Estimation of genetic and demographic parameters of extensively raised chicken populations using genome-wide single nucleotides polymorphism (SNP) data.
Year: 2015
Type: dissertation
Abstract: Village chicken populations are raised under a farming system that faces a number of challenges such as \nsmall flock size, lack of animal performance and pedigree records, lack of proper husbandry and poorly \ndefined and structured mating systems all of which can negatively influence the genetic structure of the \npopulations. Understanding of the evolutionary history, demographic structure, inbreeding levels and risk \nof a population to extinction is important in facilitating genetic improvement programs while maintaining \nbiodiversity of extensively raised chicken populations. Linkage disequilibrium (LD) is an important \nsource of information about historical events of recombination in a population and together with an \nunderstanding of the haplotype structure can provide valuable guidelines for breed improvement. This \nstudy was undertaken to investigate the existing LD level, inbreeding levels, effective population size and \nhaplotype structure of extensively raised chicken populations from Southern Africa. A total of 312 village \nchickens from Malawi (n = 30, from one ecotype), South Africa, (n = 146, from three different ecotypes) \nand Zimbabwe (n = 135, from three different ecotypes) were genotyped using the Illumina chicken \niSelect SNP60K bead chip. LD was calculated for each population from a total of 43,175 SNP after \npruning for minor allele frequency (MAF) <0.05, genotyping call rate of <0.95, and deviation from Hardy \nWeinberg Equilibrium (HWE) p <0.001 and missing genotypes of more than 5%. Linkage disequilibrium \naveraged 0.41±0.006 and was observed to extend up to a marker distance of 100 kb. From the LD, \neffective population size was estimated that indicated reduced size of the breeding population over the \npast 40 generations to less than 20 individuals. Haplo-block structure analysis resulted in a total of 649, \n2104 and 2442 blocks from Malawi, South Africa and Zimbabwe, respectively. Most of the observed \nblocks were less than 20 kb with a few that were more than 500 kb. Haplo-block genome coverage was 39 \nMbp, 64.4 Mbp and 54.5 Mbp for Malawi, South Africa, and Zimbabwe, respectively. Large haplo-blocks \non chromosome 8 spanned QTL regions associated mostly with body composition traits. The LD pattern \nwas consistent with low effective population sizes and loss of heterozygosity in the village chicken \npopulations. Potentially useful haplo-blocks spanning regions of known QTLs should be targeted for further analysis and identification of genes conferring optimal production performance of village chickens \nunder harsh and marginalized production systems. Overall, the study provides baseline information on the \nutility of genome wide SNP data in studying extensively raised village chicken populations.
Author: Khulekani Sedwell Khanyile
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W1151750582