A combined strategy for quantitative trait loci detection by genome-wide association

BMC Proceedings

Table 1 The final integrated mapping results using step-wise regression. The estimates of the allele substitution effect under the single additive QTL model are included for comparison.

SNP₁	SNP₂ ^a	logP^b	"1/2" genotype^c	"2/2" genotype^d	Accumulated Variance (%)	Single QTL allelic effect (simulated)^g
196	-	18.65	0.33	0.62	1.78	0.71 (0.62)
402	-	5.59	0.08	0.23	2.28	0.85 (0.56)
540^e	3219	10.51 (7.75)	-0.18 (-0.09)	-0.30 (0.08)	3.53
778	-	7.34	0.23	0.45	4.18	0.42 (0.37)
1257^f	3689	9.15 (6.63)	-0.56 (-0.24)	0.46 (-0.17)	5.56
1270	-	7.60	0.23	0.44	6.23	0.50 (0.35)
1483	-	10.02	-0.14	-0.36	7.13	0.43 (0.37)
2133	-	5.89	0.10	0.31	7.65	0.39 (0.30)
3033	-	20.52	0.31	0.66	9.54	0.68 (0.61)
3765	-	11.91	0.25	0.48	10.62	0.56 (0.58)
4935	-	18.38	-0.33	-0.71	12.35	0.70 (0.75)

^a: SNP₂ column has a value only for epistatic pairs.
^b: the-LOG₁₀ transformed P value for single significant SNPs, or the epistatic pairs in the nested test order. The -LOG₁₀ (P) value for epistasis tests are in brackets.
^c: estimate of the "1/2" genotype in contrast to the "1/1" genotype. The estimates of SNP₂ are in brackets.
^d: estimate of the "2/2" genotype in contrast to the "1/1" genotype. The estimates of SNP₂ are in brackets.
^e: estimates of the pair-wise interactions: 0.51, 0.23, 0.07 and 0.66 for "1/2 × 1/2", "2/2 × 1/2", "1/2 × 2/2" and "2/2 × 2/2", respectively.
^f: estimates of the pair-wise interactions: 0.57, -0.55, 0.53 and -0.47 for "1/2 × 1/2", "2/2 × 1/2", "1/2 × 2/2" and "2/2 × 2/2", respectively.
^g: Estimated allelic effect from the single SNP GRAMMAR model; the simulated value is taken from the nearest simulated QTL as provided by the organisers.

ISSN: 1753-6561