Browsing by Author "Tesfaye Kassahun (PhD)"

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    In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Biology (Applied Genetics)
    (Addis Ababa University, 1990) Gebremariam Zelalem; Bekele Endashaw (Professor); Tesfaye Kassahun (PhD)
    Three Lepus species are currently considered to occur in Ethiopia: Lepus habessinicus Hemprich and Ehrenberg 1832 (Abyssinian Hare), L. fagani Thomas 1903 (Ethiopian Hare) and L. starcki Petter 1963 (Ethiopian Highland Hare) based on limited morphologic and cytogenetic data. Analyses of morphological characters, 13 microsatellite loci, one mitochondrial (ATPase sub-unit 6 sequence) and five nuclear sequences (Transferrin (TF), Thyroglobulin (TG), Uncoupling protein two (UCP2), Uncoupling protein four (UCP4) and Thyroid stimulating hormone beta (TSHB)) were made to provide an initial comprehensive data on the evolutionary relationship among the three hare species collected from twenty six localities in Ethiopia and identified by their external phenotypes, dental and skull characters. In addition, other Lepus species: L. capensis, L. saxatilis, L. europaeus, L. timidus and L. victoriae were used for phylogenetic comparison. Multivariate skull morphometric analyses (PCA & DA) of seven Lepus species (n = 327) indicated clear distinction among the species. Lepus habessinicus had a distinct morpho shape space relative to L. capensis. Lepus fagani had a distinct morpho shape space relative to L. saxatilis and L. victoriae. Lepus starcki had a distinct morpho shape space relative to L. europaeus and L. capensis. Microsatellite analysis based on hares (n = 107) collected from Ethiopia resulted in clusters of hare species in accordance with population origin and collection sites. Individuals of L. habessinicus and L. fagani were substructured in accordance with population of origin and collection localities with some degree of SSR introgression among each other. Microsatellite introgressions were documented also between species. In all analyses (structure, FCA and NJ) L. starcki individuals were consistently clustered into a single group. All phylogenetic reconstruction methods used (Neighbour Joining, Maximum Likelihood, Bayesian Analysis and Median Joining Networks) by and large resulted in similar topologies for mitochondrial and nuclear sequences, respectively. The three hare species from Ethiopia were not monophyletic for both mitochondrial and nuclear sequences, but showed signs of both unidirectional and bidirectional introgressions among each other. Lepus habessinicus carried mtDNA distinct from South and North African L. capensis, with no sign of introgression, contrary to earlier suggestions to include L. habessinicus under L. capensis. Similarly, L. starcki had distinct mtDNA relative to L. capensis and L. europaeus as opposed to previous suggestions to include L. starcki either under L. capensis or L. europaeus. Despite the morphological distinctness of L. fagani, it shared a substantial proportion of mtDNA and nucDNA with hare species from Ethiopia and L. saxatilis from South Africa. The nuclear sequences revealed phylogenetically and geographically meaningful clusters, albeit with a fair amount of indications of recent or historical introgresions among the species. In line with ATP, the nuclear sequences indicated close phylogenetic relationships among the three Lepus species from Ethiopia, with L. fagani being surprisingly tightly connected to L. habessinicus. Furthermore, the microsatellite analysis indicated low levels of genetic differentiation (G’ST and Dest 0.384 and 0.334, respectively) between L. habessinicus and L. fagani. Moreover, the nuclear sequences suggested a closer evolutionary relationship of Cape hare from north and south Africa to hare species in Ethiopia. Although the nuclear sequence analyses supported the North American ancestry of Lepus, the results of the present analysis also suggested Africa as a potential ancestral area of Lepus. Overall, both multivariate skull morphometric and molecular analyses suggested a specific status of L. habessinicus, L. fagani and L. starcki. Keywords: Ethiopia, introgression, Lepus habessinicus, Lepus fagani, Lepus starcki, microsatellite, mtDNA, nucDNA, phylogenetics, phylogroup and skull morphometry.
