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

Paulina Ballesta,Paulino Pérez-Rodríguez,Freddy Mora,Carlos Maldonado

doi:10.3390/plants8090331

Paulina Ballesta, Paulino Pérez-Rodríguez + Show 2 more

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https://doi.org/10.3390/plants8090331

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Abstract

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.

Highlights

The number of breeding programs that use the principles of genomic selection (GS) has increased considerably in recent years
The genetic gains based on the selection with these genomic models were statistically higher than those based on pedigree information (GG = 2.9% [1.4–4.5])
The construction of the haplotype blocks was based on the confidence interval algorithm of Gabriel et al [48], which establishes that those pairs of Single nucleotide polymorphic markers (SNP) that are in a strong linkage disequilibrium have a D0 value between 0.7 and 0.98, considering a confidence interval of 95%

Summary

Introduction

The number of breeding programs that use the principles of genomic selection (GS) has increased considerably in recent years. The non-random association between two or more loci due to a low probability of recombination between them (linkage disequilibrium: LD) in a given population constitutes haplotypes [24,25], which correspond to sets of genomic regions within a chromosome that tend to be inherited together [26]. In this context, GS can be implemented using individual SNPs and haplotypes, or a combination of both, using haplotypes in conjunction with SNPs not assigned to a haplotype. Cuyabano et al [27] presented a haplotype approach for genomic prediction using high-density data in dairy cattle as an alternative to individual marker methods, demonstrating

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