Table 1.

Statistics for the QTL found from the single phenotype stepwise regression analysis performed on breeding values of the V. rupestris B38 x ‘Horizon’ (RH) and ‘Horizon’ × V. cinerea B9 (HC) F₁ families incorporating data across 2 years and multiple experiments

Name	Family	Chr	Heterozygous parenta	Phenotype	LOD thresholdb	LOD scorec	% Var. explainedd	Effect sizee	95% credible interval (Mbp)f
Rpv17	RH	8	Horizon	Hypersensitive response (HR)	3.60	6.70	12.94	0.149	11.369–11.721–12.184
Rpv18	RH	11	Horizon	Sporulation (manual)	3.59	4.69	8.77	0.159	7.038–8.138–19.921
Rpv18	RH	11	Horizon	Sporulation (computer vision)	3.65	4.21	8.51	0.006	7.038–16.995–19.921
	RH	11	V. rupestris B38	Hypersensitive response (HR)	3.60	4.11	7.66	0.117	7.609–17.753–19.857
Rpv18	RH	11	Horizon	Hypersensitive response (HR)	3.60	8.71	17.33	0.169	15.397–15.397–16.994
	RH	14	Horizon	Sporulation (manual)	3.59	7.75	15.14	0.208	23.275–24.823–25.002
	RH	14	Horizon	Sporulation (computer vision)	3.65	5.76	11.91	0.007	24.366–25.002–25.778
Rpv19	RH	14	V. rupestris B38	Sporulation (manual)	3.59	6.19	11.83	0.184	27.119–29.790–29.790
Rpv19	RH	14	V. rupestris B38	Sporulation (computer vision)	3.65	7.34	15.51	0.008	27.085–29.543–29.790
	RH	18	Horizon	Sporulation (manual)	3.59	3.79	6.99	0.146	6.598–9.684–14.528
	HC	5	Horizon	Sporulation (manual)	3.43	5.58	11.27	0.314	0.844–3.112–5.511
	HC	5	Horizon	Hypersensitive response (HR)	3.44	6.91	15.10	0.177	0.114–2.388–3.642
Rpv20	HC	6	Horizon	Hypersensitive response (HR)	3.44	4.00	8.37	0.142	0.770–0.907–13.625
Rpv21	HC	7	Horizon	Sporulation (manual)	3.43	5.42	10.90	0.312	0.994–2.129–3.150
	HC	8	Horizon	Sporulation (manual)	3.43	5.81	11.77	0.323	16.814–19.217–22.458
	HC	8	Horizon	Hypersensitive response (HR)	3.44	4.86	10.29	0.147	17.766–19.609–22.458

^aThe heterozygous parent is the one that has the heterozygous allele. SNPs for the genotypes in the families either were homozygous for one allele or heterozygous because only pseudo-testcross markers were used to build the genetic maps (Hyma et al. 2015)

^bCalculated using 1000 permutation tests with an alpha value of 0.05

^cGiven for the most significant marker in a QTL credible interval

^dCalculated as $\frac{\text{Type III SS}}{\text{Total SS}}\times 100$ for the most significant marker in a QTL credible interval. Type III sum of squares (SS) of a QTL is the SS of that QTL conditional on all other QTL in the model

^eThe absolute value of the effect of the most significant marker in a QTL credible interval when the other QTL listed for a particular phenotype within a family are included in the model. The absolute value is given because phase information of the most significant marker is not informative due to linkage with markers of opposite phase. The dimension of the effect size is the same as the dimension of the phenotype score

^fLocation intervals are based on the 12X.2 version (URGI 2014) of the grapevine reference genome. The middle value represents the location of the most significant marker