Table 4 AmpSeq marker-trait associations for acylated anthocyanins

From: A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine

Chr	Position	Family of AmpSeq design	Mean depth	CV	Missing individuals	Pooled (182) ^a			'Horizon'×Illinois 547-1 (82)			V. rupestris B38×'Horizon' (100)
						Acylated anthocyanins			Acylated anthocyanins			Acylated anthocyanins
						P-value	marker R ²	Minor allele frequency	P-value	marker R ²	Minor allele frequency	P-value	marker R ²	Minor allele frequency
chr3	14851567	HI	250	0	0	1.07E−16	0.3370	0.33	7.36E−06	0.2586	0.42	4.90E−13	0.4147	0.25
chr3	15171738	HI	247	2	0	2.05E−17	0.3491	0.28	7.31E−06	0.2587	0.30	5.33E−13	0.4137	0.25
chr3	15828002	HI	250	0	127	1.76E−10	0.3102	0.47	8.82E−03	0.1724	0.44	8.35E−09	0.4214	0.50
chr3	16007996	HI	245	3	0	1.26E−16	0.3357	0.26	5.35E−06	0.2646	0.26	4.10E−12	0.3892	0.26
chr3	16008017	HI	244	3	0	1.26E−16	0.3357	0.26	5.35E−06	0.2646	0.26	4.10E−12	0.3892	0.26
chr3	16162132	HI	250	0	67	2.70E−03	0.0763	0.31	2.73E−04	0.2502	0.43	3.78E−02	0.0710	0.21
chr3	16163517	HI	249	1	0	3.64E−17	0.3265	0.24	1.15E−06	0.2574	0.22	4.10E−12	0.3892	0.26
chr3	16246446	HI	241	5	0	5.22E−03	0.0425	0.05	6.13E−02	0.0431	0.06	5.29E−02	0.0377	0.05
chr3	16375440	HI	249	1	0	3.64E−17	0.3265	0.24	1.15E−06	0.2574	0.22	4.10E−12	0.3892	0.26
chr3	16402674	HI	113	39	1	1.61E−06	0.1385	0.42	6.88E−06	0.2599	0.35	1.35E−04	0.1678	0.50
chr3	16402706	HI	14	6	2	2.15E−15	0.3143	0.33	7.62E−06	0.2580	0.29	1.59E−10	0.3720	0.37
chr3	16473116	HI	249	1	0	1.67E−16	0.3336	0.43	2.06E−05	0.2391	0.36	1.86E−11	0.3992	0.49
chr3	16516083	HI	4	4	200	1.80E−05	0.2417	0.35	8.50E−04	0.2507	0.46	NaN	0	0.01
chr3	16520617	HI	249	1	0	8.04E−17	0.3390	0.24	1.15E−06	0.2574	0.23	4.78E−12	0.4158	0.26
chr3	16523313	HI	73	53	3	1.85E−16	0.3329	0.30	1.15E−06	0.2574	0.22	6.12E−11	0.3842	0.38
chr3	16774466	HI	249	1	0	1.06E−17	0.3356	0.26	1.26E−06	0.2557	0.29	5.02E−13	0.4145	0.24
chr3	16873018	HI	248	2	0	NaN ^b	0	0.00	NaN	0	0.01	NaN	0	0.00
chr3	16873164	HI	88	46	0	1.06E−17	0.3356	0.26	1.26E−06	0.2557	0.28	5.02E−13	0.4145	0.24
chr3	17225240	HI	20	27	2	9.37E−14	0.2861	0.22	6.59E−05	0.2163	0.18	2.53E−10	0.3393	0.27
chr3	17225412	HI	149	0	31	8.45E−03	0.0413	0.06	2.17E−02	0.0720	0.06	1.06E−01	0.0281	0.06
chr3	17225585	HI	210	14	0	2.28E−17	0.3483	0.49	6.66E−07	0.3024	0.45	1.96E−11	0.3985	0.48
chr3	17774559	HI	62	151	124	1.97E−02	0.0649	0.31	1.08E−02	0.1319	0.22	4.35E−01	0.0328	0.44

Abbreviations: CV, coefficient of variation of read depth across individuals; HI, ‘Horizon’×Illinois 547-1; QTL, quantitative trait loci.
^aPooled includes all two families. Number of progeny analyzed is presented in parentheses.
^bNaN means no association detected.

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Table 4 AmpSeq marker-trait associations for acylated anthocyanins

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