Accuracy of Measuring Population Genetic Diversity by Using Genomic Inbreeding Coefficient Based on SNP

PurposeTo investigate the accuracy of measuring population genetic diversity by using genomic inbreeding coefficient based on SNP markers (FSNP).Method Continuous 50-generation breeding in a closed population was simulated and assumed that there were 1 000 evenly spaced SNPs on a couple of autosomes which genetic length was 100 cM. The effects of population size, sire ratio, number of SNPs used to compute the FSNP (NSNP) and initial allelic frequency of each SNP (p) on the accuracy of measuring population genetic diversity by using FSNP were determined, which considered the inbreeding coefficient based on pedigree (Fped) as a control, and the correlation coefficients between FSNP, Fped and genomic observed homozygosity (HOMobs), rSNP and rped were set as the indexes of measuring the accuracy.Result The accuracy of measuring the population genetic diversity by using FSNP was higher in general, which with less influence of population size and sex ratio, and would not decrease with the increase of generations, when compared to using Fped. The accuracy of measuring the population genetic diversity by using FSNP was higher, when NSNP was larger and P was closer to 0.5.Conclusion In practice, it could be ensured that rSNP was higher than rped, and FSNP could be used to implement a timely and dynamic monitoring of the genetic diversity effectively, when the NSNP was equal or more than 20 percent of the number of whole genomic SNP (NSNP ≥ 200 in present experiment) and covered all the chromosomes; it would help to increase the accuracy of monitoring the genetic diversity and preserve the genetic variation within population that controlling the p value at medium level.