Whole Genome Based Characterization Of Indigenous Chicken Populations In Ethiopia

WHOLE GENOME BASED CHARACTERIZATION OF INDIGENOUS CHICKENrnPOPULATIONS IN ETHIOPIArnAdebabay KebedernAddis Ababa University, 2018rnIndigenous chicken are locally adapted to environmental challenges and provide subsistence tornmillions of farmers in Africa. Their productivity remains low compared to exotic chicken strains.rnEfforts are being made to combine the local adaptation of indigenous chicken with productivityrntraits of exotic chicken. Understanding the link between diversity and adaptability is opening therndoor to marker-assisted breed improvement programs. Selective breeding for genetic improvementrnis expected to leave distinctive selection signatures within genomes. The identification of selectionrnsignatures can help to elucidate the mechanisms of selection and accelerate genetic improvement.rnEthiopia has several chicken ecotypes which evolved in different agro-ecologies. This study aimsrnto characterize the genomic diversity of indigenous chicken populations from Ethiopia. The firstrnpart of this study addresses the characterization of the LEI0258 microsatellite loci in the MHCrnregion with previous study supporting links of the locus with infectious diseasesrnresistance/susceptibility in commercial chicken. Here, we report diversity of LEI0258 in 236rnchicken from 24 Ethiopian indigenous chicken populations from different agro-ecological zonesrnusing gel electrophoresis and sequencing.rnVIIrnThe number of alleles, allele frequency, and heterozygosity levels were used to measure diversityrnwithin populations whilst the Wright’s fixation indices were used to analyze the level of populationrnstructuring. Twenty-nine LEI0258 allele sizes were observed using capillary electrophoresis.rnAllele sizes ranged from 185 to 569 bp with no significant difference in allele frequencies betweenrnpopulations (P < 0.05). Allele frequencies were in Hardy and Weinberg Equilibrium in allrnpopulation except Dara chicken (P < 0.05). Excluding the tandemly repeated motif, the number ofrnmonomorphic and polymorphic sites are 412 and 35, respectively. Number of point mutation andrnindels are 33 and 17, respectively. The number of R12 CTTTCCTTCTTT repeats ranged from 2rnto 18, while R13 was found monomorphic with a single motif CTATGTCTTCTTT. Sequencesrnrelationships reveal two distinct groups of alleles. The high diversity at microsatellite LEI0258 atrnEthiopian indigenous village chicken populations supports the importance of the MHC region inrnrelation to the disease challenges diversity faced by smallholder poultry production within andrnacross Ethiopian agro-ecologies. We recommend that breed improvement programs ensure thernmaintenance of this diversity by selecting breeding stock as diverse as possible at the LEI0258rnlocus. The part of the thesis reports the genomic diversity of Ethiopian indigenous chicken throughrndiscovery and characterization of 21 million SNPs (72% novel) from 27 indigenous chickenrnpopulations (n = 260 birds) using whole genome sequencing. In each population, around 10 to 12rnmillion SNPs are present, of which, 40-47% are a heterozygote. The mean SNP density across allrnpopulation is 21 (±5) per kb, although it is much lower on the sex chromosomes (W = 0.4, Z = 11).rnPrincipal component and admixture analyses suggest the presence of four ancestral gene poolsrnacross the populations. Over 46% of the SNPs are located within genes, of which exonic andrnintronic SNPs account for 1.59% and 43.94%, respectively; while 31% of the exonic SNPs arernnon-synonymous. A large proportion of SNPs has low alternative allele frequency (AAF < 10%),rnVIIIrnalthough this proportion is higher for potentially harmful categories like missense and stoprngain/loss (> 60%) than neutral ones (40-45%). Genes with deleterious missense variants arernincluded within several important biological pathways like innate immunity. Our results confirmrnthe existence of significant genomic diversity in indigenous chicken populations of Ethiopia, withrnmost of the variants previously undescribed in commercial breeds. The last part of the thesisrnassesses the footprints of candidate signatures of positive selection from whole genome autosomalrnsequences, comprising 14,857,039 SNPs, in Improved Horro, Local Horro, Hugub, Arabo andrnJarso chicken populations of Ethiopia. We identified selection signals in 20 Kb windows size withrn10 Kb sliding steps based on estimators of pooled heterozygosity (Hp and F-statistics (Fst) withinrnand between those populations. Selective sweep analysis using Hp and Fst methods identifiedrngenomic regions associated with production and reproduction traits. A total of 595 candidate genesrnshowed high evidence of positive selection in indigenous chicken populations. These genes werernrelated to traits such as growth and egg production. Gene ontology analysis displayed severalrnbiological processes and KEGG pathways involved in oestrogen biosynthetic and nervous systemrndevelopment processes, calcium signaling and biosynthesis of unsaturated fatty acids. The regionsrnidentified in this study are expected to provide a genome landmark to enhance the ongoing breedrnimprovement operations in improved Horro and other four chicken populations. In general, thisrnstudy revealed the huge genomic diversity and taped the genomic regions under strong selectionrnin indigenous chicken populations of Ethiopia

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