Whole Genome Based Characterization of Indigenous Chicken Populations in Ethiopia
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Date
2018-12-04
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Addis Ababa University
Abstract
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
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Keywords
Chicken, Diversity, Ethiopia, Genomic, Indigenous, Population