) those with high food-feed traits such as Dukem, Gimbichu and Dega Tef; (iii) those with dual purpose such as Melko, Koye and Key Tena; and (iv) those with low food-feed traits such as Simada, Etsub and Mechare. The overall results of the present study enabled to identify tef genotypes with sufficient morpho-agronomic and molecular variations, better yield and stability, and food-feed traits having implications for collection, conservation and proper utilization of germplasm which are the basis of tef improvement.
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    Analyses of Phenotypic and Molecular Diversity, Genotype by Environment Interaction and Food-Feed Traits in Tef [Eragrostistef (Zucc.) Trotter]
    (Addis Ababa University, 2018-12-02) Jifar, Habte; Dagne, Kifle (PhD); Tesfaye, Kassahun (PhD)
    Tef [Eragrostis tef (Zucc.) Trotter] is an indigenous major cereal crop widely grown and utilized in Ethiopia. It is an excellent source of healthy and nutritious human food and livestock feed. However, its productivity is significantly lower than that of major cereals grown in Ethiopia. Although diverse constraints contribute for its inferior grain yield, the huge diversity present in tef germplasm has not been exploited. This study was, therefore, conducted to assess the phenotypic and molecular diversity, genotype by environment interactions and variation of food-feed traits in tef genotypes from various sources. The field experiments were conducted at Holetta, Debre Zeit, Alem Tena, Adet, Axum and Shambu using randomized complete block design with three replications whereas, the laboratory analyses were conducted at the University of Bern in Switzerland, Sci-Co in South Africa, International Livestock Research Institute (ILRI) in Ethiopia and International Crops Research Institute for Semi-Arid Tropics (ICRISAT) in India. Phenotypic diversity was assessed based on 12 quantitative and five qualitative traits of 188 tef genotypes while, the genotyping study was conducted using 189 genotypes with 16 SSR markers. Results from phenotypic study revealed the existence of huge variability in plant height (60.7 to 107.1 cm), panicle length (19.5 to 39.5 cm), number of fertile tillers per plant (2.1 to 5.5), number of spikelets per panicle (156.7 to 441.7), thousand kernel weight (20.7 to 33.0 mg), grain yield (3.7 to 7.3 t/ha) and lodging index (44.7 to 79.3%). Molecular diversity study generated a total of 260 alleles for the total studied loci. Cluster and STRUCTURE analyses showed four gene pools, but with high level of admixtures due xix to geographic proximity and/or trans human seed exchange. Analysis of molecular variance showed significant variation of 56.6% within individuals, 40.8% among individuals within population and 2.6% among populations. Based on SSR study, furthermore, a core collection composed of 64 genotypes (33.9%) is suffice to capture the entire alleles of studied genotypes. Significant variations were also detected for all traits due to genotypes, environments and their interaction. Based on AMMI, GGE and Eberhart Russell’s model, G6 (Melko) was identified as the highest yielding and moderately stable variety while, E5 (Debre Zeit-1) was the highest yielding and ideal environment. GGE biplot grouped the test environments into four mega environments and the studied genotypes into seven groups. Analysis of food-feed traits revealed significant (P<0.01) effect of genotypes, year, locations and their interactions. Based on this, the highest mean crude protein (CP), in vitro organic matter digestibility (IVOMD), metabolic energy (ME), total biomass (TBM) and straw yield (STY), and the lowest mean for neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL) were obtained from genotypes evaluated at Debre Zeit. Cluster analysis and PCA-biplot grouped the genotypes into four. These are, (i) those with improved feed quality traits such as Kena, Genet and Ambo Toke;(ii)) those with high food-feed traits such as Dukem, Gimbichu and Dega Tef; (iii) those with dual purpose such as Melko, Koye and Key Tena; and (iv) those with low food-feed traits such as Simada, Etsub and Mechare. The overall results of the present study enabled to identify tef genotypes with sufficient morpho-agronomic and molecular variations, better yield and stability, and food-feed traits having implications for collection, conservation and proper utilization of germplasm which are the basis of tef improvement.
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    Assessment of Genetic Diversity, Genotype by Environment Interaction, Blast (Magnaporthe Oryzae) Disease Resistance, and Marker Development for Finger Millet Germplasm from Ethiopia And Introduced
    (Addis Ababa Universty, 2015-03) Lule, Dagnachew; Tesfaye, Kassahun (PhD)
    Finger millet (Eleusine coracana subsp. coracana) is extensively cultivated in the tropical and sub-tropical regions of Africa and India. It is the major staple food for millions of resource poor people and plays an important role in the dietary habits and economy of subsistence farmers inhabiting arid and semi-arid regions of Africa and India. The crop is adapted to adverse agro-ecological conditions with minimal inputs, tolerant to moisture stress, produced on marginal land where other crops cannot perform and tolerant to acidic soils. Breeding efforts in finger millet has been limited and farmers are growing unimproved and low yielding cultivars. Improvement in any crop usually involves exploiting the genetic variability in specific traits of interest. Moreover, the use of multiple data sets, such as morphological, biochemical and molecular in combination with appropriate statistical methods are essential to identify inter and intra-species variation to develop improved cultivars. One hundred and five finger millet accessions, collected from the major finger millet producing regional states of Ethiopia (Amhara, Benishangul Gumuz, Oromia, Tigray and Southern Nations Nationalities and Peoples Region (SNNP)), supplemented by 39 introduced accessions from Kenya, Zambia, Zimbabwe and Eritrea and six improved varieties, were evaluated in the field at Gute and Arsi Negele during 2011 to assess the genetic diversity and eco-geographical patterning. The analysis of variance indicated that the mean square due to environment and genotype were highly significant (P≤0.01) for all quantitative traits except ear weight for the latter case. Erect type growth habit, open ear type, light green ear (glumes) color, enclosed grains by glumes, lower spikelet density and purple black seed color were the predominant phenotypic classes for the traits recorded in the present study. Cluster analysis for both qualitative and quantitative phenotypic traits indicated that finger millet accessions from neighboring regions of Ethiopia, neighboring African countries and proximity in altitude classes shared strong similarity. Principal component analysis at population level, geographical locations and agro-ecologies of origin indicated that grain yield per plant, thousand grain weight, days to heading, days to maturity, lodging index and biomass weight per plant were the most important traits contributing to the overall variability, implying that breeding efforts on those traits can meet the objectives in improving the trait. The higher heritability coupled with higher genetic advance noted for ear weight (71.14%), lodging index (53.49), finger length (41.94%), thousand grain weights (28.88) and grain yield per plant (26.34) indicated the ease of phenotypic selection for the improvement of those traits. About 68.4% of the total traits association showed positive correlation. The 150 finger millet test accessions were also evaluated using a set of 20 SSR markers. Results showed variable genetic polymorphism with an average polymorphic information content of 0.57. A total of 188 alleles were recorded with an average of 9.89 alleles per locus. Analysis of molecular variance revealed 69.52% variation within populations and 30.48% among populations. Relatively higher within accession polymorphism were recorded for accessions from Oromia (21.10%), Amhara (16.93%) and Tigray (13.43%) regional states of Ethiopia. Weighted neighbor joining-based clustering grouped the 138 accessions for which the SSR markers worked well, into three major clusters apart from the main node, and accessions collected from the same region or the same altitude classes did not often group entirely together within a given major cluster or sub cluster. Likewise, analysis of population structure distinguished the 138 finger millet accessions in to three subpopulation ( = 3) with the highest ΔK of around 300. The first, second and the third group comprised of accessions from the different geographical locations and the improved varieties with membership proportion 22.9%, 38.5% and 38.6%, respectively. Magnaporthe oryzea, a fungal pathogen that attacks more than 50 gramineous species, is well known to cause immense yield loss, and is particularly severe on rice and finger millet. A total of 225 finger millet materials were evaluated for blast resistance/tolerance on a sick plot supplemented with artificial inoculation at Bako Agricultural Research Center in 2011. The analyses of variance revealed the mean square due to genotypes were highly significant (P≤0.01) for leaf, sheath, neck and head blast. Based on the head blast disease severity index, the 225 test materials were classified into five groups: only one accession (Acc. BKFM0031) was resistant (head blast severity score of < 3 at maturity with both head blast severity index and relative area under disease progress curve (RAUDPC) values of less than 21%), 10 accessions were moderately resistant with blast severity index of 21-40%, the remaining 214 was in a range of moderately susceptible to highly susceptible. About 66% of the most susceptible accessions gave grain yield below the average (11.29 g/plant), indicating that grain yield reduction in most accessions were due to blast infection. Finger millet accessions collected from the same region showed different levels of disease reaction, implying that diversified materials are produced within a country or region. Both correlation and regression analysis revealed highly significant (P≤0.01) negative association of head blast to grain yield. An average of 63.2% yield loss was recorded due to head blast disease during the severe infection periods of 2011 as estimated using different yield loss assessment models. Identification of adaptable, stable and high yielding genotypes under varying environmental conditions are the first steps in plant breeding prior to release of a cultivar and this has direct bearing on the adoption of the variety, its productivity and total production of the crop. To this end, a total of 30 advanced finger millet genotypes were evaluated against two standard checks (Gute and Taddesse) across four locations (Arsi Negele, Assosa, Bako and Gute) in the 2012 and 2013. Additive Main effect and Multiplicative Interaction (AMMI), Genotype and Genotype by Environment Interaction (GGI) biplot analysis and, Eberhart and Russell model revealed that Acc. 203544 was stable and high yielding (3.16 ton ha-1) with a yield advantage of 13.7% over the best standard check, Gute (2.78 ton ha-1), and thus recommended for possible release with wider environmental adaptability. Moreover, Acc. 242111 (3.08 ton ha-1) and BKFM0051 (3.07 ton ha-1) were high yielding, but showed narrow stability and thus recommended for possible release for specific environments. Single strand conformation polymorphism (SSCP) analysis detected that only one marker was polymorphic among the thirteen primers designed from Rice Orthologous Genes with finger millet for blast resistant. Sequence analysis of this polymorphic marker (Pi9F2) for eight representative finger millet accessions and 15 clone samples revealed the average contigs measurement of 891bp and nucleotide distribution of 30.9% Thymine (T), 28.1% Adenine (A), 24.2% Cytosine (C) and 16.8% Guanine (G). Multiple sequence alignment of those sequence revealed two possible SNPs at consensus positions 460 (G/A) and 780 (G/C) in a window of 66 bp, where the consensus residue is G at both positions. Overall, this study showed the presence of divers finger millet accessions that deserve sustainable conservation and use in breeding program and generated information on the extent of genetic variation among finger millet accessions and eco-geographical regions using multiple markers. Besides, the study has of the preliminary contribution in the application of molecular tools for diversity analysis and thus variety development and identified accessions with variable level of blast tolerance for further utilization in breeding and other genomic research activities. Keywords: Finger millet (Eleusine coracana subsp. coracana), Additive main effect and multiplicative interaction (AMMI), Area Under Disease Development Curve (AUDPC), Heritability, Magnaporthe oryzae, polymorphism, Simple Sequence Repeat (SSR), Single strand confirmation polymorphism (SSCP).
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    Characterization of Ethiopian Durum Wheat Landraces and Cultivars for Processing Quality Using Phenotypic Traits and Simple Sequence Repeat (SSR) Markers
    (Addis Ababa University, 2021-09-02) Dagnaw, Temesgen; Tesfaye, Kassahun (PhD); Haileselassie, Teklehaimanot (PhD); Geleta, Mulatu (PhD)
    Durum wheat (Triticum turgidum L. ssp. durum Desf.) is getting attention in terms of production and area coverage at the global level. Its unique characteristics to produce pasta and related end-products increased the preference for durum wheat by millers and processors. Ethiopia is considered as a center of diversity for durum wheat. However, in Ethiopia, durum wheat is facing serious genetic erosion due to the expansion of teff and bread wheat, and the cultivation of exotic durum wheat materials. The genetic resource of the Ethiopian durum wheat genotypes has been limitedly explored for its processing quality attributes at the level of both phenotypic and molecular diversity. Therefore, the present study was aimed to assess the genetic diversity and evaluate the processing quality attributes of Ethiopian durum wheat genotypes using phenotypic traits and SSR markers. The field experiment was conducted at two locations (Sinana in Bale zone and Chefe Donsa in East Shewa zone) to assess the phenotypic diversity. The phenotypic characterization of genotypes showed a wide range of variability for most quantitative and qualitative traits. The combined analysis of variance (ANOVA) showed highly significant (P<0.01) variations among genotypes for the majority of the traits studied. Gluten content (GL) and grain yield (GY) showed high and intermediate heritability, respectively, combined with moderate genetic advance, and grain protein content (GPC) showed intermediate heritability combined with low genetic advance. Both, GPC and GL showed a significant and negative correlation with GY. Cluster analysis based on quantitative traits grouped the genotypes into 5 major clusters. The first four principal components (PCs) explained 64% of the total variation. Based on qualitative traits, high genetic variation was observed among genotypes. Correspondence analysis discriminated cultivars from other populations of landraces. Finally, 104 best-qualified genotypes for processing quality traits were selected and assessed using quality traits associated 14 SSR markers, which had high mean polymorphic information content (PIC) of 0.56 and gene diversity (0.61). High levels of genetic diversity was obtained among all populations (I = 0.86; He = 0.46). Analysis of molecular variance (AMOVA) revealed high genetic variation within populations (88.35%) and among populations (11.65%). The Neighbor-joining (NJ) clustering and principal coordinate analysis (PCoA) grouped the genotypes into three major clusters. In addition, Bayesian model-based population structure analysis revealed two major genetic groups. Overall, this study revealed high genetic diversity among Ethiopian durum wheat landraces and cultivars, and these genotypes can be used to identify the best genotype/s for processing quality attributes and subsequent use in the Ethiopian durum wheat improvement programs.
