Browsing by Author "Gadissa, Fekadu"

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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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    Chromosome Study in Five Endemic Kniphofia Species (Asphodelaceae) of Ethiopia
    (Addis Ababa University, 2009-09) Gadissa, Fekadu; Dagne, Kifle (PhD); Kelbessa, Ensermu (Professor))
    The karyotype of five endemic Kniphofia species of Ethiopia were studied. The studied species are: K. foliosa, K. schimperi, K. hildebrandtii, K. isoetifolia, and K. insignis. Somatic chromosomes were prepared from the root tip meristem using colchicines, 8-hydroxyquinoline or ice-cold pretreatment, followed by fixation (3:1, ethanol:acetic acid) and then enzyme maceration in pectinase-cellulase solution at 37°C for about 1 hr. Air-dry slides were prepared and stained in Giemsa stain in Sorensons phosphate buffer (pH = 6.8). The karyotype analysis has shown that K. foliosa, K. schimperi, K. hildebrandtii and K. isoetifolia are diploid with 2n = 12, where as K. insignis has 2n = 22 chromosomes which is assumed to be a polyploid on the basis of x = 6 for the genus. Polyploidy is the first report for the species. Morphologically, the chromosomes showed a gradual decrease in size in all the species with only small differences between the longest and the shortest chromosomes of each species. The size differences are relatively more pronounced in K. insignis. The karyotype formula was found to be 2m + 8sm+ 2st in K. foliosa, K. schimperi and K. hildebrandtii; 2m + 2m/sm + 8sm for K. isoetifolia and 4m + 12sm + 1sm/st + 5st for K. insignis. Generally, there is only a minor degree of differentiation observed among the karyotypes of the diploid species. One pair of small satellites were observed on the tip of short arms in K. foliosa and K. hildebrandtii, two pairs in K. schimperii and K. isoetifolia and in K. insignis, the secondary constriction is located in the middle of the long arm of a pair of chromosomes and thus delineated two large satellites. Kniphofia foliosa from ‘Laga Shore’, about 10 kms from Gedo town, west of Addis Ababa, was found to have a B-chromosome. This is the first report of B-chromosome for the species as well as the genus. In spite of the fact that samples were collected from only a limited number of sites, the cytogenetical information reported here would create only the basis for further cytological investigation of Kniphofia species. It is, thus, recommended that further cytological and molecular studies including specimens from a wider geographic area should be carried out. Key words: B-chromosome, Chromosome, Endemic Kniphofia species, Ethiopia, Karyotype, Polyploidy.