The Extent and Distribution of Linkage Disequilibrium in Extensively Raised Chicken Populations of Southern Africa

The amount of linkage disequilibrium (LD) is an important source of information about historical events of recombination and allows inferences about genetic diversity and genomic regions that have undergone selection. Linkage disequilibrium is equally important in studying effective population size and rate of inbreeding particularly in extensively raised and wild animal populations where pedigree records are scarce. The objective of this study was to investigate LD in village chicken populations of Southern Africa. These chickens are raised under scavenging systems of production characterized by uncontrolled breeding and frequent population bottlenecks due to disease outbreaks and fluctuations in feed supplies. DNA samples from 312 extensively raised chickens from South Africa, Malawi and Zimbabwe were genotyped using the Illumina iSelect chicken SNP60K BeadChip. A panel of 43,157 out of the total 57,636 (74.8%) SNPs was used in the final analysis after screening for those that had a minor allele frequency of less than 5%, were out of Hardy-Weinberg equilibrium (P<0.01) and had a call rate of less that 95%. Results indicated that LD averaged between 0.45 and 0.58 for SNPs that had a pairwise distance of less than 20 kb. LD dropped to 0.34 for SNPs between 20 and 100 kb after which it remained constant. LD was further analyzed for its decay over marker distance and differences between populations from different geographic locations. Results are discussed in terms of historical changes in effective population size and resultant recombination rates. The utility of the iSelect chicken SNP60K beadchip in investigating free-range chicken population genetics is demonstrated.