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.