How to achieve a higher selection plateau in forest tree breeding? Fostering heterozygote x homozygote relationships in optimal contribution selection in the case study of Populus nigra

In breeding, Optimal Contribution Selection (OCS) is one of the most
effective strategies to balance short- and long-term genetic responses, by
maximizing genetic gain and minimizing global coancestry. Considering
genetic diversity in the selection dynamic – through coancestry – is
undoubtedly the reason for the success of OCS, as it avoids intial loss of
favorable alleles. Originally formulated with the pedigree relationship
matrix, global coancestry can nowadays be assessed with one of the
possible formulations of the realized genomic relationship matrix. Most
formulations were optimized for genomic evaluation, but few for the
management of coancestry. We introduce here an alternative formulation
specifically developed for Genomic OCS (GOCS), intended to better control
heterozygous loci, and thus better account for Mendelian sampling. We
simulated a multi-generation breeding program with mate allocation and
under GOCS for twenty generations, solved with quadratic programming. With
the case study of Populus nigra, we have shown that, although the dynamic
was mainly determined by the trade-off between genetic gain and genetic
diversity, better formulations of the genomic relationship matrix,
especially those fostering individuals carrying multiple heterozygous
loci, can lead to better short-term genetic gain and a higher selection
plateau.