Table 1. Comparison of mean R ² and mean number of significant SNPs across 100 cross-validation runs, calculated for two models and four traits.

Trait	R2val		R2train		Number of significant SNPs
	'IBS-M'	'IBD-M × F'	'IBS-M'	'IBD-M × F'	'IBS-M'	'IBD-M × F'
HEA	0.62	0.63	0.85	0.76	80	6
TGW	0.52	0.31	0.77	0.40	74	2
THR	0.78	0.82	0.89	0.86	54	3
GrCol	0.71	0.85	0.93	0.95	80	5
Mean	0.66	0.65	0.86	0.74	72	4

Abbreviations: GrCol, grain colour; HEA, heading; IBD, identical by descent; IBS, identical by state; R²train, model fit of the training set; R²val, prediction ability; SNP, single-nucleotide polymorphism; TGW, thousand grain weight; THR, threshability.

Traits studied: HEA, TGW, THR and GrCo; Models applied: only marker main effects based on IBS (‘IBS-M’) and only marker-by-family effects based on IBD genotypes (‘IBD-M × F’). The last row indicates the mean across traits.