Institute for Biotechnology Research (IBR)
http://localhost/xmlui/handle/123456789/1280
2024-03-28T09:44:40ZEvaluation of Extremophilic Bacteria from Lakes Bogoria and Magadi for Biocontrol of Fusarium Solani and Rhizoctonia Solani in Phaseolus Vulgaris L.
http://localhost/xmlui/handle/123456789/6231
Evaluation of Extremophilic Bacteria from Lakes Bogoria and Magadi for Biocontrol of Fusarium Solani and Rhizoctonia Solani in Phaseolus Vulgaris L.
Wekesa, Tofick Barasa
Common Bean (Phaseolus vulgaris L.) is some significant vegetable crop rich in
protein, carbohydrates, and Vitamin B complex, used as a source of protein or cooked as
a vegetable. It is associated with improving capillary resistance, inhibiting inflammation
and act as an anticancer. Common beans face a major challenge of pests and disease
hence lowering production yield. Some of the diseases are root rot triggered by
Rhizoctonia solani and Fusarium solani. Application of chemical products and cultural
practices are not effective in managing these diseases. Therefore, a sustainable,
affordable, and effective control method needs to be devised to minimize the effect of
bacterial plant diseases on the quality and quantity of bean yield. The use of bio-control
agents is hypothetically self-sustaining, provides a non-target approach, spreads on its
own, and is environmentally friendly. This study evaluated the biocontrol potential of
extromophilic bacterial isolates from Lakes Bogoria and Magadi for against Fusarium
solani and Rhizoctonia solani pathogens in beans. To explore biocontrol frontiers, a total
of 110 bacteria were isolated from water, sediments, and soil of both lakes. Their
antifungal properties were determined by co-culturing analyzed using SAS (ANONA)
were; 17 (34.7%) isolates from L. Bogoria and 25 (41%) isolates from L. Magadi had
varying mycelium inhibition rate for both Fusarium solani and Rhizoctonia solani. The
characterization of the bioactive isolates revealed that 84.2% were Gram-positive and
15.8% were Gram-negative. The graphical analysis of bacterial isolates grew well at pH
7.0 and 8.5 though there was recorded growth in pH 5.0 and 10.0. In terms of
temperature, the optimum temperature recorded was 30-35ºC with optimum salinity of
0-0.5M NaCl. The bioactive isolates were assayed for their ability to produce secondary
metabolites whereby; most of the isolates produced phosphatase, pectinase, chitinase,
protease, Indole-3-acetic acid and Hydrogen Cyanide making them potential biocontrol
agents. Analysis of the partial sequence using BLASTn indicated 84.2% of the isolates
were affiliated to Bacillus spp and 15.8% were affiliated to members of
Gammaproteobacterial. Isolates B7, B11, B20, B21, B26, B29, B30, B32, B38, B39,
M9, M10, M16, M47, M50 and M60 clustered with Bacillus at 98.71-100% similarity
index. Isolates B12, B17 and B19 clustered to Gammaproteobacterial with 99.59-100%
similarity index. In assessment for the selected isolates in greenhouse experiment, seed
bio-priming showed significant change in terms of root mortality, germination rate, plant
height, plant biomass, chlorophyll content, Phenylalanine ammonia-lyase, Polyphenol
oxidase, Peroxidase and phenolic content compared to pathogen inoculated controls. In
conclusion, lakes Bogoria and Magadi harbors beneficial microbes that can be used as
biocontrol agents against Fusarium solani and Rhizoctonia solani.
Master of Science in Biotechnology
2024-02-02T00:00:00ZComparative Genomics and Transcriptomics of Heat Stress in Chicken and Guineafowl Populations from Selected Countries in Africa, Asia, and Europe
http://localhost/xmlui/handle/123456789/6214
Comparative Genomics and Transcriptomics of Heat Stress in Chicken and Guineafowl Populations from Selected Countries in Africa, Asia, and Europe
Kennedy, Grace Moraa
Poultry farming is a crucial component of the global agriculture industry, providing a significant source of protein and economic livelihoods to millions of people worldwide. However, climate change has led to an increase in extreme weather conditions, including rising temperatures, which can negatively impact poultry production. Heat stress, a physiological response to high temperatures, has been identified as a major challenge affecting poultry health and performance, leading to reduced growth rates, decreased egg production, and increased mortality rates. Understanding the genetic and molecular mechanisms underlying heat stress response in different poultry breeds is essential for developing effective strategies to mitigate its impact on poultry farming.
