Modelling of population structure through contemporary groups in genetic evaluation

Abstract

BackgroundForest trees can occupy extensive geography and environmentally highly variable areas which result in high genetic variability in the direction of pressure from natural selection. At the same time, the majority of conifer species are wind-pollinated from both short and long distances, resulting in wide-spread gene flow, which can lead to maladaptation to local conditions. Quantitative analyses of provenance/progeny tests correct for genetic differences between populations to ensure unbiased genetic parameters are obtained. Commonly, the provenance effect is fitted as a fixed term or can be implemented as a contemporary group in the pedigree.ResultsThe use of a provenance effect, either as a fixed term or as the same contemporary groups in both maternal and paternal sides of the pedigree, resulted in fairly similar precision of genetic parameters in our case. However, when we developed a phantom contemporary group for the paternal side of the pedigree that considered a different genetic quality of pollen compared with the maternal contribution from trees in the local environment, the model fit and accuracy of breeding values increased.ConclusionConsideration of the mating dynamics and the vector of gene flow are important factors in modelling contemporary genetic groups, particularly when implementing pedigrees within a mixed model framework to obtain unbiased estimates of genetic parameters. This approach is especially important in traits involved in local adaptation.

Marker Selection in Multivariate Genomic Prediction Improves Accuracy of Low Heritability Traits

“…The E. nitens population used in this study included 691 individuals, part of the third generation of open-pollinated progeny established within New Zealand's breeding program. The experimental design contained 30 replications of randomized complete blocks of these "sets" with each replication of the "set" comprising the same families but different individuals within these families (Klápště et al, 2019). Missing relatedness information in this population was recovered using sib-ship reconstruction as genomic information was not available for all possible parents (Klápště et al, 2017).…”

Accounting for population structure in genomic predictions of Eucalyptus globulus

“… Callister et al 2011 ; Lee et al 2015 ; Ukrainetz et al 2018 ). Thoughtful genetic group definitions for unpedigreed individuals can elucidate patterns of gene flow as well as improve predictions ( Klápště et al 2019 ). There is growing interest in the HBLUP approach to integrate genomic, pedigree, and phenotypic information and provide unbiased predictions of genetic merit for tree breeding programs ( Callister et al 2021 ).…”

“…Forest geneticists have widely adopted genetic groups to account for population differences in linear mixed models (LMM) (e.g. McRae et al 2004 ; Brawner et al 2010 ; Callister et al 2011 ; Klápště et al 2019 ), typically as unknown parent groups (UPGs) that were developed to account for missing parents in livestock populations ( Quaas 1988 ; Westell et al 1988 ). This approach treats provenances as fixed effects, and it results in more conservative estimates of heritability relative to treating founders as unrelated individuals ( Callister et al 2021 ).…”

Multi-trait selection to build resilience in conifer forests: a case study on spruce-shoot weevil interactions

“…Therefore, the older plant material could pass previous disease outbreaks and the tree height is the result of the level of resistance to pest attack rather than an independent trait. For example, Dungey et al [58], and later Klápště et al [59], investigated Swiss needle cast in Douglas-fir introduced in New Zealand. While the Californian provenances were the most productive on South Island which is pest free, their productivity was severely affected by Swiss needle cast on North Island where the Oregon provenances were the most productive due to a higher level of tolerance to the pest.…”