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    Estimation of Breeding Parameters within and between Malt Barley (Hordeum Vulgare L) Crosses using Phenotypic Traits and Kasp SNP Markers
    (Addis Ababa University, 2021-12-31) Tadesse, Endeshaw; Tesfaye, Kassahun (PhD)
    The genetic variation in a breeding program is created by crossing genetically divergent parents. The resulting genetic variation between and within crosses is the determining factor for the offspring’s performance, which is defined as the level of compliance of the offspring with preset breeding goals. Estimation of breeding parameters plays a key role in crop improvement. The aim of this study was to (i) estimate and compare mid-parent value and the cross mean (ii) estimate and compare the variance between means of crosses (σ²c) and segregation variance of recombinant inbred line within crosses (σ²g) (iii) estimate correlation among the traits measured and their heritability (iv) estimate and compare Rogers Distances (RD) of parental lines and their correlation to the segregation variance within crosses, and (v) estimate usefulness of crosses. 900, F4:5 recombinant inbred lines randomly derived from 30 crosses were evaluated at two locations in modified split plot p-rep design whereas the parental where genotyped using SNP-KASP markers. The variance component analysis revealed significant (P <0.05) genetic variation among parents, crosses and RIL for almost all traits. Based on generation mean analysis, the means of recombinant inbred line did not deviate significantly from the means of parental lines. The range of σ²g for the individual crosses was very high for days to heading, days to maturity, plant height, thousand kernel weight and grain protein concentration and for these traits the respective standard deviation were high. Heritability for parents ranged from 49.50 % (malt extract) - 93.60 % (plant height), heritability for crosses ranged from 29.52 % (grain protein concentration) - 87.0% (days to maturity), whereas heritability for RIL was lowest with 27.40% (beta-glucan) - 73.60% for thousand kernel weight. Significant (P<0.01) genotypic correlations with high impact for practical breeding were found between malting traits. Significant (P<0.01) regression of cross mean on mid-parent value were obtained for all traits demonstrating that cross means can accurately be predicted from mid parent values and selection among crosses at an early stage of line development is highly effective. Further, based on the usefulness criteria, 16 outperforming crosses were identified that surpass Planet as the actual leading malt variety. Diversity analysis revealed an average RD between lines was 0.46 with a range of 0.32- 0.64 and homogeneity within the 17 parental lines varied from 71-100%. The dendrogram grouped the lines into three clusters. Importantly, the high malting European lines were grouped together with some of the ICARDA and Ethiopian lines Correlations of RD to σ²g ranged from -0.19 to 0.34 and were not significantly deviating from zero for all traits except DH, hence, RD proved to be not predictive for σ²g. In this study the two variances, σ²c and σ²g, proved to be significantly deviating from zero for almost all traits; hence breeder can exploit both of them for selection. Generally, differences between generation means (Parental lines vs. RIL) were small across all crosses. But when grouping into crosses with and without Planet as a parental line, deviation between parent and RIL were larger possibly due to epistastic effects. Hence breeder should estimate breeding values rather than genetic values of parental lines. The use of mid-parent value and usefulness for cross selection were found to be promising. The national barley breeding program should exploit this result by starting with a large number of initial crosses and reducing them to the most promising crosses. Some heterogeneity was observed within the lines. When originating from technical mixture this should be considered as a wake-up call for the breeder to closely follow maintenance breeding. RD based on KASP markers was not predictive for σ²g; hence further research will be required by improving accuracy of σ²g estimate and linkage disequilibrium between markers and quantitative trait loci (QTL). Over all, the large diversity revealed among lines indicates the potential that the genotypes have to improve the productivity and quality of the crop and the uses of molecular markers can benefit the breeding program in order to have an effective breeding program by selecting diverse parental genotypes with complementary gene action.
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    Genetic Analysis of Agro-Morphological Traits and Molecular Diversity Study (ISSR and Snps) of Quality Protein Maize (Zea Mays L.) Inbred Lines in Drought Stressed Areas of Ethiopia
    (Addis Ababa University, 2017-11-05) Tilahun, Lealem; Tesfaye, Kassahun (PhD)
    Genetic studies along with characterization of elite breeding lines provide understanding of the genetic diversity and relationship among the inbred lines. They also offer information on the type of gene action controlling the inheritance of desirable quantitative traits. The information enables breeders to define a systematic breeding strategy and to select suitable parents and hybrids for further breeding activities and commercialization. Thus, the purposes of this study were to estimate combining abilities and heterosis and to determine genetic variation, correlation, heritability and expected genetic advance of elite quality protein maize (QPM) inbred lines for grain yield and other agronomic traits as well as to investigate their genetic diversity and relationship using SNP and ISSR markers. A total of 116 QPM test cross hybrids developed by crossing 58 QPM inbred lines with two QPM testers was evaluated for 17 morphological traits along with two conventional maize (CM) and two QPM standard checks in drought stressed areas of eastern Ethiopia – Melkassa Agricultural Research Center (MARC), Edo Gojola and Mieso. The inbred lines were also evaluated separately adjacent to the hybrid trial at each site and the inbred lines were genotyped by SNP and ISSR markers. Significant differences were observed among the inbred lines and hybrids for grain yield and most considered agronomic traits indicating that genetic variations existed among the genotypes to allow good progress from selection for improvements of those traits. Across sites, the highest mean grain yield was observed for the hybrid L52/CML159 (5.38 t ha-1) followed by L18/CML159 (5.07 t ha-1) and L35/CML159 (5.02 t ha-1) in the hybrid trial while inbred line L52 showed the highest mean GY which was 3.15 t ha-1 followed by L38 (2.94 t ha-1), L47 (2.88 t ha-1), L17 (2.43 t ha-1), L48 (2.33 t ha-1) and L40 (2.06 t ha-1) in the inbred line trial. The combining ability analysis showed that general combining ability (GCA) of lines was significant while specific combining ability (SCA) was non-significant for grain yield, anthesis date, plant height, ear height, plant aspect, ear length and thousand kernel weight indicating that the variability observed among the hybrids was attribuable to additive effects for most traits. The contribution of line iv GCA was found to be higher than the contribution of tester GCA and line  tester SCA for all considered traits except for thousand kernel weight where the contribution of tester GCA was higher. Inbred lines L35 (0.83 t ha-1), L45 (0.68 t ha-1), L53 (0.63 t ha-1), L4 (0.57 t ha-1), L21 (0.56 t ha-1), L52 (0.54 t ha-1) and L32 (0.49 t ha-1) had significant positive GCA effects for grain yield. Hybrid combination L52/CML159 had the best SCA effects for grain yield and other most important traits and the maximum standard heterosis over MH140 (19.7%) and MH130 (21.4%). Grain yield had positive and highly significant genotypic and phenotypic correlations with plant height, ear length and thousand kernel weight while negative and highly significant with days to 50% anthesis, anthesis-silking interval, ear position, shoot lodging and ear aspect. The present study showed that root lodging was not important characteristics to be considered while shoot lodging played an important role in determining grain yield. It also showed that ear height is more important than plant height to develop high yielding hybrids and that it is possible to select high yielding varieties which are early but tall with low ear placement. The ISSR markers were found to be as effective as SNP markers in clustering inbred lines into seven sub-groups which are in agreement with pedigree information. All the three multivariate analyses viz. cluster analysis, model-based population structure analysis and principal component analysis using SNPs consistently identified the same seven distinct populations and revealed similar membership of inbred lines in each population. In general, the results from this diversity study based on SNP and ISSR markers will be useful to breeders in selecting best parental combinations for starting new breeding populations, mapping population and marker assisted breeding.
