Quantitative trait loci for resistance to Flavobacterium psychrophilum in rainbow trout: effect of the mode of infection and evidence of epistatic interactions

Table 1 Results of QTL analyses for resistance traits after an injection challenge with F. psychrophilum

Trait	QTL	LRTmax	Position (cM)	CI (95%)	QTL effect	Resistance origin	Survival rate (%) according to allele origin at the QTL		% of phenotypic variance explained in DH progeny
Trait	QTL	LRTmax	Position (cM)	CI (95%)	QTL effect	Resistance origin	AP2	B57	% of phenotypic variance explained in DH progeny
RESISTANCE	Omy3	21.24**	89	67–97	0.25	AP2	76	34	–
	Omy10	10.31*	23	4–93	0.35	AP2	67	50	–
	Omy26	9.49*	21	1–41	0.38	AP2	73	40	–
	Omy29	23.94***	48	26–49	0.22	AP2	76	38	–
STATUS	Omy3	21.28***	89	68–95	+ 0.29	AP2	76	34	14%
	Omy25a	11.06*	14	0–27	− 0.21	B57	49	60	7%
	Omy29	19.06***	48	25–49	+ 0.27	AP2	76	38	12%
ENDURANCE	Omy15	10.99*	11	0–78	+ 2.63	AP2	–	–	nc
ENDURANCE	Omy29	9.90*	43	18–49	+ 2.63	AP2	–	–	11%

RESISTANCE: overall resistance, analysed with a Cox model survival analysis that takes failure, time to death and final survival (censored observations) into account; STATUS: (dead/surviving) phenotype at the end of the challenge, analysed as a binary trait; ENDURANCE: time to death in days after infection for dead fish only, analysed as a Gaussian trait; LRTmax = maximum of likelihood ratio test; Position in the genetic map in centimorgans (cM); CI = confidence interval; Chromosome-wide significant at *P ≤ 0.01; Genome-wide significant at **P ≤ 0.05 or ***P ≤ 0.01; The QTL effect was measured as the relative risk for RESISTANCE (B57 as the reference, risk = 1), as half the difference between the mean values of the two classes of homozygous progeny (individual values fixed as 1 for survivors and 0 for dead fish) for STATUS and as half the difference (in days) between the mean date of death of the two classes of homozygous progeny for ENDURANCE

ISSN: 1297-9686