RNA-Seq Transcriptome Profiling of Ethiopian Lowland Bamboo (Oxytenanthera Abyssinica (A.Rich) Munro Under Drought and Salt Stresses and SSR Based Genetic Diversity Analysis o f Ethiopian Highland Bamboo (Arundinaria Alpina K. Schum).
| dc.contributor.advisor | Beyene, Dereje (PhD) | |
| dc.contributor.advisor | Feyissa, Tileye (PhD) | |
| dc.contributor.advisor | Tingbo, Jiang (Professor) | |
| dc.contributor.author | Adem, Muhamed | |
| dc.date.accessioned | 2020-02-04T09:20:11Z | |
| dc.date.accessioned | 2023-11-08T16:39:23Z | |
| dc.date.available | 2020-02-04T09:20:11Z | |
| dc.date.available | 2023-11-08T16:39:23Z | |
| dc.date.issued | 2019-07-02 | |
| dc.description.abstract | Bamboos are perennial grasses classified under family Poaceae and subfamily Bambusoideae and are among the fastest growing plants on earth. Although bamboos have ecological and economic importance in Ethiopia, scientific inquiry particularly on genomics, transcriptomics and genetic diversity and structure is lacking. Ethiopian lowland bamboo (O. abyssinica) adapted in hot areas of Ethiopia hence inquiry on global transcriptome profiling is very important to elucidate the most important genes, transcript factors and metabolic pathways associated to abiotic stress. To do so, plastic pot germinated seedlings of lowland bamboo were subjected to 200 mM NaCl and 25% PEG-6000 (Poly Ethylene glycol) to induce salt and drought stress, respectively. Using the Illumina sequencing platform, fifteen cDNA libraries were constructed and sequenced to generate the first drought and salt stress global transcriptome profiling of the species. Following quality control, 754,444,646 clean paired-ends reads were generated, and then de novo assembled into 406,181 unigenes. Functional annotation against the public databases presented annotation of 217,067 (53.4%) unigenes, where NCBI-Nr 203,777, Swissport 115,741, COG 81,632 and KEGG 80,587. Prediction of Transcripts Factors (TFs) has generated 4,332 TFs organized into 64 TF families. Analysis of Differentially Expressed Genes (DEGs) provided 65,471 genes where 569 genes belongs to all stresses. Transcript factors (TFs) with a higher number of differentially expressed genes include bZIP (49), WRKY (43), MYB (38), AP2/ERF (30), HD-ZIP (25) and MYB related (21). Such 569 genes could serve for engineering plants for multiple abiotic tolerances. Despite the important role of bZIPs in plants, particularly in abiotic tolerances, bZIP family members and their corresponding functions remain elusive in the lowland bamboo. Through genome-wide analysis, a total of 162 bZIP lowland bamboo TFs having the bZIP binding domain (PF00170) were identified. For the identified bZIPs, functional annotation, phylogenetic relationship and their expression under drought and salt stress were investigated. The expression profile of the bZIP TFs revealed that majority of the bZIPs were highly responsive to drought and salt stress as 99 of the 162 TFs were up-regulated. Metabolic pathway analysis revealed that environmental information processing and genetic information processing categories were the only represented pathway which implies that the bZIPs are associated to drought and salt stress. Understanding on the genetic diversity and structure of highland bamboo is important particularly for conservation. For genetic diversity analysis 150 samples, representing 15 populations, 10 samples from each population were collected. The sources of SSR primers were; first, primers developed through reduced-representation genome sequencing of lowland bamboo were checked for their polymorphism and transferability, then 7 primers were selected and used for highland bamboo. Second, primers were directly taken from literature from Chinese Moso bamboo, after checking their transferability 9 primers were used. The genetic diversity indices (H= 0.398 and I= 0.639) for the 16 SSR markers used were moderate in capturing genetic variability. Both individual phylogeny and population structure merged the 15 populations in to nine clusters, with less geographic origin or collection based pattern. UPGMA clustered the 15 populations in 2, while NJ clustered in to 3, however pattern of their grouping is not in line with their pattern of origin of collection. The principal component analysis revealed that individuals are highly dispersed and did not group the populations into stridently distinct clusters which tells the presences of high genetic admixture possibly attributed to gene flow or the reproductive biology of the species. In conclusion, the RNA-Seq based global transcriptome profiling has generated transcriptomics resources for lowland bamboo which can be employed for itself and related species for further research. Most importantly the study uncovered key stress responsive genes, transcription factors, metabolic pathways and even genes differentially expressed to all stress groups which could be used as the basis for further studies aiming to confer plants for multiple abiotic stress tolerances. The study on bZIPs genome wide analysis also provided valuable information on how bZIPs are highly associated to abiotic stress tolerance since only pathways related to stress tolerances were represented in metabolic pathway analysis. The genetic diversity and population structure analysis of highland bamboo uncovered the presences of moderate genetic variability with high genetic admixture. The information could be used as a basis particularly for conservation interventions and for further investigations. | en_US |
| dc.identifier.uri | http://etd.aau.edu.et/handle/123456789/20550 | |
| dc.language.iso | en | en_US |
| dc.publisher | Addis Ababa University | en_US |
| dc.subject | Arundinaria Alpina | en_US |
| dc.subject | Abiotic Stress | en_US |
| dc.subject | Differentially Expressed Genes | en_US |
| dc.subject | Genetic Diversity | en_US |
| dc.subject | Oxytenanthera | en_US |
| dc.subject | Abyssinica | en_US |
| dc.subject | Rna-Seq | en_US |
| dc.subject | Ssr | en_US |
| dc.subject | Transcriptomics | en_US |
| dc.title | RNA-Seq Transcriptome Profiling of Ethiopian Lowland Bamboo (Oxytenanthera Abyssinica (A.Rich) Munro Under Drought and Salt Stresses and SSR Based Genetic Diversity Analysis o f Ethiopian Highland Bamboo (Arundinaria Alpina K. Schum). | en_US |
| dc.type | Thesis | en_US |