Genomic Prediction of Growth and Stem Quality Traits in Eucalyptus globulus Labill. at Its Southernmost Distribution Limit in Chile

Abstract

The present study was undertaken to examine the ability of different genomic selection (GS) models to predict growth traits (diameter at breast height, tree height and wood volume), stem straightness and branching quality of Eucalyptus globulus Labill. trees using a genome-wide Single Nucleotide Polymorphism (SNP) chip (60 K), in one of the southernmost progeny trials of the species, close to its southern distribution limit in Chile. The GS methods examined were Ridge Regression-BLUP (RRBLUP), Bayes-A, Bayes-B, Bayesian least absolute shrinkage and selection operator (BLASSO), principal component regression (PCR), supervised PCR and a variant of the RRBLUP method that involves the previous selection of predictor variables (RRBLUP-B). RRBLUP-B and supervised PCR models presented the greatest predictive ability (PA), followed by the PCR method, for most of the traits studied. The highest PA was obtained for the branching quality (~0.7). For the growth traits, the maximum values of PA varied from 0.43 to 0.54, while for stem straightness, the maximum value of PA reached 0.62 (supervised PCR). The study population presented a more extended linkage disequilibrium (LD) than other populations of E. globulus previously studied. The genome-wide LD decayed rapidly within 0.76 Mbp (threshold value of r2 = 0.1). The average LD on all chromosomes was r2 = 0.09. In addition, the 0.15% of total pairs of linked SNPs were in a complete LD (r2 = 1), and the 3% had an r2 value >0.5. Genomic prediction, which is based on the reduction in dimensionality and variable selection may be a promising method, considering the early growth of the trees and the low-to-moderate values of heritability found in the traits evaluated. These findings provide new understanding of how develop novel breeding strategies for tree improvement of E. globulus at its southernmost range limit in Chile, which could represent new opportunities for forest planting that can benefit the local economy.

SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus

“…For instance, Callister et al [53] reported a range in branching quality (measured as branch thickness) of 0–0.16 in full-sib families of E. globulus (at age 3.5). Ballesta et al [43] reported that the pedigree-based heritability estimate of BQ in E. globulus at 4 years of age was less than 0.1. In other tree species, traits related to branch quality have been described to be moderately heritable [66,67].…”

“…It should be noted that there are few studies that have evaluated the combined use of GS and haplotypes in plants [29,41,42]. In particular, these methods have been implemented in predominantly self-pollinated (autogamous) species—for example, soybean and wheat [41,42]—in which extensive LD values can be found in their genomes, which favors the identification of haplotypes, while in outcrossing species (allogamous) such as Eucalyptus and most species of forest interest, LD usually decays at short genomic distances [43,44], which allows the identification of smaller haplotype blocks and those conformed by a smaller number of alleles.…”

Genomic Predictions Using Low-Density SNP Markers, Pedigree and GWAS Information: A Case Study with the Non-Model Species Eucalyptus cladocalyx

“…Several studies have explored the potential of the selection based on genomic tools in forest species [33][34][35][36], including E. cladocalyx [12,37,38]. According to the results, GSq models outperformed traditional GS models in terms of predictive ability when at least ten significant marker-trait associations were included in GSq.…”

“…According to Silva et al [19], the superior performance of the models that include QTL information compared with GS model can be due to GSq model exploiting relevant regions not directly considered in GS model, improving the performance of the prediction model. Additionally, previous studies have reported that a pre-selection of SNPs or the use of genome-wide association analyses to identify and rank markers could increase predictive ability [38,44,45].…”

Bayesian analysis of growth, stem straightness and branching quality in full-sib families of Eucalyptus globulus

“…E. globulus is the second most important woody species in the Chilean forest industry (Ballesta et al 2018), where it comprises approximately 21% of national plantations (Morales et al 2015). Traditionally, the species has experienced a rotation period that varies between eight and 12 years.…”