Data from: Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations

Though epistasis has long been postulated to play a critical role in
genetic regulation of important pathways as well as provide a major source
of variation in the process of speciation, the importance of epistasis for
genomic selection in the context of plant breeding is still being debated.
In this paper, we report the results on the prediction of genetic values
with epistatic effects for 280 accessions in the Nebraska Wheat Breeding
Program using adaptive mixed LASSO. The development of adaptive mixed
LASSO, originally designed for association mapping, for the context of
genomic selection is reported. The results show that adaptive mixed LASSO
can be successfully applied to the prediction of genetic values while
incorporating both marker main effects and epistatic effects. Especially,
the prediction accuracy is substantially improved by the inclusion of
two-locus epistatic effects (more than one fold in some cases as measured
by cross validation correlation coefficient), which is observed for
multiple traits and planting locations. This points to significant
potential in using non-additive genetic effects for genomic selection in
crop breeding practices.