Favorable Conditions for Genomic Evaluation to Outperform Classical Pedigree Evaluation Highlighted by a Proof-of-Concept Study in Poplar

Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris

“…Spearman's rank correlations may have amplified the benefits of genomic models in black poplar (Pégard et al, 2020) whereas in Norway spruce they were similar between pedigree-based and genomic-based models (Chen et al, 2019), coinciding with our results.…”

“…(Ukrainetz and Mansfield, 2020). Given that the correlation between an individual phenotype and its true breeding value cannot be larger than the square root of heritability, r 2 is recognized as an unbiased estimation of accuracy of selection from n-fold-cross validation (Legarra et al, 2008;Meuwissen et al, 2013), thus r 2 has begun to be more standard used in forest tree GS studies (Lenz et al, 2019(Lenz et al, , 2020Calleja-Rodríguez et al, 2020;Klápšte et al, 2020;Pégard et al, 2020;Zhou et al, 2020). Similar r 1 were observed, for all models and traits evaluated for Scots pine, which agrees with previous studies (Bouvet et al, 2016;de Almeida Filho et al, 2016;Chen et al, 2019), but differs from other eucalyptus reports in which the genomic models performed better (Tan et al, 2018), yet in the same study inconsistencies in the original pedigree were detected, and a pseudo-pedigree was used.…”

“…Low estimates of nonadditive genetic variation may not necessarily mean this source of variation is not present since a suitable family structure and a proper mating design are also needed to obtain reliable estimates of nonadditive genetic effects (Munoz et al, 2014 ; Chen et al, 2020 ). Also, the lack of a good mating design would lead to a poor estimation power of variance components (Framton and Huber, 1995 ; Pégard et al, 2020 ) and attention should be paid when exploiting full-sib family structures. The role of dominance effects in many clonal and full-sib breeding programs is well studied, whereas less is known of epistatic variance.…”

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

“…The population used in the study included 1009 individuals from the French breeding population of Populus nigra (Pégard et al, 2020). All of them were genotyped with a 12k Infinium array (Faivre-Rampant et al, 2016) resulting in 5253 usable SNP markers after quality and frequency filtering (minor allele frequency higher than 0.05).…”

“…The resulting genotypes were phased, imputed and a consensus recombination map derived (Pégard et al, 2019) by using FImpute software (Sargolzaei et al, 2014). The allelic effects were estimated from a genomic multitrait evaluation using breedR (Muñoz & Sanchez, 2020). In this study, we considered the trunk circumference as a focal trait.…”