Browsing by Author "Kebede Adebabay"

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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