Genomic Diversity of Livestock Conserved Population under Different Initial Frequencies of SNP Alleles

Purpose To reveal the genomic diversity of livestock conserved population under different initial frequencies (IFs) of SNP alleles.

Methods A continuous 50-generation breeding by random selection and mating in a closed population with a constant size was simulated by Monte Carlo method, assumed that there were 1 000 evenly spaced SNPs on a couple of autosomes with a genetic length of 100 cM. The minor allele frequency (MAF) and its distribution, genomic heterozygosity (H_G), genomic observed homozygosity (HOM_obs), and the number of allele loss of each generation were analyzed under three different IFs (0.1, 0.3 and 0.5).

Results Regardless of the IFs, with the increment of breeding generations, the average MAF and H_G within the population decreased continuously, while HOM_obs increased gradually, and the number of SNPs with MAFs in the 0, 0.1 interval as well as the number of allele losses increased constantly. Compared to lower IFs, when the IF of SNP allele was 0.5, the same generation had the highest average MAF and H_G, lowest HOM_obs, the minimum number of SNPs with MAFs in the 0, 0.1 interval, and the minimum number of allele losses.

Conclusion Too low or too high IF will lead to a decrease in population H_G and an increase in the probability of allele loss or fixation. However, when the IF is close to 0.5, it can be effectively maintain a higher H_G and reduce the risk of gene loss or fixation, which is conducive to the maintenance of genetic diversity in the population.