Abstract
Non-additive genetic effects can be effectively exploited in control-pollinated families with the availability of genome-wide markers. We used 41,304 SNP markers and compared pedigree vs. marker-based genetic models by analysing height, diameter, basic density and pulp yield for Eucalyptus urophylla × E.grandis control-pollinated families represented by 949 informative individuals. We evaluated models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance). We showed that the models can capture a large proportion of the genetic variance from dominance and epistasis for growth traits as those components are typically not independent. We also showed that we could partition genetic variances more precisely when using relationship matrices derived from markers compared to using only pedigree information. In addition, phenotypic prediction accuracies were only slightly increased by including dominance effects for growth traits since estimates of non-additive variances yielded rather high standard errors. This novel result improves our current understanding of the architecture of quantitative traits and recommends accounting for dominance variance when developing genomic selection strategies in hybrid Eucalyptus.
Highlights
Hybrids between inbred lines within species or between different species are commonly used for commercial production in both crops and tree species
It has been reported that rooting ability, flowering time, drought and freezing resistance were all inherited in a predominantly additive manner, while partial dominance was detected for freezing resistance in first generation population false discovery rate (FDR) (F1) hybrids of E. camaldulensis × E. globulus and E. torelliana × E. citriodora, respectively [18]
Since we found considerable inconsistencies between the registered pedigree and the realized relationships in our previous study [48], we carried out a parentage assignment test in this study to better understand the reasons of these inconsistencies and to construct a pseudo-pedigree that was later used to estimate genetic parameters and make predictions compared to genomic-based ones
Summary
Hybrids between inbred lines within species or between different species are commonly used for commercial production in both crops and tree species. The main reason of conducting crosses between pure lines of a single species or between contrasting species is the exploitation of hybrid superiority (heterosis) or to combine complementary traits of different species [1,2,3]. For Eucalyptus hybrids, the relative contribution of dominance has been shown to vary between traits and species combinations. Dominance effects seem to be important and widespread for growth traits [1, 19,20,21] and a ratio of dominance to additive variance close to 1.2 was estimated during the growth period for the E. grandis x E. urophylla hybrid [11]. Pulp yield appears to show dominance or partial dominance towards the low yielding parents [18]
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