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    Genetic and Virulence Variability of Zymoseptoria Tritici Populations and Genome Wide Association Studies for Septoria Tritici Bloch Resistance and Yield Potential in Wheat (Triticum Aestivum L.) in Ethiopia
    (Addis Ababa University, 2021-08-25) Mekonnen, Tilahun; Tesfaye, Kassahun (PhD); Hailesilassie, Teklehaimanot (PhD); Abeyo, Bekele (PhD)
    Septoria tritici blotch (STB) caused by the fungus Zymoseptoria titici is the major bottleneck to wheat production in Ethiopia and worldwide. The present study was targated to investigate genetic and virulence variability of Zymoseptoria tritici populations; and Genome-Wide association studies for STB resistance and yield potential in bread wheat in Ethiopia. Genetic structure analysis of 182 Z. tritici isolates representing eight populations from major wheat growing areas of Ethiopia using 14 polymorphic microsatellite markers confirmed the presence of high genetic diversity (h = 0.45) where 92% of the total genetic variation resides within populations. Cluster (UPGMA), PCoA and STRUCTURE analyses did not group the Z. tritici populations into sharply genetically distinct clusters according to their geographical areas of sampling. All individual samples shared alleles from two subgroups (K=2). Pathogenicity assay conducted with eight Z. tritici isolates on a set of 45 bread wheat genotypes showed highly significant differences for isolate-by-genotype interaction on both percentage of necrosis leaf area (NLA) and pycnidia coverage (PC). The isolates showed significantly higher differences in virulence patterns. Isolate I1 sourced from Bale was found to be the most virulent (93%) and aggressive (NLA = 58%) isolate. Among tested Stb genes, Stb16 conferred broad-spectrum resistance to 75% of the isolates. Three genotypes (MURGA, Km7 and Hidase) conferred the greatest level of seedling resistance to the tested isolates. Molecular screening for major Stb genes in 180 genotypes using 16 tightly linked markers identified a number of Stb genes ranging from 6.67% for Stb12 to 96.1% for Stb13 gene. Field evaluation conducted on 180 wheat genotypes across six environments revealed a very highly significant difference among the wheat genotypes for most traits. Top 5% selected genotypes showed 10.8 - 21.99% and 52.25- 74.25% superior grain yield performance and STB resistance to standard check (King-bird), respectively. Moreover, population structure, linkage disequilibrium (LD), and GWAS for adult-plant STB resistance, yield, yield- related and phenological traits were conducted for 178 wheat genotypes using 7,776 SNPs resulted from Illumina HiSeq2500 Genotype-by-sequencing. STRUCTURE and PCA confirmed two sub-populations with greater degree of genetic admixture. In all chromosomes, LD between pairs of SNPs declined at r2 = 0.2 within physical distance of 2.26 -105.62 Mbp, with an overall mean of 31.44 Mbp.The association analysis identified 53 loci significantly associated with STB resistance pointing to 33 putative QTLs. Most of these shared similar chromosome locations with already published Septoria resistance genes and QTLs, and were distributed across chromosomes 1B, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 5A, 5B, 6A, 7A, 7B and 7D. However, five of the putative QTLs identified on chromosomes 1A, 5D and 6B appeared to be novel. Predicting the possible functions of the detected loci from the IWGSC RefSeq Annotation v2.1 revealed the existence of disease resistance-associated genes in the identified QTL regions which are involved in plant defense responses. Seven of the QTLs for STB resistance also co-localized with MTAs for agronomic traits. In conclusion, the study provides new insights into the genetic structure and virulence variability of Z. tritici in Ethiopia to design effective and durable management strategies. The identified Stb genes, QTLs and resistance source materials could be used in wheat genome-assisted resistance breeding against STB. Therefore, the information generated in the present study is useful to improve STB resistance and grain yield performance in wheat which ultimately leads to increased and stable wheat production to ensure food security in Ethiopia and the region at large.
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    Genetic Characterization and Estimation of Genotype by Environment Interaction of Ethiopian Sesame (Sesamum Indicum L.) Germplasm
    (Addis Ababa University, 2021-07-02) Tesfaye, Tewodros; Tesfaye, Kassahun (PhD)
    Sesame is one of the major oil crops that has great economic importance for the country. In Ethiopia, sesame is among the foremost important oil crops both in terms of area coverage and total national annual production. However the crop suffers from low productivity due to biotic and abiotic stresses. Therefore, the present study conducted in different sets to generate information that can be used to design the future breeding program of sesame in the country. The first set of experiments was to study the morphological and molecular genetic diversity of the sesame germplasm collected from Ethiopia and other countries (Asian and other African countries). The same genotypes planted at three locations for phenotyping and genotyping using the two high throughput diversity array technology (DArT) markers (silicoDArT and SNP). Further to understand the impact of different putative genes Genome-wide association study of yield-related traits using 2997 SNPs in two environments was performed. The second set of experiments was conducted in 19 environments to assess the performance and stability of sesame varieties, and to characterize sesame growing environments in Ethiopia. Based on morphological characterization, genotypes showed wide variability for most morphological traits, except for plant growth type, leaf glands, anther filament color, and anther connective tip gland. High heritability combined with high genetic advance was recorded for plant height, primary branch, days to flower initiation, days to 50% flowering, pod bearing zone, seed yield per plant, and bacterial blight reaction indicating the potential of improving the population through a direct selection for these traits. Grain yield showed a significant and positive genotypic correlation with plant height, the number of capsules per plant, and pod bearing zone, the magnitudes of the positive genetic correlation suggest that the selection by those characters produces a significant increase in grain yield. Genetic divergence using Mahalanobis D2 statistics was computed, and the genotype lines were grouped into six different clusters. Clustering was not associated with the geographical distribution; instead, genotypes were grouped mainly based on morphological differences. The maximum inter-cluster distance was observed between clusters IV and VI (D2 =342.56, followed by clusters I, and VI (D2 =217.9783). Maximum genetic recombination and variation in the subsequent generation are expected from crosses that involve parents from the clusters characterized by maximum distances. The genetic diversity analysis showed that the average nucleotide diversity of the panel was 0.14. Considering the genotypes based on their geographical origin, Africa collections (0.21) as a whole without Ethiopian collection was more diverse than Asia and when further portioned Africa, North Africa (0.23) collection was more diverse than others, but at the continent level, Asia (0.17) was more diverse than Africa (0.14). The genetic distance among the sesame populations ranged from 0.015 to 0.394, with an average of 0.165. The structure analysis divided the panel into four hypothetical ancestral populations and 21 genotypes were clustered as an admixture. Under Genome-wide association study (GWAS) a total of 21 significant SNPs with 7 yield-related traits in two environments were identified and, these explaining the phenotypic variation ranged from 7.02 (DF) to 16.11% (CAPL), with an average of 9.76%, suggesting a moderate contribution to the traits. All significant loci found in LG 2, 6, and 11 associated with capsule length except one associated with the physiological period. The significant loci found in LG 3, 7, and 8 associated with a physiological period (Days to flower initiation, Days to 50% flowering, and Days to physiological maturity) except one associated with capsule length. Dissecting genetic control of flowering time and maturity is importance to foster sesame breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time and maturity strongly affect yield and plant adaptation ability. Since several favorable alleles detected in this study have not yet been intensively selected, our GWAS results will assist in incorporating further useful alleles into the elite sesame germplasm for a seed yield increase in the future. Based on the genotype x environment interaction study the test locations were divided into six groups. Humera, Banat, and Tach Armacho were highly discriminating and representative in the first, the second, and the third group respectively, and were identified as a core test site in that group. While Alemaya, Worer, and Mender67 were identified as the only test site in groups four, five, and six. The core testing sites identified would be used to facilitate the identification of superior sesame varieties and to reduce testing costs in the country. Environment Tach Armacho in 2017/18 and 2018/19 were close to the ideal environment. The GGE biplot analysis identified genotype G2 (setit-1) as the “ideal” genotype and among the highest mean seed yield. Setit-1 considered the most stable across variable environments.
