Genetics and immunity of indigenous chicken in Kenya

Abstract

Indigenous chicken (IC) are the most common poultry in developing world, found in almost every homestead and constitute over 89% of total chicken populations in Kenya. Contributions of IC to economy include source of income, food security and nutrition. The IC productivity is compromised by diseases that contribute to over 50% of economic losses. This study was undertaken to contribute to improved productivity of indigenous chicken (IC) of Kenya through sustainable breeding for disease tolerance and enhanced immunity by searching for appropriate probiotics. The specific objectives of the study were: 1) to determine the sources of variation of Natural antibodies (Nabs) (IgG, IgM and IgA) binding keyhole limpet hemocyanin (KLH) amongst the IC, 2) to estimate the repeatability and variation of the ELISA assay (Nabs) with time within the IC, 3) to assess the diversity and population structure of IC using LEI0258 Marker, 4) to determine the effects of probiotic on IgM titre levels on IC 5) to determine composition and diversity of microbial populations in the chickens and 6) to identify potential bacterial species for use as probiotics for enhanced immunity. Blood was drawn from the wing vein of IC and plasma separated. Natural antibodies (IgM, IgA, IgG) titre values binding KLH were determined by indirect ELISA. One way ANOVA and Mixed model analyses were used to determine sources of Nab titre variation and estimate repeatability parameter. The IC genetic diversity and population structure was achieved by DNA extraction from blood and genotyping using the MHC linked LEI0258 marker and sequencing of subset of representative alleles. Polymorphism and population genetic parameters were determined using bioinformatic tools. Effect of commercial probiotics on IgM titre values was done by comparing treatment and control means using one factor ANOVA. Metagenomics employed usage of DNA from fecal samples and next generation sequencing. Qiime pipeline was used to call operational taxonomic units OTU) and for alpha and beta diversity analysis of microbial composition. The microbiome abundance between immune competency levels was compared using one factor ANOVA. The results showed presence and variation of Nabs amongst the IC. The variance estimate for chicken components were high and significant for IgM (p=0.003), IgG (p=0.0001) and IgA (p=0.0001).The repeatability of the ELISA assay to Nabs was high in all the immunoglobulin isotypes. Repeatability were 0.68, 0.99 and 0.99 for IgM, IgG and IgA respectively. The LEI0258 locus showed high diversity and presence of four gene pools among the IC. The locus observed high diversity as revealed by the average Shannon's information index of 2.768. The vii

mean overall observed heterozygosity and Polymorphic information Content (PIC) was 0.844 and 0.932 respectively for the total population sampled. The central population had the highest observed heterozygosity (0.878) while coastal had the lowest (0.792). Use of commercial probiotic did not have significant effect on IgM titre values of IC. The metagenomics revealed extensive microbial diversity. Candidate bacterial species differed significantly for immune response level. The study recommended routine management practices (e.g. vaccination) for disease control and evaluation of candidate bacterial species for enhanced immunity. Using genetic approaches to improve IC disease tolerance and the proposed bacterial candidates for probiotic will improve animal welfare, ensure friendly environment, has sustainable improvements and address consumer concerns about drug use and reduce the risk of food poisoning.