This study aimed to investigate the comparative genomics and transcriptomics of heat stress in chicken and guineafowls from selected countries in Africa, Asia, and Europe. Chicken (Gallus gallus domesticus) and guineafowls (Numida meleagris) are two important poultry breeds widely raised for their meat and egg production, as well as for their cultural significance in various regions of the world. By comparing the genetic and molecular responses to heat stress in these two poultry species from different geographic locations, this study sought to identify candidate genes, and molecular pathways that are associated with heat stress tolerance. This study utilized the “omics” techniques (genomics and transcriptomics), to investigate the signatures of selection for heat stress in chicken, and guineafowls. Three methods: Fixation index (FST), Integrate Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XP-EHH) were used for the detection of signatures of selection for heat stress. Blood samples from 20 chicken were obtained for whole genome sequencing from Lamu, Kilifi, Mombasa, and Kwale. An additional 14 chicken whole genome sequences were downloaded from the NCBI SRA archive for comparative genomics. For the guineafowls, 16 blood samples from Laikipia, Lamu, Kilifi, and Taita Taveta were obtained for whole genome sequence analysis. An additional 56 guineafowl whole genome sequences were downloaded from the NCBI SRA archive. Through the signatures of selection methods, several candidate genes such as CNBP, COL1A1, YWHAE, PPARG, SREBF1, ATP6V0 and LRRC8A ATP2A2, TBXAS1, PER2, BOK, and RAF1 were selected in the chicken genomes. These candidate genes were subjected to annotation and several pathways including response to oxidative stress, localization, metabolic process, cellular process, developmental process, response to stimuli, signaling, and homeostatic process, that play a role in heat stress were identified. In the guineafowl genomes, some of the significant candidate genes that were selected included the MAPK1, SLC27A4, ATP5MF, PPARG, SREBF1, ATP6V0 and LRRC8A BRAF, CRYGN, and ANGPT2. These genes were annotated and found to play a role in several significant pathways like localization, metabolic process, positive regulation of the biological process, cellular process, signaling, and response to stimuli. Some pathways that were significant for both the chicken and guineafowl genomes included the metabolic process, localization, signaling, cellular process, and response to stimuli. Some of the candidate genes that were selected for both chicken and guineafowls include the PPARG, SREBF1, ATP6V0 and LRRC8A. RNA sequencing was used to profile the kidney tissue of 13 chicken and 13 guineafowls from Lamu and Mombasa Counties. At a false discovery rate (FDR) < 0.05, 278 DEGs were identified in chicken kidney tissue samples from these regions. Among these, 129 were upregulated (e.g., CD36, ANGPTL4, PLIN1, GLRA3, GABRA4) and 149 were downregulated (e.g., GABRA2, C3, GHRHR, GHSR, GRIA3, ACSL6, VTN). In guineafowl kidney tissue samples, a total of 349 DEGs were identified, among these, 190 were upregulated (e.g., SDR16C5, RETSAT, ALDH1A1, BCO1, ACSM3, AKR1D1, MDH2, CYP24A1) and 159 were downregulated (e.g., PAH, MAPK12, GRM1, RAG1, CARNS1, CNDP1, FTCD, HTR2A, MYLK2, AOX1). Gene Ontology (GO) enrichment analysis revealed that in the chicken samples, these genes were significantly enriched for metabolic and developmental processes, whereas in guineafowls, they were prominently enriched for metabolic biological processes. Similarly, when conducting KEGG pathway analysis on the DEGs from chicken kidney tissue samples, it was observed that pathways related to neuroactive ligand-receptor interaction, the PPAR signaling pathway, the Adipocytokine signaling pathway, and ECM-receptor interaction were differentially enriched. In guineafowls, the KEGG pathway analysis of DEGs indicated differential enrichment in metabolic pathways, neuroactive ligand-receptor interaction, the calcium signaling pathway, and the FoxO signaling pathway. The study's discoveries have offered fresh perspectives on the intricate relationship between genetic and environmental elements in poultry's response to heat stress. The identification and selection of genes associated with heat tolerance enhances our comprehension of the molecular mechanisms implicated in heat stress among poultry. Consequently, this provides a promising and sustainable approach for breeding heat-tolerant poultry. This approach effectively addresses the challenges posed by heat stress, particularly in the context of climate change, and ultimately contributes to ensuring food security.
