Weighted GP maintained genetic variance in later generations by sacrificing initial genetic gain, and therefore increased the selection limit.
Irrespective of the number of QTL simulated, BL is superior to RR in maintaining genetic variance and therefore results in higher long-term genetic gain.
Moreover, even when epistatic effects exist, this does not reduce the importance of maintaining genetic variance and rare favourable alleles by weighting methods.
Balancing selection refers to any type of selection that maintains genetic variance in a population, such as frequency-dependent selection, temporally or spatially fluctuating selection, and overdominance.
Although a QTL with a small effect and/or with a low frequency of the favourable allele may not be important for short-term gain, it potentially contributes more to long-term genetic gain by maintaining genetic variance over time.
To achieve this, we first monitored (i) the fixation and loss of favourable alleles, (ii) the maintained genetic variance, and (iii) the accuracy of selection when employing genomic or conventional selection methods.
This study shows that without weighting methods, BL is superior to RR in maintaining genetic variance and controlling inbreeding, and therefore can result in higher long-term genetic gain, regardless of the number of QTL affecting the trait and length of the planning horizon.
Finally, to understand the mechanisms leading to GS success or failure, population variables were analyzed including the maintained genetic variance, realized accuracies, LD and distance between QTL and markers remaining polymorphic, inbreeding over generations and the fixation of QTL and marker alleles.
This management activity therefore potentially contributes to maintain genetic diversity by generating gene flow among different rearing sites as well as reducing genetic drift, possibly resulting in maintained additive variance.
