. 2013 Oct 9;8(10):e75749. doi: 10.1371/journal.pone.0075749

Table 3. Significant and suggestive QTL for SI using half-sib family regression analysis¹ in rainbow trout family 2008132.

					F_ChromWide	F_ExperWide			Closest marker¹⁰
Category	Omy²	cM³	LR⁴	F- value⁵	_P = 0.05 ⁶	_P = 0.05 ⁷	⁸	95% C.I.⁹	Left	Right
*Dam HS family*	1	5	10.76	11.09*	7.12	13.64	0.07	0.0–27.0	Ssa20_19NUIG	OMM1205
	8	39	9.27	9.52*	7.02	13.64	0.06	19.0–71.0	OMM1579	OMM1055
	13	25	7.46	7.63*	6.63	13.64	0.05	0.0–60.0	OMM1330a	OMY1UoG
	18	70	6.47	6.59*	6.36	13.64	0.04	2.0–70.0	OMM1303	OMM1352
	19	29	25.91	27.81**	6.65	13.64	0.18	16.0–34.0	OMM5216	OMM5327
	26	1	10.78	11.12*	5.97	13.64	0.07	0.0–22.0	OMY1189b	OMM5231a
*Sire HS family*	1	30	8.01	8.02*	5.97	12.28	0.05	4.0–45.0	OMM1152	OMM1355
	2	10	6.54	6.67*	4.93	12.28	0.04	4.0–81.0	OMM1391a	OMM1131
	3	48	8.89	9.12*	5.54	12.28	0.06	4.0–75.0	OMM4025	OMM1080
	5	57	25.31	27.12**	6.08	12.28	0.18	29.0–80.0	OMM1439	OMM5213
	11	4	6.78	6.92*	4.45	12.28	0.04	0.0–40.0	OMM3093	OMM1433
	16	0	12.33	12.77**	4.62	12.28	0.09	0.0–42.0	OMM1221	OMYRGT6TUFa
	17	10	7.17	7.32*	6.07	12.28	0.05	0.0–58.0	OMM1306	OMM1607

Half-sib regression interval mapping was performed with web-based software GridQTL [24].

Rainbow trout chromosome number [21], [22].

The chromosome location with the highest estimated F-value was defined as the most likely QTL location. The map cM units are based on genetic maps developed for this QTL genome scan study.

⁴

The likelihood ratio test statistic was estimated as Inline graphic where L₀ is the log likelihood of polygenic model and L₁ is the log likelihood of the QTL model at the tested location (cM).

⁵

Asymptotically F-test statistic with the degrees of freedom(DF) being the number of sires or dams included for the numerator, and the total number of offspring minus twice the number of sires or dams for the denominator [25]. The QTL with F-value ≥ F_{ChromWide P = 0.05} was defined as suggestive QTL (*) and QTL with F-value ≥ F_{ExperWide P = 0.05} was defined as significant QTL (**).

⁶

Chromosome-wide F-value at P = 0.05 was estimated using 10,000 permutations with GridQTL [24].

⁷

Experiment-wide F_{ExperWide P = 0.05} was estimated using 10,000 bootstraps with re-sampling with GridQTL [24].

⁸

The proportion of phenotypic variance explained by the QTL was calculated as Inline graphic where MSE_full and MSE_reduced are the mean squared error of the full and reduced model, respectively [25]. The estimated was corrected for selective genotyping according to Darvasi and Soller [61].

⁹

The 95% confidence intervals for each suggestive and significant QTL was determined using 10,000 bootstraps with re-sampling with software GridQTL [24].

¹⁰

The closest markers flanking (left and right) the chromosome location with the highest estimated F-value in the QTL scan.

Table 3. Significant and suggestive QTL for SI using half-sib family regression analysis1 in rainbow trout family 2008132.

Table 3. Significant and suggestive QTL for SI using half-sib family regression analysis¹ in rainbow trout family 2008132.