DataSheet_3_Improving Short- and Long-Term Genetic Gain by Accounting for Within-Family Variance in Optimal Cross-Selection.pdf

The implementation of genomic selection in recurrent breeding programs raises the concern that a higher inbreeding rate could compromise the long-term genetic gain. An optimized mating strategy that maximizes the performance in progeny and maintains diversity for long-term genetic gain is therefore essential. The optimal cross-selection approach aims at identifying the optimal set of crosses that maximizes the expected genetic value in the progeny under a constraint on genetic diversity in the progeny. Optimal cross-selection usually does not account for within-family selection, i.e., the fact that only a selected fraction of each family is used as parents of the next generation. In this study, we consider within-family variance accounting for linkage disequilibrium between quantitative trait loci to predict the expected mean performance and the expected genetic diversity in the selected progeny of a set of crosses. These predictions rely on the usefulness criterion parental contribution (UCPC) method. We compared UCPC-based optimal cross-selection and the optimal cross-selection approach in a long-term simulated recurrent genomic selection breeding program considering overlapping generations. UCPC-based optimal cross-selection proved to be more efficient to convert the genetic diversity into short- and long-term genetic gains than optimal cross-selection. We also showed that, using the UCPC-based optimal cross-selection, the long-term genetic gain can be increased with only a limited reduction of the short-term commercial genetic gain.

在反复育种程序中实施基因组选择引发了一个担忧，即更高的近交率可能会损害长期遗传增益。因此，一种优化配种策略，旨在最大化后代的表现并维持多样性以实现长期遗传增益，显得尤为关键。最佳杂交选择方法旨在确定一组最佳的杂交方案，在后代遗传多样性受限的条件下，最大化预期遗传值。通常，最佳杂交选择并未考虑到家族内部的选拔，即仅使用每个家族中选定的部分作为下一代父母的现实。在本研究中，我们考虑了家族内部变异，并考虑到数量性状位点之间的连锁不平衡，以预测一组杂交选育后代中预期平均表现和预期遗传多样性。这些预测依赖于有用性标准亲本贡献（UCPC）方法。我们比较了基于UCPC的最佳杂交选择与在考虑重叠代际的长期模拟反复基因组选择育种程序中的最佳杂交选择方法。基于UCPC的最佳杂交选择被证明在将遗传多样性转化为短期和长期遗传增益方面比最佳杂交选择更为高效。我们还展示了，利用基于UCPC的最佳杂交选择，即使在短期内商业遗传增益仅有限度降低的情况下，也能提高长期遗传增益。