Table 3.

SNPs significantly associated with each of the quality traits based on single marker regressions.

Trait	SNP 1	Chromo-some	p Value	Allele Frequency (%) 2	Genetic Effect	Explained Genetic Variance (%)	Gene ID	Annotation
Flour yield	NOS_WW_ SNP_688	5D	2.44 × 10−9	28	0.96 ± 0.14	13.3	TraesCS5D02G004300	Nontranslating coding sequence
Alveo P	NOS_WW_ SNP_5054	1D	6.22 × 10−7	15	7.99 ± 1.29	5.0	TraesCS1D02G322300	Uncharacterized protein
	NOS_WW_ SNP_688	5D	1.02 × 10−6	28	6.01 ± 0.99	4.4	TraesCS5D02G004300	Nontranslating coding sequence
Alveo L	NOS_WW_ SNP_2731	4A	9.59 × 10−8	37	4.87 ± 0.82	8.0	TraesCS4A02G447000	Glycosyl-transferase
Alveo W	NOS_WW_ SNP_11809	1B	1.77 × 10−13	64	14.58 ± 1.66	8.8	TraesCS1B02G329600	Uncharacterized protein
	NOS_WW_ SNP_6663	1B	1.21 × 10−9	64	12.04 ± 1.67	6.0	TraesCS1B02G016400	Uncharacterized protein
	NOS_WW_ SNP_3056	1D	6.30 × 10−13	13	20.18 ± 2.35	8.3	TraesCS1D02G317100	Histone deacetylase
	NOS_WW_ SNP_688	5D	4.16 × 10−6	28	9.41 ± 1.74	3.2	TraesCS5D02G004300	Nontranslating coding sequence

¹ Only the most significant SNP for each peak in the Manhattan plots is shown. ² Allele frequencies are for the allele that is positively associated with the trait.