Figure 1.
Production of experimental families and QTL design.
DH: doubled haploid individuals (all homozygous), obtained by mitogynogenesis (fertilization of ova with UV irradiated sperm followed by inhibition of the first embryonic mitosis); VREFT values: viral replication in excised fin tissue (in pfu.mg−1); in each lineage, F1 females are isogenic, and their progeny were pooled into a single family. *:offspring used to measure VREFT values were produced one year later, from a single F98 female.
Table 1.
Main characteristics of DH families until infectious challenge.
Figure 2.
Cumulative survival curves after waterborne infection of the two DH families used for selective genotyping.
Kaplan-Meier estimation of survival functions after infectious challenge for the two DH families. Fish were infected by incubation for 2 h with the VHSV strain 07–71. All fish, including heterozygous individuals detected after genotyping of the phenotypic tails, were conserved to draw the curve. (A) Hazard function of DH-F98 progeny (1125 fish challenged, 9 aquaria). (B) Hazard function of DH-F00 progeny (1200 fish challenged, 10 aquaria).
Figure 3.
Survival-associated QTL detected in DH-F98 and DH-F00 families after VHSV waterborne infection using a bidirectional selective genotyping strategy.
The figure shows significant QTL identified in DH-F98 (A) and DH-F00 families (B). In each family, about 20% of the entire population (1125 and 1200 fish respectively) were genotyped, i.e. about 10% extremely susceptible individuals (first to die) and 8% (DH-F98) to 10% (DH-F00) resistant fish (survivors) according to the survival at the end of the challenge. Only linkage groups with significant QTL are shown. Linkage groups are labelled according to (Guyomard et al. 2012). C indicates the position of centromere. Marker positions are given on the linkage groups rebuilt for each family from all genotyped individuals. At every marker position, a P-value <0.01 at the chromosome-wide level (χ2-test with Bonferroni correction) was taken as the significance threshold. For each linkage group, the black line indicates the significance threshold χ2 value at the chromosome-wide level. The QTL on RT31 was also significant at the genome-wide level.
Figure 4.
Likelihood ratio profiles for survival and VREFT values associated QTL on linkage group RT31 in DH-F98 and DH-F00 families.
Analyses for the survival-associated QTL were performed with the complete post challenge life-time dataset (3 aquaria per family, i.e. 354 fish in HD-F98 family and 360 fish in HD-F00 family, heterozygous individuals excluded). For VREFT-associated QTL, 133 and 300 fish respectively were analysed in the two families. A total of 8 and 10 markers located on RT31 were genotyped in DH-F98 and DH-F00 respectively. Marker names and positions are available on supplementary Table 1S. Likelihood values were obtained using the QTLMap software. Likelihood thresholds for significant QTL (P<0.01 at the genome-wide level) were determined from LRT distribution of 10000 simulations under the null hypothesis (no QTL). Survival-associated QTL locate at 105 and 106 cM in DH-F98 and DH-F00 respectively. VREFT-associated QTL locate at 106 cM in both families (confidence intervals estimated at about 1 cM in length).
Figure 5.
Effect of allelic status at OMM5005 marker (RT31) on cumulative survival curves during infectious challenge and distribution of VREFT values in the two DH families.
(A) Cumulative hazard functions (Kaplan-Meier estimator) for the alternative R/S alleles. (B) Frequency distribution of VREFT values in the two families for the alternative R/S alleles. VREFT values (pfu.mg−1) are log-transformed.
Table 2.
Performances (means and standard deviations) according to the alternative alleles at OMM5005 marker and percentage of the phenotypic variance explained for time to death (TTD) and viral replication in fin explants (VREFT).
Table 3.
Characteristics of additional DH families and marker-trait associations at OMM5005 in extreme phenotypes (early dead/surviving).