Multienvironment genomic variance decomposition analysis of open-pollinated Interior spruce (Picea glauca x engelmannii)

Abstract

The advantages of open-pollinated (OP) family testing over controlled crossing (i.e., structured pedigree) are the potential to screen and rank a large number of parents and offspring with minimal cost and efforts; however, the method produces inflated genetic parameters as the actual sibling relatedness within OP families rarely meets the half-sib relatedness assumption. Here, we demonstrate the unsurpassed utility of OP testing after shifting the analytical mode from pedigree- (ABLUP) to genomic-based (GBLUP) relationship using phenotypic tree height (HT) and wood density (WD) and genotypic (30k SNPs) data for 1126 38-year-old Interior spruce (Picea glauca (Moench) Voss x P. engelmannii Parry ex Engelm.) trees, representing 25 OP families, growing on three sites in Interior British Columbia, Canada. The use of the genomic realized relationship permitted genetic variance decomposition to additive, dominance, and epistatic genetic variances, and their interactions with the environment, producing more accurate narrow-sense heritability and breeding value estimates as compared to the pedigree-based counterpart. The impact of retaining (random folding) vs. removing (family folding) genetic similarity between the training and validation populations on the predictive accuracy of genomic selection was illustrated and highlighted the former caveats and latter advantages. Moreover, GBLUP models allowed breeding value prediction for individuals from families that were not included in the developed models, which was not possible with the ABLUP. Response to selection differences between the ABLUP and GBLUP models indicated the presence of systematic genetic gain overestimation of 35 and 63% for HT and WD, respectively, mainly caused by the inflated estimates of additive genetic variance and individuals’ breeding values given by the ABLUP models. Extending the OP genomic-based models from single to multisite made the analysis applicable to existing OP testing programs.

Effect of number of annual rings and tree ages on genomic predictive ability for solid wood properties of Norway spruce

“…Generally, pedigree-based PA estimates in conifer species have been reported to be higher or comparable to marker-based models [11,15,16,19,20,23], but there are also some studies reporting marker-based PA estimates to be higher [13,24,36]. Our results for density and Pilodyn follow the general finding in forest trees, whereas for MFA, a low heritability trait, the PA estimation based on GBLUP model is substantially higher (0.16) compared to the ABLUP model (0.04).…”

Quantitative Genetics and Genomics Converge to Accelerate Forest Tree Breeding

“…In the past 2 years, a number of additional experimental GS studies have been reported (Cappa et al, 2017 , 2018 ; Duran et al, 2017 ; Lenz et al, 2017 ; Müller et al, 2017 ; Ratcliffe et al, 2017 ; Tan et al, 2017 , 2018 ; Thistlethwaite et al, 2017 ) (Table 1 ; Resende et al, 2017b ; Chen et al, 2018 ; De Moraes et al, 2018 ; El-Dien et al, 2018 ; Kainer et al, 2018 ; Suontama et al, 2018 ). Many of them in species of Eucalyptus for which public high-throughput genotyping platforms of DArT (Sansaloni et al, 2010 ) and SNPs (Silva-Junior et al, 2015 ) have been available.…”

“…GS can increase the rate of genetic gain of breeding cycle by increasing ( i ) because the phenotypes of a much larger number of seedlings in the nursery can be predicted with marker data compared to the number of trees that can be tested in conventional field progeny trials. Additionally, the use of realized genomic relationships is associated with increased accuracy in estimating σ A and breeding values (r) (Hayes et al, 2009 ; El-Dien et al, 2018 ). Yet, in forest trees, the potentially greatest impact of GS on the rate of genetic progress will originate from decreasing ( L ).…”

“…Accordingly, the realized genetic covariances are now based on the actual fraction of the genome that is identical by descent or by state between individuals (Vanraden, 2008 ). It has been shown in a number of studies in forest trees that realized genomic relationships can produce more accurate predictions than pedigrees alone (Munoz et al, 2014 ; El-Dien et al, 2015 , 2018 ; Bouvet et al, 2016 ; Cappa et al, 2017 , 2018 ; Tan et al, 2018 ). Additionally, the realized genomic relationships of a small subset of the progeny testing population have been effectively combined with a substantially large proportion of un-genotyped individuals in a single-step analysis (Legarra et al, 2009 ).…”

Genomic Studies Reveal Substantial Dominant Effects and Improved Genomic Predictions in an Open-Pollinated Breeding Population of Eucalyptus pellita

“…Application of markers in open-pollinated (OP) families is particularly useful as markers can uncover half-sib and full-sib relationships within the OP families ( El-Kassaby et al 2011 ). This will have a significant impact on the precision and accuracy of the estimated genetic parameters as demonstrated by a number of studies ( Bush and Thumma 2013 ; Gamal El-Dien et al 2016 , 2018 ; Müller et al 2017 ; Klápště et al 2017 ; Klápšte et al 2018 ). In traditional methods, all individuals of an OP family are treated as half-sibs.…”