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    Genetic Diversity Analysis of Ethiopian Orobanche Crenata Population Using Microsatellite Markers (SSR)
    (Addis Ababa University, 2015-06) Belay, Gashaw; Tesfaye, Kassahun (PhD); Hamwieh, Aladdin (PhD); Kemal, Seid (PhD)
    Orobanche crenata (Broomrape) is a parasitic weed which imposes considerable yield losses on food legume crops particularly on faba bean. In Ethiopia more than 0.5 million ha of faba bean production have been at risk of Orobanche infestation. Attempts have been made on the development of O. crenata control strategies; however there is no single approach to control such parasitic weed. Information on genetic diversity and virulence genetics of O. crenata are limited in our country. Moreover, understanding such information has valuable input on the control and diagnosis of parasitic weeds. However, no attempts were made to study population genetics of parasitic weed on faba bean in Ethiopia. Hence, this study was designed with the aim to assess the genetic diversity of O. crenata populations from Ethiopia; using transferable SSR markers. A total of 96 samples were collected from South Tigray (30), South Gondar (30), South Wollo (31), and North Wollo (5). Genomic DNA was isolated from Silca gel dried O. crenata samples using modified CTAB method. Out of 79 O. cumana SSR markers 30 SSR markers were selected for cross amplification on O. crenata. Reaction amplification was performed by using touchdown PCR program and amplicon were processed to QIAxcel gel electrophoresis. From 30 tested SSR loci; 11 SSR markers were identified and determined as functional and transferable markers. Different biological software was used for molecular data analysis. An average number of allele, gene diversity, heterozygosity, and PIC values for the SSR loci were 9.6, 0.82, 0.38, and 0.80, respectively. An average of 59 percent of polymorphic loci per population was recorded; the mean observed and expected heterozygosity, allelic range, gene number and diversity, and Garza-Williamson index values for the all population was 0.37, 0.78, 21.68, 48, 0.77 and 0.45, respectively. South Wollo population was exhibited high gene diversity as compared to others. The Nie’s genetic distance revealed that population of South Wollo and South Gondar has 88% similarity whereas individual from North Wollo showed divergent to others. The Analysis of Molecular Variation (AMOVA) has also shown that 97% and 3 % of the total variation was due to the within and among populations variation, respectively. Cluster analysis demonstrated that the 96 samples clearly divided into two major group and six sub-groups. Principal coordinate analysis (PCO) also separated the entire sample into three major groups and fully supported by STRUCTURE, that assigned all samples in to three sub-populations. However, there is no clear distinction were made about the distribution of genotypes in different groups based on their geographical origins. Overall, high level of genetic diversity achieved from this study could be used as pioneer information for O. creanta control strategies and diagnosis mechanism in Ethiopia. Furthermore the findings could be applied for the improvement of faba bean breeding. Key words: Orobanche crenata; Broomrape; SSR markers; Genetic diversity
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    Genetic Diversity and Population Structure of Common Bean (Phaseolus Vulgaris L.) Germplasm from Ethiopia
    (Addis Ababa University, 2015-07) Fisseha, Zelalem; Tesfaye, Kassahun (PhD); Gepts, Paul (Professor))
    The common bean is one of the most important diet components and cash crops in Ethiopia and Africa. However, despite having such major benefits, the production and productivity of the crop has been highly constrained by: inadequacy of improved varieties; complex myriads of biotic and abiotic constraints, and narrow genetic base of germplasm used in breeding. The multiple centers of domestication accompanied by heterogenous farming practices adopted by farmers, ever since its introduction to Ethiopia, and recent variety development projects have resulted in a range of morphologically diverse landraces via the preservation and exploitation of useful alleles. To this end, assessing the morphological and molecular diversity; and population structure of common bean landrace accessions in Ethiopia is sine qua non vis-à-vis establishing an efficient breeding and conservation scheme, nationally. Genetic diversity and population structure of 125 common bean accessions were studied using agro-morphological and SSR DNA markers. The morphological diversity assessment was conducted in the main rainy season of 2013 at Melkassa Agricultural Research Center, main research station, Ethiopia. The molecular diversity study was conducted from August 2012 to February 2013 at the lab of the BecA-ILRI hub, Nairobi, Kenya, using 24 fluorescent SSR markers. Higher and significant genetic variability among accessions was evidenced, with respect to 8 quantitative and 11 qualitative agro-morphological traits. On the other hand, results of the association analyses revealed that 100-seed weight and seed diameter had positively-significant correlation and higher positive direct effects on the seed yield of the common bean accessions. Hence, these two traits, 100-seed weight and seed diameter, were recommended, as important traits to be used in the indirect selection of high- yielding common bean cultivars, in conjunction with seed yield. On the other hand, results of the morphological (phenotypic) diversity analyses revealed that both the Tocher and Neighbor-joining clustering methods identified similar five clusters with almost identical members in each. Of these, three and two clusters were predominated by Andean and Mesoamerican accessions, respectively. However, a comparable proportion of accessions had intermediate features between the two gene pools, suggesting the significant presence of inter-gene pool introgressions. The Mahalanobis (D2) analysis of the five clusters indicated mostly significant differences between all the combinations of cluster pairs. This indicated there may be a great opportunity to obtain transgressive segregants and maximum heterosis in future common bean breeding programs. With regards to the molecular genetic diversity using SSR markers among the common bean accessions sampled from different geographical regions, it indicated that most allelic parameters had values comparable to previous similar study results. Specifically, the geographical populations, ‗Amhara‘ and SNNP had the highest number of effective alleles; Shannon‘s diversity index (I); and heterozygosity values. Furthermore, results of Analysis of Molecular Variance (AMoVA) indicated that the greater proportion of the genetic variation was explained between individuals from different populations (58%) and between individuals within the same population (40%). In comparison, only 2% of the genetic variation was due the variation among the populations themselves. In addition, the calculated Fst value was small (Fst=0.015), associated with a high gene flow value (Nm=16.282), indicating lower differentiation of the populations, which, in turn, implied significant exchange of planting materials among farmers in the studied populations. Finally, Neighbor-Joining (NJ) cluster and Principal Coordinate analyses (PCoA) revealed that accessions from different collection sites tended to cluster together, probably owing to the high gene flow among the populations. Moreover, five groups of clusters were identified in the NJ dendrogram. In addition to the aforementioned, analysis of structure of genetic diversity of the Ethiopian common bean accessions was undertaken with respect to the Andean and Mesoamerican gene pools of origin. Results indicated at cluster K=2, accessions separated into the Mesoamerican and Andean gene pools. In view of this, the number of accessions from the Mesoamerican gene pool was higher than that of their Andean counterparts. Moreover, STRUCTURE identified K=5, as the optimum cluster number. At K=5, five clusters: three from the Andean gene pool; and two from the Mesoamerican gene pool were identified. On the other hand, based on calculations of hybrid/non-hybrid accessions (from membership coefficient values), 72 out of the 125 accessions were found to be inter-gene pool introgressions. Moreover, results of NJ cluster analysis and PCOA done with the remaining 55 non-hybrid accessions identified at K=5 revealed common bean genetic diversity in Ethiopia, as organized into the Andean and Mesoamerican gene pools. This was exhibited by the clustering of accessions with either of the Andean or Mesoamerican control genotypes. The other peculiar event was mixed membership of Andean/Mesoamerican accessions in some of the clusters. Finally, yet equally importantly, Principal Component Analysis (PCA); stepwise discriminant and