Table 2.

Summary of multi-environment QTL detected in this study using the single-marker ANOVA additive effects model

Trait	Na	Thresholdb	ICMc	cMd	− log10(p)e	Expl. Varf	Peak markerg	Marker phaseh
Stem length	121	4.9	2	14.6	5.1	0.15	M36499_924	oooo × QQoo
Stem width	121	4.7	7	47.6	6.0	0.18	K3954_219	oooQ × oooo
Prickles on stem	121	4.8	3	21.4	7.4	0.22	K7826_576	ooQo × ooQo
			4	72.2	6.7	0.20	K5629_995	SxS
Prickles on petiole	121	4.8	4	66.9	7.7	0.24	G38418_730	QooQ × oQQo
Chlorophyll content	121	4.9	4	45.9	5.9	0.19	K5520_777	oooQ × oQoo
Num. petals	121	4.8	2	98.3	6.6	0.20	G66895_409	oooo × ooQo
			3	31.5	6.4	0.19	K599_2377	ooQo × ooQo

^aN number of offspring for which genotype and phenotype data were available for each trait

^bThreshold experiment-wide significance threshold, determined by permutation test with N = 1000 and α = 0.05

^cICM chromosomal linkage group, using the integrated consensus map (ICM) numbering of Spiller et al. (2011) and Bourke et al. (2017)

^dcM centiMorgan position of QTL peak

^e − log₁₀(p) = significance at QTL peak, using the p value from the model fit

^fExpl. Var. fraction of phenotypic variance explained by the QTL model at the peak position (adjusted R² from the regression)

^gPeak marker marker with the highest trait association above the threshold on that linkage group

^hMarker phase parental marker phase (consistent with homologue numbering from Table 1 and Fig. 4). In cases where the marker was not phased due to insufficient linkage to 1 × 0 markers, the segregation type is given instead