Estimation of the Effective Population Size in Sheep Based on Recombination Rate By the LD Method

Effective population size (Ne) is a key parameter in population genetics and is widely applied in determining the rate of genetic drift and loss of genetic variability. It is crucial to consider in animal breeding, selection and conservation. The linkage disequilibrium (LD) method performs better in the Ne estimation when genome-wide SNPs applied. Ne estimated by the LD method is also related to the recombination rate that was not taken into account in most studies. Genome-wide SNP data of three commercial sheep breeds, including Texel, Merino and Suffolk, were downloaded from the ISGC database (http://www.sheephapmap.org/). Chromosome-specific recombination rates were estimated for all autosomes from estimated LD between SNP pairs <500 kb apart and the known map length of chromosome. For each chromosome the pairwise r² was calculated for all pairs of SNP in sliding windows of 500 kb with a 250 kb overlap. The average recombination rate for each window was estimated from the average LD within that window by fitting the model of relationship between recombination rate and r². The average recombination rates were scaled over the entire chromosome and adjusted to the known map length of the corresponding chromosome before applying for the Ne estimation. We found that the decay in LD over distance between SNPs within sheep populations is consistent with the recent population decrease. However, our estimated Ne for these sheep populations were about 40% higher than the previously report, possibly because we used the estimated recombination rate, not the theoretical value of 100 Mb = 1 Morgan.