Table 3.

Predictability of the five traits based on the BLUP model, just inclusion of one type of kinship matrix

SNP sets	YD	HD	PH	GL	GW
Regulatory	0.451 ± 0.008a	0.562 ± 0.011	0.697 ± 0.006	0.551 ± 0.007	0.693 ± 0.006
Intron	0.447 ± 0.008	0.545 ± 0.011	0.687 ± 0.008	0.545 ± 0.008	0.691 ± 0.006
Exon	0.443 ± 0.008	0.544 ± 0.011	0.692 ± 0.007	0.536 ± 0.008	0.685 ± 0.006
Intergenic	0.455 ± 0.008	0.556 ± 0.011	0.697 ± 0.006	0.552 ± 0.008	0.697 ± 0.006
Gene	0.445 ± 0.008	0.542 ± 0.011	0.687 ± 0.007	0.539 ± 0.008	0.688 ± 0.006
Non-gene	0.453 ± 0.008	0.559 ± 0.011	0.695 ± 0.007	0.552 ± 0.008	0.695 ± 0.006
GBLUP (whole)	0.451 ± 0.008	0.555 ± 0.011	0.693 ± 0.007	0.549 ± 0.008	0.694 ± 0.006

Regulatory, intron, exon, intergenic, gene and non-gene represents the kinship matrix inferred from genetic variants within this kind of category

GBLUP (whole) represents that all the variants are used to infer the kinship matrix

^aDenotes the standard error of predictability of traits, calculated from 100 replicates of tenfold cross-validation