Experiment
To map regions of the genome responsible for differences in influenza susceptibility 53 BXD lines derived from a cross between C57BL/6J and DBA/2J strains and the parental strains were infected with influenza A virus PR8, H1N1. DBA/2J mice are highly susceptible to many influenza A virus subtypes; in contrast C57BL/6J mice are more resistant. Body weight, survival, and mean time to death were monitored for 13 days post infection.
Four strains, BXD9, BXD13, BXD43, and BXD97 were highly resistant indicating that the infection may not cause any major pathology. In contrast, strain BXD28 lost body weight much more rapidly than even the highly susceptible DBA/2J parent.
Interval mapping of body weight loss detected the largest and most significant time-dependent locus on Chromosome 5 (NCBI Build 37):
QTL Ifvrq4 (influenza virus resistance QTL 4) mapped between 140-153 Mb on Chr 5 and exhibited wide genome significance on days 5, LRS:19.0, p<0.05, effect size 30%, and 6, LRS:19.4, effect size 31%. Interestingly the resistance allele at Ifvrq4 was inherited from the nominally sensitive DBA/2J parental strain.
Suggestive loci (LRS values between 10-15) mapped to Chromosomes 2, 6, 9, proximal and distal 16, and chromosome 17. The effect of these loci was also time-dependent.
Another suggestive locus was identified on Chromosome 10 on day 1 (LRS:14.1, p<0.37, effect size 23%). Its effect was lower at day 2 and not apparent at later days.
Analysis of survival rate traits on days 7, 8 and 11 post infection revealed significant peaks:
QTL Ifvrq5 (influenza virus resistance QTL 5) mapped between 140-153 Mb on Chromosome 5 and was significant at days 7 (LRS:24.8, p<0.05, effect size 37%) and at day 8 (LRS:19.7, effect size was 31%.
QTL Ifvrq6 (influenza virus resistance QTL 6) mapped between 37-45 Mb on Chromosome 19 and was significant at day 8 (LRS:19.4, p<0.05 effect size 29%). The resistance allele for both Ifvrq5 and Ifvrq6 was inherited from the DBA/2J parental strain.
Analysis of mean time if death (MTTD) identified a time-dependent significant locus on Chromosome 5:
QTL Ifvrq7 (influenza virus resistance QTL 7) mapped between 140-153 Mb on Chr 5, LRS:20.5, p<0.05, effect size 32%. The resistance allele for Ifvrq7 was also inherited from the DBA/2J parental strain. In addition suggestive QTL were revealed on Chrs 2 and 17 for the MTTD trait.
Potential interactions were found between Ifvrq5 and a new locus on Chromosome 9 as well as between Ifvrq5 and Ivfrq6 for the survival trait at day 8. For both interactions the allele combination of homozygous DBA/2J alleles showed the highest, and the combination of homozygous C56BL/6J alleles the lowest, survival scores.
For candidate gene searches the critical regions of the QTL were investigated.
Within the critical region (between 140-153 Mb, Chr 5) for QTL Ifvrq4, Ifvrq5 and Ifvrq7, genes Eif3b, Sdk1, Eif2ak1 and Rnf6 met the selection criteria from the 179 candidate genes profiled.
Within the critical region for QTL Ifvrq6 ( between 37-45 Mb, Chr 19) genes Sorbs1, Tctn3, Hps1 and Dnmbp met the selection criteria.
Potential candidate genes are also listed for the identified suggestive QTL, Table 2.
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