Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing

Authors: Palti, Yniv; Vallejo, Roger; Gao, Guangtu; Liu, Sixin; HERNANDENZ, ALVARO - University Of Illinois; Rexroad, Caird; Wiens, Gregory - Greg

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/31/2015
Publication Date: 9/16/2015
Citation: Palti, Y., Vallejo, R.L., Gao, G., Liu, S., Hernandenz, A., Rexroad III, C.E., Wiens, G.D. 2015. Detection and validation of QTL affecting bacterial cold water disease resistance in rainbow trout using restriction-site associated DNA sequencing. PLoS One. 10(9):e0138435. doi: 10.1371/journal.pone.0138435.

Interpretive Summary: The work reported here is a major component of our efforts to identify genes affecting resistance to Bacterial cold water disease (BCWD) which is caused by the bacterium Flavobacterium psychrophilum, a major concern for rainbow trout aquaculture production and managers of recreational fisheries. Genetic markers representing the entire rainbow trout genome were analyzed on two pedigreed families, which revealed a single chromosome region with large effect on this trait in one family and several other chromosome regions with moderate effects in the experimental population of the national center for cool and cold water aquaculture (NCCCWA). Three of the chromosome regions affecting BCWD resistance in this population were also found to affect stress level in response to handling and confinement in a separate rainbow trout population. Several candidate genes that may be involved in immune or stress response on those chromosomal regions were identified through alignment of the genetic markers and the trout reference genome sequence. Further genetic analyses are currently underway to validate the impact of those genome regions in the response to BCWD infection in other rainbow trout breeding populations important for aquaculture production in the US, and to increase our confidence in the likely underlying causative genetic polymorphisms in those chromosome regions.

Technical Abstract: Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. Using microsatellites genome scan we have previously detected significant and suggestive QTL with major effects on the phenotypic variation of survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). In this study, we used selective genotyping of SNPs from SbfI restriction-site associated DNA (RAD) sequence data from two pedigreed families to validate the major QTL from the previous work and to detect new QTL. The use of RAD SNPs in the genome scans increased the number of mapped markers from ~300 to ~5,000 per family. The significant QTL detected in the microsatellites scan on chromosome Omy8 in family 2009070 was validated explaining up to 58% of the phenotypic variance in that family, and a second QTL was also detected on Omy8. Two novel QTL on Omy11 and 14 were detected in the same family, and the previously suggestive QTL on Omy1, 7 and 25 were validated. The significant QTL on Omy6 and 12 were validated and a new QTL on Omy8 was detected in family 2009196, but none of the previously detected suggestive QTL were validated in this family. The two Omy8 QTL from family 2009070 and the Omy12 QTL from family 2009196 were found to be co-localized with handling stress response QTL that our group has previously identified in a separate pedigreed family. However, with the currently available data we cannot determine if the co-localized QTL are the result of genes with pleiotropic effects or mere physical proximity on the same chromosome segment. The genetic markers linked to BCWD resistance QTL were used to query the scaffolds of the rainbow trout reference genome assembly and the QTL-positive scaffold sequences were found to contain 100 putative candidate genes from our previous RNA-seq study. Several of the candidate genes located on or near the two Omy8 QTL detected in family 2009070 suggest potential linkages between stress response and the regulation of immune response in rainbow trout.