Genomic Prediction in a Self-Fertilized Progenies of Eucalyptus spp.

Abstract

Genomic selection in <i>Eucalyptus</i> enables the identification of superior genotypes, thereby reducing breeding cycles and increasing selection intensity. However, its efficiency may be compromised due to the complex structures of breeding populations, which arise from the use of multiple parents from different species. In this context, partial inbred lines have emerged as a viable alternative to enhance efficiency and generate productive clones. This study aimed to apply genomic selection to a self-fertilized population of different <i>Eucalyptus</i> spp. Our objective was to predict the genomic breeding values (GEBVs) of individuals lacking phenotypic information, with a particular focus on inbred line development. The studied population comprised 662 individuals, of which 600 were phenotyped for diameter at breast height (DBH) at 36 months in a field experiment. The remaining 62 individuals were located in a hybridization orchard and lacked phenotypic data. All individuals, including progeny and parents, were genotyped using 10,132 SNP markers. Genomic prediction was conducted using four frequentist models-GBLUP, GBLUP dominant additive, HBLUP, and ABLUP-and five Bayesian models-BRR, BayesA, BayesB, BayesC, and Bayes LASSO-using k-fold cross-validation. Among the GS models, GBLUP exhibited the best overall performance, with a predictive ability of 0.48 and an R² of 0.21. For mean squared error, the Bayes LASSO presented the lowest error (3.72), and for the other models, the MSE ranged from 3.72 to 15.50. However, GBLUP stood out as it presented better precision in predicting individual performance and balanced performance in the studied parameter. These results highlight the potential of genomic selection for use in the genetic improvement of <i>Eucalyptus</i> through inbred lines. In addition, our model facilitates the identification of promising individuals and the acceleration of breeding cycles, one of the major challenges in <i>Eucalyptus</i> breeding programs. Consequently, it can reduce breeding program production costs, as it eliminates the need to implement experiments in large planted areas while also enhancing the reliability in selection of genotypes.