Doctor of Philosophy in Biotechnology
2023-11-30T00:00:00ZPhenotypic Features and Genetic Characterization of Galla Goats from Selected Regions in Kenya Using Mitochondrial DNA and HSP70 Gene Polymorphisms
http://localhost/xmlui/handle/123456789/6202
Phenotypic Features and Genetic Characterization of Galla Goats from Selected Regions in Kenya Using Mitochondrial DNA and HSP70 Gene Polymorphisms
Masila, Ednah Mutindi
Galla goats are mainly found in arid and semi-arid regions of Kenya, which are mostly affected by climate change. Indiscriminate crossbreeding has led to the erosion of genetic pool of indigenous goats, which are hardy and better adapted to the local climatic conditions including hot environment as compared to exotic goat breeds. Hot climatic conditions result in heat stress that suppresses productivity and reproducibility. Thermotolerance is therefore an important trait to be considered during breeding. Breeding programmes need to conserve and incorporate desirable traits from the indigenous goats. For this to be accomplished, there must be understanding of the genetic diversity of the indigenous goat population. This study reports on the adaptation and diversity of this indigenous genetic resource. Specifically, the study reports on phenotypes of heat tolerance, the genetic diversity and polymorphisms in the Heat Shock Protein 70 (HSP70) gene among the Galla goats’ population in Garissa, Isiolo and Tana River Counties. Phenotypic data was collected from 149 Galla goats by the use of a checklist. Blood samples were collected for molecular characterization. Both qualitative and quantitative data for the phenotypic features was carried out. For molecular work, bioinformatics and biostatistics analyses were carried out to infer genetic diversity of the 90 Galla goat samples from all the populations. Analysis of variance for the phenotypic features was determined in response to environmental temperature. Horn and beard presence showed a significant relationship to the environmental temperature. For molecular analysis, a fragment of the D-loop region of the Mitochondrial DNA and that of heat shock protein 70 gene for 96 samples were amplified using convectional Polymerase chain reaction, purified and Sanger sequencing done. A total of 68 mtDNA haplotypes were discovered. Phylogenetic relationship analysis for the haplotypes clustered them into 3 goat haplogroups (haplogroup A, D and G). Analysis of molecular variance showed a huge diversity within populations at 94.39%. For HSP70, 21 haplotypes were discovered. Phylogenetic analysis showed that the haplotypes cluster with sequences from Iraq, China and India. The genetic variation using AMOVA was greatest within populations among groups at 64.66% and showed a high FIS index. This information lays the foundation for informed and controlled genetic breeding for heat tolerant goats and conservation of the Galla goats’ genetic resources. Therefore, the study provides information on the huge diversity
Master of Science in Biotechnology
2023-11-20T00:00:00ZGenetic Background and Signatures of Selection Assessment in Wild African Harlequin and Domestic Japanese Quails Using a Genomic and Transcriptomic Approach
http://localhost/xmlui/handle/123456789/6193
Genetic Background and Signatures of Selection Assessment in Wild African Harlequin and Domestic Japanese Quails Using a Genomic and Transcriptomic Approach
Ogada, Stephen Omondi
Quails are increasingly becoming a vital complementary protein source, contributing to food security. In Kenya, the indiscriminate and destructive harvesting of wild African harlequin quails using traditional methods has been ongoing for generations. Yet, their genetic diversity and evolutionary history are largely unknown, thus posing a threat to extinction and genetic diversity. In this study, the genetic variation and demographic history of captured wild African harlequin quails (n = 78) were determined using mitochondrial DNA (mtDNA) and genotyping by sequencing (GBS) data. Selection signatures were also examined using composite likelihood ratio (CLR) and integrated haplotype score (iHS) tests in comparison to domestic Japanese quails (n = 22). Domestic Japanese quail transcriptome data (n = 6) was also examined. The genetic variation in wild African harlequin quails was predominantly among individuals rather than populations. Demographic analyses indicated a signal of rapid expansion. The estimated time since population expansion was 150 to 350 thousand years ago (kya), corresponding to around the Pliocene–Pleistocene boundary. A gradual decline in their effective population size was also observed, which raised concerns about their conservation status. 352 and 424 candidate genes were detected in the wild African harlequin quail and domestic Japanese quail through the CLR test, respectively, whereas 150 and 457 candidate genes were identified through iHS analysis. Candidate genes under positive selection identified in the wild African harlequin quail were associated with important traits such as immune response (MAPK13, CREB1, ITGB3, and PPP1CA) and morphological traits (WNT5A, GRIA1, and ALK), whereas, in domestic Japanese quail, production-related genes such as VIPR2, DYNLL2, PRF1, COL11A1, and GNA12 were identified. RNA-Seq analysis revealed differentially expressed genes associated with production processes such as spermatogenesis and muscle structure development. This is the first study on the wild African harlequin quails to provide information useful in biodiversity conservation and proper utilization of its genetic resources.
Doctor of Philosophy in Biotechnology
2023-11-17T00:00:00Z