canonical correlation analyses; and data recorded in some agro-morphological traits distinguishing the Andean and Mesoamerican gene pools were used in conjunction, in order to determine the identities of the five cluster groups, identified at K=5 of the molecular structure analysis into the ecogeographic races of the Andean or Mesoamerican gene pools. To this end, PCA, done with the 125 accessions identified at K=2 of the molecular analysis, revealed that Mesoamerican and Andean groups of accessions separated along the first Principal Component (PC) axis. Nonetheless, several accessions occupied intermediate positions between the Andean and Mesoamerican control genotypes, which supported the presence of inter-gene pool introgressions detected in both the morphological and molecular analyses. Furthermore, stepwise discriminant and canonical correlation analyses, using the non-hybrid accessions at the molecular analysis STRUCTURE preset K=5, displayed that there was fair level of separation among the Andean and Mesoamerican cluster groups, with some overlaps. Ultimately, the identities of the five cluster groups identified in the molecular structure analysis were determined. In line with this, it was concluded that Ethiopian common bean accessions from the Andean gene pool had a broader base, belonging to ecogeographic races in the gene pool. In other words, the three Andean cluster groups were found to be from two of the three races in the Andean gene pool-‗Nueva Granada‘ and ‗Peru‘, whereas the Mesoamerican accessions had a narrower genetic base, belonging only to race ‗Mesoamerica‘ in the same gene pool. In summary, results of the present study showed that common bean landrace genotypes in Ethiopia had adequate genetic diversity, organized in to the Andean and Mesoamerican gene pools. Importantly, this rich genetic diversity should be harnessed in order to maximize genetic variability in future common bean improvement programs in Ethiopia. On the other hand, the significant presence of inter-gene pool introgressions, by itself, can be used as opportunity, for such introgressions were previously reported to be rich in many adaptation and nutritional genes. This, in turn, can be used as an advantage in prospective common bean breeding works. On the other hand, the higher/significant variations among accessions vis-à-vis qualitative and quantitative agro-morphological traits should be directed towards broadening genetic variability and developing transgressive genotypes, excelling their parents in relation to these traits. Key words: AMoVA, Genetic Diversity, landrace, accessions NJ, PCA, PCoA, Population Structure,STRUCTURE,
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    Genetic Diversity and Population Structure, Trait Interrelationships, Yie Stability and Socioeconomic Importance of White Lupin (Lupinus Albus L.) Landraces in Ethiopia
    (Addis Ababa Universty, 2017-06) Atnaf, Mulugeta; Tesfaye, Kassahun (PhD)
    White lupin (Lupinus albus L.) is one of four economically important species of the Lupinus genus, and has been traditionally cultivated for several thousand years along the Nile valley, including Ethiopia. Lupins are known to perform multifaceted functions, such as for human food and beverage, livestock feed, ecological importance, pharmaceutical values and social contributions. In Ethiopia, white lupin has been sustaining quite long in the farming system, and is produced exclusively by smallholder subsistence farmers. However, despite it has long been produced in the country, the crop received little attention by different development actors and have several undesirable characteristics. To address these, setting up practical lupin breeding program targeting the aforementioned major lupin production constraints is quite essential and necessary. Hence, the present study attempted to avail various pertinent socioeconomic and genetic and/or breeding information which are fundamental to realize lupin improvement in the country. Detailed baseline survey involving 303 households sampled from white lupin production areas of north western Ethiopia was conducted, to ascertain the extent of lupin production constraints and document farmers experiences and practices on lupin cropping, processing and utilization and marketing. Study results identified the major production practices and constraints to lupin production in the areas. The results would form a useful guide for the development of well‐tailored breeding objectives for the improvement of white lupin for Ethiopian farmers and consumers. This approach is useful not only to document farmers experiences and practices, but also ensures participation of farmers to develop demand led lupin technologies. A phenotyping experiment aiming at characterizing the landraces using agronomic and phenological traits which comprises 143 landrace accessions was under taken at Merawi, Ethiopia. Further characterization of genetic diversity and population structure of 212 landraces using 15 polymorphic SSR markers were done. Another experiment with objectives to evaluate the performance and stability of white lupin landraces in different locations; and characterize white lupin growing environments in Ethiopia was conducted at six different locations in north western Ethiopia. The phenotyping and over‐locations experiments were considered to understand the relationships among traits, and to document trait profile of white lupin landraces. Phenotypic characterization revealed that Ethiopian white lupin landraces were significantly different for most of the traits studied, and a significant number of local accessions performed as high as 5 metric tonnes per hectare of grain yield. Cluster analysis showed that landraces were grouped into 17 clusters of different sizes, of which five were singletons. Some landraces were grouped together regardless of their geographic origin. On the other hand, landraces from Awi, South Gondar and West Gojam were distributed over many clusters. Genetic distances between many pairs of clusters were significant, justifying crosses between parents from them would be desirable genetic recombinations. Molecular characterization further revealed the genetic diversity vested on the landraces. The SSR markers revealed 98 from 212 landraces, 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 allele 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 two control genotypes and five landraces remaining distinct and ungrouped. Population differentiation and genetic distance were relatively high between Gondar and populations collected by Australians. High level of gene flow (Nm), ranging from 10.60 to 31.46, was detected between the four major populations namely West Gojam, Awi, East Gojam and Gondar. 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 and some from Awi, were grouped together with significant admixtures. The study also suggested that 34, as core collections, were sufficient to retain 100% of SSR diversity. Higher heritability and genetic advance as percent of mean was observed for grain yield, indicating the possibility of improving this trait through selection. Different patterns of associations and accession by trait interactions were observed in different environments. However, genotype by trait biplots consistently indicated that grain yield had positive associations with most of the traits; especially, with number of pods per plant, plant height and seeds per pod. The study identified some accessions with desirable performances as good for specific trait and/or trait groups that could be considered as sources of genes for the traits they have best performed. The genotype by environment interaction study depicted that the white lupin landraces studied had differential performances at different test locations implying the presence of crossover interaction. The first two principal components (PC1=41.6% and PC2=21.8%) of the genotype plus genotype by environment interaction (GGE) explained 63.4% of the GGE sum of squares. Two white lupin growing mega‐environments were identified in north western Ethiopia. All test locations were found to be representative with different degrees of reliability whereby Fenote Selam and Dibate were found to be most representative. In addition, all test locations, except Mandura and Injibara had generally similar and good discriminating power. Fenote Selam and Dibate were found to be the most representative and discriminating environments and are characterized as most desirable test locations for white lupin improvement in north western Ethiopia. Genotype 2 (G2) was found to be the highest yielding and most stable landrace across the test environments, and hence identified as most desirable genotype for production. Key words: Discriminating power, Ethiopian farming system, Farmers' experiences, Genotype by location interaction, Genotype by Trait, Landrace populations, Mega‐environment, Representativeness, White lupin.