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    Morphological and Molecular Characterization, Assessment of Nutritional Composition and Micropropagation of Cocoyam (Xanthosoma Sagittifolium (L.) Schott) from Ethiopia
    (Addis Ababa University, 2018-06-03) Wada Eyasu; Feyissa Tileye (PhD); Tesfaye Kassahun (PhD); Asfaw Zemede (Professor)
    Morphological and Molecular Characterization, Assessment of Nutritional Composition and Micropropagation of Cocoyam (Xanthosoma sagittifolium (L.) Schott) from Ethiopia Eyasu Wada Wachamo, PhD Dissertation Addis Ababa University, June 2018 Cocoyam (Xanthosoma sagittifolium (L.) Schott) is a tuberous root crop in the Araceae family. It is an exotic crop to Ethiopia that was introduced fairly recently but has spread widely and already become part of the agricultural and food systems of the people, wherein tuber and root crops play an important role as sources of food. However, cocoyam has not been given research attention commensurate to its importance as it is a neglected crop by research and development community. This study was conducted to characterize cocoyam diversity at morphological and molecular levels through documenting farmers’ knowledge, perceptions and management practices; determining nutritional composition; and developing a micropropagation protocol for this neglected crop. The present ethnobotanical survey results showed that the crop is given different local names by farmers and that it is locally used for food, fodder, medicine and other purposes. Furthermore, the results showed that the uses of cocoyam as a food crop and fodder are the most preferred traits as perceived by the farmers while hardness, sour taste, unpleasant smell and low market demand were the major constraits for cocoyam production. Green- and purple-colored cocoyam plants were observed during our survey. The field study helped to distinguish two classes of qualitative traits for petiole color, lamina orientation, color of veins on leaf surfaces, position of cormel apex and shape of cormels. Analysis of variance (ANOVA) revealed significant variation in 11(84.6%) of the 13 studied quantitative traits. Principal Component Analysis (PCA) reduced the 13 quantitative traits to 3 Principal components (PCs) with the eigen values >1, which explained 69.2% of the observed variations. In the genetic diversity analysis using 11 SSR markers, a total of 36 alleles were detected (mean 3.273). High SSR marker diversity was detected within populations (average Ho = 0.503 and He = 0.443) and when all collections were considered as single population (Ho: 0.508, He: 0.566). Supporting these results, genetic diversity analysis using AFLP markers revealed high Nei’s gene diversity (He) within populations (He = 0.349) and at the entire collection level (He = 0.389). SSR markers revealed strong genetic differentiation among populations and between green and purple cocoyam morphotypes by Fst values 0.196 and 0.463, respectively. However, unlike SSR markers, AFLP marker-based analysis showed low genetic differentiation among populations (Gst = 0.072) as well as between green and purple cocoyam morphotypes (Gst = 0.024). The nutritional composition analysis showed that both the green- and purple-cocoyam morphotypes can provide nutrient-rich products, albeit slight differences in the quantities of proximate, minerals and antinutritional factors. A micropropagation protocol was successfully developed in which the green- and purple-cocoyam shoot tip explants were best initiated on Murashige and Skoog (MS) medium containing 2.0 mg/l BAP, best multiplied on MS medium containing 2.5 mg/l BAP and 0.5 mg/l NAA and the best IBA concentration for rooting was MS medium supplemented with 2.0 mg/l IBA. Overall, a lot of useful indigenous knowledge exists within the farming communities in the rural areas, but cocoyam is poorly studied and underutilized crop in spite of its nutritional value & its potential as food crop. The findings of this study are very important to enhance the future use of cocoyam in the country. Collaborative research intervention involving the development of varieties, making available high quality planting material for farmers & promoting value chains and market opportunities are valuable for sustainable use of the exiting diversity & to safeguard the potential end users of cocoyam in the country.
