For traits with presence of a few large and several small effect QTL, alternative biometrical approaches have been proposed to maximally profit from a combined marker-assisted and genomic selection [ 8, 9].
Even so, for multi-environment analyses, the percentage of phenotypic variance attributable to genetic effects was as expected for a complex trait, which is governed by several small effect QTLs/genes located in different genomic regions, and where the environment interactions play an important role.
One major QTL for ovary size was detected in each backcross, along with several smaller effects and two QTL for ovary asymmetry.
These results confirm the current understanding that the complex traits are highly polygenic in nature and are the outcome of several small-effect genetic factors.
Previous QTL studies of heading date have identified several small-effect QTLs (Hd4, Hd7, Hd8, Hd9, Hd10, Hd12, Hd13, and Hd17 [ 27, 49- 51]).
For example, in two studies several small-effect QTL affecting flowering time were detected only after FLC was down-regulated through vernalization (Alonso-Blanco et al. 1998; Werner et al. 2005; Strange et al. 2011).
Several small-effect single-SNP or haplotype-based associations were detected in this species, indicating wood properties are quantitative traits controlled by multiple alleles, and limited statistical power for single-marker or haplotype-based association methods (Beaulieu et al. 2011; Du et al. 2013).
However, it should be noted that we only used 384 SNP panels in this study; therefore, we may have overlooked several QTL with small effects.
In breeding, quantitative resistance is more difficult to implement as it is mostly controlled by several genes with small effects, and it demands more effort to introgress quantitative resistance.
This may indicate that the PTA milk is a phenotype that is influenced by several markers with small effects on it, besides the possibility of epistasis and dominance, however, such genetic effects cannot be proven by the method suggested in this work.
