<p>Stochastic simulation was used to test the hypothesis that optimum-contribution selection with
genomic relationships using marker loci with low minor allele frequency (MAF) below a predefined
threshold (referred as TGOCS) to control inbreeding maintained more genetic variation than
pedigree relationships (POCS) at the same rate of true genetic gain (∆<i>G</i>_<i>true</i>). Criteria to measure genetic variation were the number of segregating QTL loci (quantitative trait loci) and the average number of founder alleles per locus. Marker alleles having a MAF below 0.025 were used in forming
the genomic relationships in TGOCS strategy. For centering in establishing genomic relationships,
when the allele frequency of marker loci with low MAF set to 0.5 the TGOCS strategy maintained
66% fewer founder alleles than POCS and there were 30% fewer QTL segregating. This TGOCS
strategy maintained 61% fewer founder alleles than GOCS and 28% fewer segregating QTL loci.
When the allele frequency of marker loci with low MAF was set to observed allele frequency these
figures were 8%, 2%, 5% and 2%, respectively. Using marker loci with low MAF in the TGOCS
strategy was inferior to both GOCS and POCS. Both TGOCS and GOCS were affected by the same
constraint that is LD (linkage disequilibrium) between markers and QTL. Therefore, POCS is a more
efficient method to maintain genetic variation in the population until a better way to use genomic
information in optimum-contribution selection is identified.</p>