Table 3. Genomic Control Inflation Factor (λ_GC) analyses of GWAS models as a function of three different methods^a for adjusting population structure.

Q only models	λGC			Model Rankingb
Trait	nMDSQ	PCAQ	STRQ	nMDSQ	PCAQ	STRQ
After Cooking Blackening	1.569	1.586	1.571	1	3	2
Brightness	1.823	2.105	1.785	2	3	1
Days to Emergence	1.286	1.378	1.244	2	3	1
Dormancy Break	1.086	1.25	1.186	1	3	2
Dry Matter	2.453	2.45	2.494	2	1	3
Enzymatic Browning	1.388	1.613	1.457	1	3	2
Ethylene treated tubers sprouting	1.59	1.562	1.519	3	2	1
Eye Depth	1.666	1.481	1.578	3	1	2
Flesh Color	1.922	3.062	1.966	1	3	2
Foliage	1.168	1.302	1.132	2	3	1
Frying Color	2.254	2.4	2.244	2	3	1
Maturity	1.449	1.428	1.622	2	1	3
Plant Height	1.554	1.692	1.426	2	3	1
stems per Plant	1.444	1.474	1.297	2	3	1
Stolon Attachment	1.678	1.289	1.601	3	1	2
Total Tubers	1.404	1.991	1.319	2	3	1
Tuber Shape	1.888	2.035	2.075	1	2	3
Tuber Uniformity	1.593	1.548	1.621	2	1	3
Tubers per Stem	1.629	1.572	1.653	2	1	3
Yield	1.693	1.86	1.723	1	3	2

QK modelsc	λGC
Trait	nMDSQK	PCAQK	STRQK
After Cooking Blackening	0.944	0.977	0.956
Brightness	0.906	0.91	0.92
Days to Emergence	0.991	0.975	0.976
Dormancy Break	0.97	0.974	1.003
Dry Matter	0.925	0.953	0.931
Enzymatic Browning	0.945	0.964	0.947
Ethylene treated tubers sprouting	0.971	0.991	0.955
Eye Depth	0.977	0.908	0.93
Flesh Color	0.878	0.861	0.9
Foliage	0.964	0.991	0.927
Frying Color	0.957	0.993	0.969
Maturity	0.928	0.943	1.001
Plant Height	1.026	1.086	1.037
stems per Plant	0.97	0.988	0.965
Stolon Attachment	0.968	0.954	0.951
Total Tubers	0.972	0.949	0.914
Tuber Shape	0.975	0.968	0.981
Tuber Uniformity	1.007	1.025	1.021
Tubers per Stem	0.956	0.969	0.952
Yield	0.978	1.011	0.982

^anMDS, non-metric multidimensional scaling; PCA, principal component analysis; STR, STRUCTURE.

^b1, first; 2, second; 3, third.

^cQK models not ranked as inclusion of K in GWAS models brought λGC close to 1 for all three Q methods tested.