Abstract
Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years that ought to be characterized and utilized. Surveys that can reveal a population's genetic structure and provide an insight into its demographic history will give valuable information that can be used to manage and conserve important indigenous animal genetic resources. This study reports population diversity and structure, linkage disequilibrium and effective population sizes of Southern African village chickens and conservation flocks from South Africa. DNA samples from 312 chickens from South African village and conservation flocks (n = 146), Malawi (n = 30) and Zimbabwe (n = 136) were genotyped using the Illumina iSelect chicken SNP60K BeadChip. Population genetic structure analysis distinguished the four conservation flocks from the village chicken populations. Of the four flocks, the Ovambo clustered closer to the village chickens particularly those sampled from South Africa. Clustering of the village chickens followed a geographic gradient whereby South African chickens were closer to those from Zimbabwe than to chickens from Malawi. Different conservation flocks seemed to have maintained different components of the ancestral genomes with a higher proportion of village chicken diversity found in the Ovambo population. Overall population LD averaged over chromosomes ranged from 0.03 ± 0.07 to 0.58 ± 0.41 and averaged 0.15 ± 0.16. Higher LD, ranging from 0.29 to 0.36, was observed between SNP markers that were less than 10 kb apart in the conservation flocks. LD in the conservation flocks steadily decreased to 0.15 (PK) and 0.24 (VD) at SNP marker interval of 500 kb. Genomewide LD decay in the village chickens from Malawi, Zimbabwe and South Africa followed a similar trend as the conservation flocks although the mean LD values for the investigated SNP intervals were lower. The results suggest low effective population sizes particularly in the conservation flocks. The utility and limitations of the iselect chicken SNP60K in village chicken populations is discussed.
Highlights
Extensively raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years, that could be useful in future for improvement in response to climate change and consumer demands (Delany, 2004)
SNP MARKER CHARACTERISTICS Minor allele frequency averaged 0.29 (Table 1) and over 8.5% of the SNPs on the Illumina iSelect chicken SNP60K panel had a minor allele frequency (MAF) of less than 0.05 (Supplementary Figure 1)
The proportion of SNPs used for further analysis was 51% for the whole population for estimation of population structure and was over 80% for the village chickens from Malawi, South Africa and Zimbabwe and ranged from 67 to 77% in the conservation flocks for the estimation of Linkage disequilibrium (LD)
Summary
Raised village chickens are considered a valuable source of biodiversity, with genetic variability developed over thousands of years, that could be useful in future for improvement in response to climate change and consumer demands (Delany, 2004). This diversity ought to be characterized, conserved and manipulated to suit production systems such as free-range organic farming. Its patterns are useful in understanding the levels of inbreeding (García-Gámez et al, 2012) the genetic background of animal populations (Porto-Neto et al, 2014) and assists in the fine mapping of genes and quantitative trait loci (QTL) of economically important traits (Wragg et al, 2012). LD will be of use in extensively raised chicken populations in smallholder www.frontiersin.org
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