GENETIC EVALUATION OF IMMUNOGENETIC VARIATIONS, MUTATIONAL LOAD AND EFFECTIVE POPULATION SIZE IN INDIGENOUS CHICKEN

Abstract

Modern poultry production houses large flock of birds at high stocking density thus increasing risk of diseases, and disease spreading. Control of diseases through improved management, vaccination and prophylaxis to a large extend increases costs and affects animal welfare negatively. One promising strategy to increase general disease resistance is by selectively breeding for immune traits using antibody titers against particular pathogen. The study aimed to examine the population structure of 150 Indigenous chickens (IC) at genome level. Secondly, it aimed to identify the impacts of deleterious mutations with relation to disease resistance and undertaking functional characterization of deleterious variants. Lastly, the study aimed to estimate Linkage Disequilibrium -based effective population size, rate and levels of inbreeding. Objective one addresses phenotypic and genetic clustering. Phenotypic clustering based on body weight and antibody titers revealed two significantly (P < 0.001) distinct groups of IC. Cluster with high mean in bodyweight and low mean in titers and vice versa. Genetic characterization at whole genome level grouped the IC into two groups providing a deeper understanding of the structure of IC population to supplement the use of phenotypes. At chromosome 16 level grouped IC as a single population. Part two of the study identified deleterious alleles and carry out gene ontology analysis. Using whole genome data, 182 deleterious genes were identified, of which, six were related to immune traits. The six genes included; FANCA, RBBP5, CRB1, RUFY3, FBXO38, and PDE3A. Results revealed numerous biological and KEGG processes that are involved in immune and disease resistance traits. Analysis of the ontology of the ENSGALG00000046739 candidate gene that was identified in chromosome 16 (MHC region) was linked with missense variants associated with the regulation of RNA polymerase II transcription. The third part of the study confirmed that effective population size of IC is decreasing whereas the inbreeding rate is increasing as the number of generations increase. The rate and levels of inbreeding seem to be in line with low effective population size thus leading to loss of diversity in IC. The findings in this thesis provide insight understanding on the immuno-genetic variations, genomic diversity. The knowledge generated in this study is useful for the development of a sustainable IC breeding programme for enhanced IC productivity and improve disease resistance. Consequently, reducing the need for vaccine and antibiotic treatments, thereby reducing drug residues in IC products.