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    Whole Genome Based Characterization of Indigenous Chicken Populations in Ethiopia
    (Addis Ababa University, 2018-12-04) Kebede Adebabay; Tesfaye Kassahun (PhD); Belay Gurja (PhD)
    WHOLE GENOME BASED CHARACTERIZATION OF INDIGENOUS CHICKEN POPULATIONS IN ETHIOPIA Adebabay Kebede Addis Ababa University, 2018 Indigenous chicken are locally adapted to environmental challenges and provide subsistence to millions of farmers in Africa. Their productivity remains low compared to exotic chicken strains. Efforts are being made to combine the local adaptation of indigenous chicken with productivity traits of exotic chicken. Understanding the link between diversity and adaptability is opening the door to marker-assisted breed improvement programs. Selective breeding for genetic improvement is expected to leave distinctive selection signatures within genomes. The identification of selection signatures can help to elucidate the mechanisms of selection and accelerate genetic improvement. Ethiopia has several chicken ecotypes which evolved in different agro-ecologies. This study aims to characterize the genomic diversity of indigenous chicken populations from Ethiopia. The first part of this study addresses the characterization of the LEI0258 microsatellite loci in the MHC region with previous study supporting links of the locus with infectious diseases resistance/susceptibility in commercial chicken. Here, we report diversity of LEI0258 in 236 chicken from 24 Ethiopian indigenous chicken populations from different agro-ecological zones using gel electrophoresis and sequencing. VII The number of alleles, allele frequency, and heterozygosity levels were used to measure diversity within populations whilst the Wright’s fixation indices were used to analyze the level of population structuring. Twenty-nine LEI0258 allele sizes were observed using capillary electrophoresis. Allele sizes ranged from 185 to 569 bp with no significant difference in allele frequencies between populations (P < 0.05). Allele frequencies were in Hardy and Weinberg Equilibrium in all population except Dara chicken (P < 0.05). Excluding the tandemly repeated motif, the number of monomorphic and polymorphic sites are 412 and 35, respectively. Number of point mutation and indels are 33 and 17, respectively. The number of R12 CTTTCCTTCTTT repeats ranged from 2 to 18, while R13 was found monomorphic with a single motif CTATGTCTTCTTT. Sequences relationships reveal two distinct groups of alleles. The high diversity at microsatellite LEI0258 at Ethiopian indigenous village chicken populations supports the importance of the MHC region in relation to the disease challenges diversity faced by smallholder poultry production within and across Ethiopian agro-ecologies. We recommend that breed improvement programs ensure the maintenance of this diversity by selecting breeding stock as diverse as possible at the LEI0258 locus. The part of the thesis reports the genomic diversity of Ethiopian indigenous chicken through discovery and characterization of 21 million SNPs (72% novel) from 27 indigenous chicken populations (n = 260 birds) using whole genome sequencing. In each population, around 10 to 12 million SNPs are present, of which, 40-47% are a heterozygote. The mean SNP density across all population is 21 (±5) per kb, although it is much lower on the sex chromosomes (W = 0.4, Z = 11). Principal component and admixture analyses suggest the presence of four ancestral gene pools across the populations. Over 46% of the SNPs are located within genes, of which exonic and intronic SNPs account for 1.59% and 43.94%, respectively; while 31% of the exonic SNPs are non-synonymous. A large proportion of SNPs has low alternative allele frequency (AAF < 10%), VIII although this proportion is higher for potentially harmful categories like missense and stop gain/loss (> 60%) than neutral ones (40-45%). Genes with deleterious missense variants are included within several important biological pathways like innate immunity. Our results confirm the existence of significant genomic diversity in indigenous chicken populations of Ethiopia, with most of the variants previously undescribed in commercial breeds. The last part of the thesis assesses the footprints of candidate signatures of positive selection from whole genome autosomal sequences, comprising 14,857,039 SNPs, in Improved Horro, Local Horro, Hugub, Arabo and Jarso chicken populations of Ethiopia. We identified selection signals in 20 Kb windows size with 10 Kb sliding steps based on estimators of pooled heterozygosity (Hp and F-statistics (Fst) within and between those populations. Selective sweep analysis using Hp and Fst methods identified genomic regions associated with production and reproduction traits. A total of 595 candidate genes showed high evidence of positive selection in indigenous chicken populations. These genes were related to traits such as growth and egg production. Gene ontology analysis displayed several biological processes and KEGG pathways involved in oestrogen biosynthetic and nervous system development processes, calcium signaling and biosynthesis of unsaturated fatty acids. The regions identified in this study are expected to provide a genome landmark to enhance the ongoing breed improvement operations in improved Horro and other four chicken populations. In general, this study revealed the huge genomic diversity and taped the genomic regions under strong selection in indigenous chicken populations of Ethiopia