Table 2.

Summary of significant associations between selected traits and SNP markers from the mixed-linear model (MLM) analysis. Only results in the major loci from chromosome 1 are shown.

Trait	SNP	Allele	Position, bp	P-value	Candidate genes and mid-position
Color chart	S1_24121306	A/T†	24,121,306	1.74 × 10–22	Phytoene synthase (Manes.01G124200; 24,155,070 bp)
Color chart	S1_30543382	A†/G	30,543,382	2.91 × 10–11	NA‡
Chromameter b*	S1_24159585	C/T†	24,159,585	1.79 × 10–19	Phytoene synthase (Manes.01G124200; 24,155,070 bp)
Chromameter b*	S1_30543382	A†/G	30,543,382	1.66 × 10–11	NA
Dry matter	S1_24121306	A†/T	24,121,306	1.86 × 10–12	UDP-glucose pyrophosphorylase (Manes.01G123000; 24,061,652 bp); sucrose synthase (Manes.01G123800; 24,142,314 bp)

^†Nucleotide linked to the favorable allele at each SNP.

^‡NA, not available; no known candidate gene was found around the locus.