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    Genetic Diversity and Selection Efficiency of Ethiopian Durum Wheat (Triticum Durum Desf.) Landrace Collections
    (Addis Ababa University, 2016-09) Asmamaw, Meseret; Tesfaye, Kassahun (PhD)
    Durum wheat (Triticum durum Desf) is an economically important crop because of its unique characteristics and end products like semolina for pasta making. In Ethiopia, durum wheat is among the most important Triticum species with higher morphological variability among landraces. Knowledge of the extent and pattern of genetic diversity within and among populations is very crucial to identify useful breeding materials and design appropriate collection and conservation strategies. Genetic diversity of 160 durum wheat accessions were studied using 17 morpho-agronomic traits and 12 SSR markers. A field and laboratory experiments were also undertaken in 2014-2016 in Ethiopia to characterize and evaluate durum wheat germplasm for attributes of morphological and molecular characterization. The field studies for morphological characterization was undertaken at Adadi Maryam and Ginchi using randomized complete block design with two replications while the molecular characterization study was conducted in Holeta national agricultural biotechnology laboratory (HNABL) at Holetta in Ethiopia. The average linkage technique of clustering produced a more understandable portrayal of the 160 durum wheat accessions by grouping them into seven clusters with inter-cluster D2 values ranged from 13to 235 . According to genotypic correlation grain yield had highly significant positive correlation coefficient with harvest index, biomass yield, grain filling efficiency, biomass production rate and economic growth rate. In the present study spike length, grain yield, stem rust disease reaction, harvest index, economic growth rate, biomass production rate and biomass yield exhibited relatively higher broad sense heritability. In genetic progress study of 19 released varieties, empirical experimental evidence of gains in durum wheat yield showed that at average rate of increase in yield potential per year of release over 46 years period from the slope of linear regression shown in the graph was 30.99 kg/ha (0.74%) per year over the oldest variety Arendato. Analysis Molecular of Variance (AMOVA) showed higher variation within populations (81%) while the remaining 19% attributed for among population. The degree of polymorphism between populations varied from 74% for the collections from Eastern Tigray to 98.86 % for collections from Harergie, with the average of 88%. The dendogram of cluster analysis based on neighbor-joining algorithm categorized the 160 durum wheat accessions into three major clusters consisting of 47, 64, and 49 of the accessions in cluster I, II, and III, respectively. The highest values of genetic distance ranges from North Gonder and East Tigray (0.576) to smallest genetic distance between accessions from Bale and Harergie (GD=0.092).The HWE test for 12 loci were exhibited that loci (BARC 153, CFD 257, WMS 493, and WMS 516) were in Hardy-Weinberg equilibrium in all the populations analyzed. However, significant deviation from HWE was observed in some of the locus through tested populations. In 2D, most individuals of the respective populations were observed to form three major cluster groups with some sub cluster groups with higher intermixing from the other population. Thus, most of accessions from all 15 populations were intermixed with one another. Key Words: Triticum durum Desf, Genetic Diversity, Trait association, Heritability, SSR primers, Polymorphism, Disease resistance.
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    Genetic Diversity Assessment of Yams (Dioscorea Spp.) From Ethiopia Using Inter Simple Sequence Repeat (Issr) Markers
    (Addis Ababa University, 2015-04-04) Mohammed, Kedra; Tesfaye, Kassahun (PhD); Haileselassie, Teklehaimanot (PhD)
    The genetic diversity and relationships of 70 accessions of yam belonging to Dioscorea cayenensis/Dioscorea rotundata complex (55), Dioscorea bulbifera (13) and Dioscorea alata (2 as a reference) were assessed using six ISSR primers. DNA was extracted from a bulk of two plants per accession using a modified CTAB method. Six ISSR primers amplified 77 fragments with 75 (97.40%) polymorphism at genus level. The genetic diversity, estimated by Gene diversity and Shannon’s index were 0.36 and 0.53, respectively, revealing a high level of genetic variation at genus level. At species level 75 bands were amplified for D. cayenensis/D. rotundata complex, out of which 71 were polymorphic accounting for 92.2% polymorphism. Gene diversity and Shannon's index for D. cayenensis/D. rotundata complex were 0.33 and 0.49, respectively. In case of D. bulbifera a total of 64 bands were scored, out of which 55 were found to be polymorphic which resulted in 71.4% polymorphism. Gene diversity and Shannon's index for this species were 0.24 and 0.47, respectively. Genetic diversity analysis of D. cayenensis/D. rotundata complex accessions showed that Gedeo were the most diverse among populations and South among groups. Analysis of molecular variance (AMOVA) indicated the presence of higher proportion of variation within species (63.9%) than among species (36.1%) which could be due to presence of several shared bands. AMOVA for D. cayenensis/D. rotundata complex also showed higher within population variation (53.6) than among populations (46.4). This could be due to gene flow through seed materials exchange among local farmers. Cluster analysis showed grouping of most of the accessions according to their species. In addition, cluster analysis for relationship between D. cayenensis/D. rotundata complex accessions showed grouping of some of the accessions according to their population but it failed to produce clear species boundary between D. cayenensis/D. rotundata complex. The results suggested that there exists a high level of genetic diversity in yams of Ethiopia to be exploited for future improvement (breeding) of the crop.
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    Genetic Diversity of Ethiopian Tef (Eragrostis tef (Zucc.) Trotter) Varieties as Revealed by Morphological and Microsatellite Markers
    (Addis Ababa Universty, 2016-10) Fikre, Tsion; Tesfaye, Kassahun (PhD)
    Tef (Eragrostis tef (Zucc.) Trotter) is a gluten free cereal crop mainly grown in Ethiopia for food, feed and cash. This study was designed to assess the genetic diversity using morphological and molecular marker, and investigate trait association among tef varieties of Ethiopia. The experiment was conducted at two locations (viz. Debre Zeit and Alem Tena) for morphological study and National Agricultural Biotechnology Research Center, Holetta for molecular study in 2014/15 using 49 and 51 tef varieties based on 23 phenotypic traits and 9 microsatellites, respectively. In morphological study, combined analysis of variance over location revealed highly significant variation (P≤0.01) among the tested varieties for all recorded traits except for plant height and genotype x location interact significantly (P≤0.01) on 11 of the traits. The phenotypic coefficient of variation ranged from 3% for days to maturity to 30% for grain yield per plant, and the genotypic coefficient of variation ranged from 0% for second basal culm internode diameter to 21% for number of fertile tiller per plant. Estimates of broad sense heritability varied from 0% for second basal culm internode diameter to 95% for days to heading. The expected genetic advance as percent of the mean varied from 0% for second basal culm internode diameter to 32% for number of spikelets per main shoot panicle. The cluster analysis grouped the varieties into seven major groups consisting of one to 29 varieties. The first six principal components with eigenvalues greater than one explained 76% of the total variation. Grain yield showed significant positive correlation with panicle length, culm length, number of fertile tillers per plant, number of spikelets and primary branches per main shoot panicle, thousand seed weight, grain yield per plant and biomass yield. On the other set of experiment, the molecular study detected a total of 52 alleles with a mean of six alleles per locus ranged from five to seven. With a mean 0.69 the polymorphic information content (PIC) ranged from 0.59 for marker CNLTs27 to 0.77 for CNLTs86. The gene diversity ranged from 0.65 to 0.80 with a mean of 0.73. The degree of polymorphism among the groups varies from 67% for improved varities obtained from hybridization to 57% for wild relatives with the average of 63%. The lowest level of genetic differentiation and high level of gene flow were observed among the varieties obtained through hybridization and direct selection. Molecular analysis of variance higher percentage of variation within individuals (60%) and the variation among groups was the least (10%). Cluster analysis based on SSR data grouped the varieties into three major cluster groups. Principal Co-ordinate Analysis showed that the first three most informative principal coordinates accounted for 29% of the genetic variation. Generally, the present studies showed the existence of low genetic diversity among the released varieties which calls for timely action to widen the genetic diversity of Ethiopian released tef varieties. Moreover, both marker systems identified distinct varieties such Simada, Gola, Tsedey and Were Kiyu in the early maturing category that is suitable for terminal drought-prone area, and Etsub in late maturing category that is meant for optimum rainfall areas using both marker systems. The incorporation of these selected varieties and other divergent varieties as parent materials will strengthen the future tef breeding program through developing distinct varieties in the respective agro-ecologies. Key Words: Tef, Eragrostis tef, Genetic diversity, Morphological traits, Microsatellite markers, Trait Association.
