Estimation of genetic and demographic parameters of extensively raised chicken populations using genome-wide single nucleotides polymorphism (SNP) data.
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Date
2015
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Abstract
Village chicken populations are raised under a farming system that faces a number of challenges such as
small flock size, lack of animal performance and pedigree records, lack of proper husbandry and poorly
defined and structured mating systems all of which can negatively influence the genetic structure of the
populations. Understanding of the evolutionary history, demographic structure, inbreeding levels and risk
of a population to extinction is important in facilitating genetic improvement programs while maintaining
biodiversity of extensively raised chicken populations. Linkage disequilibrium (LD) is an important
source of information about historical events of recombination in a population and together with an
understanding of the haplotype structure can provide valuable guidelines for breed improvement. This
study was undertaken to investigate the existing LD level, inbreeding levels, effective population size and
haplotype structure of extensively raised chicken populations from Southern Africa. A total of 312 village
chickens from Malawi (n = 30, from one ecotype), South Africa, (n = 146, from three different ecotypes)
and Zimbabwe (n = 135, from three different ecotypes) were genotyped using the Illumina chicken
iSelect SNP60K bead chip. LD was calculated for each population from a total of 43,175 SNP after
pruning for minor allele frequency (MAF) <0.05, genotyping call rate of <0.95, and deviation from Hardy
Weinberg Equilibrium (HWE) p <0.001 and missing genotypes of more than 5%. Linkage disequilibrium
averaged 0.41±0.006 and was observed to extend up to a marker distance of 100 kb. From the LD,
effective population size was estimated that indicated reduced size of the breeding population over the
past 40 generations to less than 20 individuals. Haplo-block structure analysis resulted in a total of 649,
2104 and 2442 blocks from Malawi, South Africa and Zimbabwe, respectively. Most of the observed
blocks were less than 20 kb with a few that were more than 500 kb. Haplo-block genome coverage was 39
Mbp, 64.4 Mbp and 54.5 Mbp for Malawi, South Africa, and Zimbabwe, respectively. Large haplo-blocks
on chromosome 8 spanned QTL regions associated mostly with body composition traits. The LD pattern
was consistent with low effective population sizes and loss of heterozygosity in the village chicken
populations. 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
under harsh and marginalized production systems. Overall, the study provides baseline information on the
utility of genome wide SNP data in studying extensively raised village chicken populations.
Description
M. Sc. University of KwaZulu-Natal, Pietermaritzburg 2015.
Keywords
Chickens -- Breeding., Chickens -- Genetics., Farms, Small -- Africa., Theses -- Genetics.