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Haplo-block structure of Southern African village chicken populations
A total of 290 village chickens from Malawi (n=30), South Africa, (n=132) and Zimbabwe (n=128) were analysed for haploblock structure and diversity using the Illumina iselect chicken SNP60K bead chip data. Results showed 649, 2104, and 2442 haploblocks for the three populations, respectively. More haploblocks were observed in macro-chromosomes (range 118 to 402) compared to micro-chromosome (range from 13 to 125). The median block lengths were 13.6 Kb, 10.8 Kb and 9.7 Kb whilst genome coverage was 39 Mbp, 64.4 Mbp and 54.5 Mbp for Malawi, South Africa and Zimbabwe, respectively. Majority of the haploblocks were smaller than 25Kb and only five blocks were bigger than 2 Mbp. Significant haploblock sharing was observed between populations. Results imply transferability of genetic parameters between populations and suggest that unique haploblocks could be emanating from isolated evolutionary events specific to the agro-ecological zones of the sampled countries.
Keywords:
chickens
haplotype
diversity
