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Open AccessArticle

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

Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
Colegio de Postgraduados, Statistics and Computer Sciences, Montecillos, Edo. de México 56230, Mexico
Author to whom correspondence should be addressed.
Plants 2019, 8(9), 331;
Received: 25 July 2019 / Revised: 2 September 2019 / Accepted: 3 September 2019 / Published: 5 September 2019
(This article belongs to the Special Issue Genomics for Plant Breeding)
Eucalyptus globulus (Labill.) is one of the most important cultivated eucalypts in temperate and subtropical regions and has been successfully subjected to intensive breeding. In this study, Bayesian genomic models that include the effects of haplotype and single nucleotide polymorphisms (SNP) were assessed to predict quantitative traits related to wood quality and tree growth in a 6-year-old breeding population. To this end, the following markers were considered: (a) ~14 K SNP markers (SNP), (b) ~3 K haplotypes (HAP), and (c) haplotypes and SNPs that were not assigned to a haplotype (HAP-SNP). Predictive ability values (PA) were dependent on the genomic prediction models and markers. On average, Bayesian ridge regression (BRR) and Bayes C had the highest PA for the majority of traits. Notably, genomic models that included the haplotype effect (either HAP or HAP-SNP) significantly increased the PA of low-heritability traits. For instance, BRR based on HAP had the highest PA (0.58) for stem straightness. Consistently, the heritability estimates from genomic models were higher than the pedigree-based estimates for these traits. The results provide additional perspectives for the implementation of genomic selection in Eucalyptus breeding programs, which could be especially beneficial for improving traits with low heritability. View Full-Text
Keywords: genomic prediction; haplotype blocks; predictive ability; Bayesian models genomic prediction; haplotype blocks; predictive ability; Bayesian models
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Ballesta, P.; Maldonado, C.; Pérez-Rodríguez, P.; Mora, F. SNP and Haplotype-Based Genomic Selection of Quantitative Traits in Eucalyptus globulus. Plants 2019, 8, 331.

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