Table 5.

Performance (average r²) of rrBLUP for the single marker model (Formula 1) and epistasis model (Formula 2) under the traditional encoding vs. the data-driven encoding.

Dent
Phenotype	rrBLUP (T)	rrBLUP (D)	Epistasis (T)	Epistasis (D)
1	0.590	0.616	0.590	0.616
2	0.552	0.58	0.552	0.58
3	0.321	0.349	0.356	0.349
Flint
Phenotype	rrBLUP (T)	rrBLUP (D)	Epistasis (T)	Epistasis (D)
1	0.470	0.492	0.476	0.493
2	0.301	0.308	0.316	0.312
3	0.057	0.068	0.096	0.102

rrBLUP (T) is the single marker model under the traditional encoding. rrBLUP (D) is the single marker model under the data-driven encoding. Epistasis (T) is the epistasis model under the traditional encoding. Epistasis (D) is the epistasis model under the data-driven encoding.