Marine Biotechnology

, Volume 16, Issue 3, pp 349–360 | Cite as

Detection of QTL in Rainbow Trout Affecting Survival When Challenged with Flavobacterium psychrophilum

  • Roger L. Vallejo
  • Yniv PaltiEmail author
  • Sixin Liu
  • Jason P. Evenhuis
  • Guangtu Gao
  • Caird E. RexroadIII
  • Gregory D. Wiens
Original Article


Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation in survival following challenge with Flavobacterium psychrophilum (Fp), the causative agent of BCWD in rainbow trout (Oncorhynchus mykiss). A family-based selection program to improve resistance was initiated in 2005 at the USDA National Center for Cool and Cold Water Aquaculture. Select crosses were made in 2007 and 2009 to evaluate family-based disease survival using Fp injection challenges. From each putative F2/BC1 family generated in 2009, 200–260 fish were challenged in 4–7 replicates per family. Whole genome QTL scans of three F2/BC1 families were conducted with about 270 informative microsatellite loci per family spaced at an average interval size of 6 cM throughout the rainbow trout genome. Markers on chromosomes containing QTL were further evaluated in three additional F2/BC1 families. The additional F2/BC1 families were sire or dam half-sibs (HS) of the initially genome scanned families. Overall, we identified nine major QTL on seven chromosomes that were significant or highly significant with moderate to large effects of at least 13 % of the total phenotypic variance. The largest effect QTL for BCWD resistance explaining up to 40 % of the phenotypic variance was detected on chromosome OMY8 in family 2009070 and in the combined dam HS family 2009069–070. The nine major QTL identified in this study are candidates for fine mapping to identify new markers that are tightly linked to disease resistance loci for using in marker assisted selection strategies.


QTL Bacterial cold water disease Disease resistance Flavobacterium psychrophilum Rainbow trout 



We would like to acknowledge the following people for providing technical assistance including Kristy Shewbridge, Roseanna Long, Brian Smith, Lindsey Pierce, Nathan Johnson, Renee Fincham, Tim Welch, Jeff Silverstein, Tim Leeds, Travis Moreland, Jen Harper, Ryan Lipscomb, Jessica Thompson, Kathryn Hovatter, Kyle Jenkins, Jenea McGowan, James Everson, David Payne, Josh Kretzer, Kevin Melody, and Mark Hostuttler. RLV is very grateful to Dirk-Jan de Koning for his generous lengthy discussions and suggestions on mapping QTL for complex traits in outbred populations. Mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

Supplementary material

10126_2013_9553_MOESM1_ESM.pdf (308 kb)
ESM 1 (PDF 307 kb)


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Copyright information

© Springer Science+Business Media New York 2013

Authors and Affiliations

  • Roger L. Vallejo
    • 1
  • Yniv Palti
    • 1
    Email author
  • Sixin Liu
    • 1
  • Jason P. Evenhuis
    • 1
  • Guangtu Gao
    • 1
  • Caird E. RexroadIII
    • 1
  • Gregory D. Wiens
    • 1
  1. 1.National Center for Cool and Cold Water AquacultureNAA-ARS-USDAKearneysvilleUSA

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