Table 4.

Results of genomic prediction tests on PD recombinant inbred lines (RILs) by training subset using the all-marker set [18,663 single-nucleotide polymorphisms (SNPs)] and 2rd set (9,282 SNPs).

Subset of core collection	Trait a	gblupRR		RKHS		Random forest
		18,663 SNPs	9,282 SNPs	18,663 SNPs	9,282 SNPs	18,663 SNPs	9,282 SNPs
Capsicum annuum complex (302 lines)	FL	0.352	0.317	0.336	0.318	0.285	0.333
	FS	0.443	0.387	0.487	0.397	0.594	0.583
	FWd	0.457	0.484	0.468	0.499	0.320	0.343
	FWg	0.403	0.436	0.430	0.483	0.353	0.351
C. annuum only (229 lines)	FL	0.363	0.329	0.345	0.330	0.328	0.277
	FS	0.408	0.387	0.433	0.397	0.498	0.468
	FWd	0.452	0.481	0.436	0.494	0.373	0.407
	FWg	0.401	0.437	0.427	0.480	0.415	0.434
Capsicum chinense and Capsicum frutescens (73 lines)	FL	−0.308	−0.205	−0.156	−0.196	−0.006	−0.042
	FS	0.245	0.391	−0.008	0.357	−0.190	0.018
	FWd	0.006	0.126	−0.033	0.079	−0.129	−0.127
	FWg	−0.034	0.033	−0.148	0.000	−0.134	−0.094

^aFL, fruit length; FS, fruit shape; FWd, fruit width; FWg, fruit weight; PT, pericarp thickness.