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    Genetic Diversity of Sesame (SesamumindicumL.) Revealed by ISSR Marker Conservation
    (Addis Ababa University, 2011-07) Teshome, Dagmawi; Tesfaye, Kassahun (PhD)
    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. Intersimple sequence repeat (ISSR) marker was used to assess the level of geneticdiversity, genetic structure and genetic distance, and to indirectly estimate the level of gene flowamong populationsof sesame in Ethiopia.A total of 120 (82 Ethiopian and 38 exotic) sesame accessions and six ISSR primers, five of which were dinucleotides (810, 818, 834, 844, 860) and one pentanucleotides (880) 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. A total of 58 clear and reproducible bands were amplified, out of which 44(75.86%) were observed to be polymorphic. The number of polymorphic loci ranged from four for primer-834 to eight for the other primers.Comparative assessment of Ethiopian accessions (considering as a single large population) verses exotic accessions indicated the presence of higher polymorphism among accessions collected from Ethiopia (75.85)than the exotic accessions (65.52). Primers 810, 818 and 860 showed the highest percent polymorphism (88.89%) and the least polymorphic bandswere scored by primer 834 which is only 40.00 %. Grouping Ethiopian accessions into administrative region-based populations and the exotic accessions in to country based populations showed samples from Welega were 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. The average gene diversity relative to the overall population was 0.24 considering accession from different administrative region of Ethiopia and exotic accessions as independent population. AMOVA without grouping revealed that higher percentage of variation (94.09%) is attributed to the within population variation while the remaining variation is due to the among population variation (5.90%). Inter-population genetic distance (D) ranged from 0.031 to 0.165 for the overall population. Among the pairwise population comparisons made within Ethiopian populations,accessions from Welega and Harerge showed the highest genetic distance (0.16) and accessions from Shewa and Harerge show the least genetic distance (0.041). From the exotic accession,samples of South East Asia are distantly related to most of the Ethiopian accessions. Genetic distance between the other pairwise combinations of populations was very low, with the least genetic distance being between samples of Mexico and Tanzania (0.031).UPGMA analysis of Ethiopian sesame populations revealed two major groups and three outliers (Cultivated, Welega and Illubabore). The first major cluster again forked into two sub groups the first containing Tigray, Harerge and Shewa populations, while the second contained Gamo Goffa, and Wello populations. The second major cluster comprise of accessions from north western part of Ethiopia mainly from Gojam, Benishangul Gumuz and Gonder.In the 3D plot, with the exception of few accessions that come from Welega, Wello and Ilubabore, most of the individual accessions that represent different populations spread all over the 3D space. Key words:Ethiopia, genetic diversity, ISSR, Sesame (Sesamum indicum L.)
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    Genetic Diversity of Wild Coffee (Coffea Arabica L.) Populations from Southwestern Ethiopia as Revealed by ISSR Markers
    (Addis Ababa University, 2012-06) Getenet, Biruk; Tesfaye, Kassahun (PhD)
    Coffea arabica L., is indigenous to the highland of southwestern Ethiopia and southeastern Sudan. It is the afromontane rain forest species of south west and south east part of Ethiopia and grown naturally at altitudes ranging from 1,300 and 1,800 meter above sea level. Human population pressure and land use change in and around the afromontane rain forest highly threatened the wild coffee populations of Ethiopia. Inter simple sequence repeats (ISSRs) molecular markers were analysed. In the present study five wild populations of Coffea arabica from, Bench Maji-1(Maji), Bench Maji-2(Jeba), Dawero Banja, Limmu and Anfilo were included. A total of 71 individual plants were analyzed using four ISSR primers, three dinucleotides (810, 812,818) and one penta nucleotides (880) primers. A total of 30 clear and reproducible bands were amplified, and 100% were found to be polymorphic. The highest polymorphic loci were revealed by primer 812 with 9 polymorphic loci. Among the populations studied, Bench Maji-1 and Dawero showed 100% polymorphism, while Limmu and Anfilo showed moderate polymorphism of 56.67% and 63.33%, respectively, whereas Bench Maji- 2showed the least polymorphism(30%). The average gene diversity relative to the overall population was 0.45. AMOVA without grouping revealed that higher percentage of variation (79.4%) is attributed to the within population variation while the remaining variation is due to the among population variation (20.6%). Forest based UPGMA analysis based on Jaccard’s coefficient revealed one major group with Limu and Anfilo and two outliers (Bench Maji and Dawero Banja). NJ analysis based on individuals of wild Coffea arabica showed two distinct major clusters and sub-clusters within both major clusters; and individuals from Bench Maji-1 and Anfilo tend to form their own separate groups while others tends to speared all over the tree. In 3D PCO, most of Dawero Banja and Bench Maji individuals were intermixed with each other and made separate group from the other two populations but individual of Anfilo and Limmu were spread all over the plot. Key words: Coffee, Coffea arabica, genetic markers, genetic diversity and ISSR
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    Genetic Diversity Study of Ethiopian Faba Bean (Vicia Faba L.) Varieties Using Phenotypic Traits, Issr and Snp Markers
    (Addis Ababa Universty, 2016-11) Mulugeta, Behailu; Tesfaye, Kassahun (PhD)
    Faba bean (Vicia faba L.) is one of the earliest food legumes of the world used as source of high protein for human and animal consumption. In Ethiopia, no studies were conducted on faba bean varieties genetic diversity assessment based on molecular markersand this study is designed to fill this gap. The study was designed to reveal the genetic diversity existing among Ethiopian faba bean varieties using phenotypic traits, ISSR and SNP markers. Field experiment was conducted at three locations (Sinana, Agarfa and Selka) for agro-morphological performance, while the molecular part was conducted at Addis Ababa University (ISSR) and UK, LGC genomics (KASP SNP genotyping). A total of 32 faba bean varieties were used for phenotypic and ISSR markers, whereas 16 additional breeding lines were included for SNP markers. A total of 23 phenotypic traits,11 ISSR and 37 SNP primers were used to assess genetic diversity and interrelationship among Ethiopian faba bean varieties. The genomic DNA extraction was made based on modified CTAB method and Oktopure extraction kit method from bulked young leaf sample for ISSR and SNP markers, respectively. The combined analysis of variance over the three locations showed highly significant (p<0.01) variations among the varieties for the majority of traits. Genotype by environment interaction showed highly significant difference (p< 0.01) among traits. UPGMA constructed based on phenotypic traits revealed five major clusters and the first six principal components (PCs) accounted for 85% of the entire diversity among the varieties for all the 23 traits and the first three PCA revealed 66% of the total variation. Eleven ISSR primers amplified 120 bands, of which 107 loci were polymorphic. The highest gene diversity (0.38) and Shannon index (0.56) were recorded by primer 860, while the least gene diversity (0.18) was revealed by primer 848 and 857. UPGMA cluster and PCO analysis grouped the cultivars into three major clusters based on Jaccard’s similarity coefficient ranging from 0.41 to 0.77. Out of the 37 scoreable SNP markers, one was monomorphic across all the 48 genotypes and 36 SNP showed polymorphism with rate of 95.58%. Relatively high average Nei’s genetic diversity (0.41) and PIC (0.32) were revealed by SNP markers. Based on obtained PIC value, 31 SNP primers were found to be reasonably informative. Genetic dissimilarity between different pairs of varieties varied from 0.15 (Dosha and Mesay) to a maximum of 0.80 (Tumsa and Kulumsa local varieties) with an average mean of 0.45. STRUCTURE, UPGMA and PCOA suggested that the varieties were divided into three main genetic groups. Therefore, the observed genetic variation in the study indicated the opportunity of using these materials in future faba bean breeding program via introgression with other germplasm resources for improvement of better genotypes. Key Words: Genetic distance, Genetic diversity, ISSR, Phenotypic traits, SNPs, Vicia faba