This research was supported by in-house funding of the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Cool and Cold Water Aquaculture (NCCCWA) CRIS Project 8082-31000-012 “Integrated Research Approaches for Improving Production Efficiency in Salmonids” and in part by an appointment of DGP to the ARS Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the USDA. ORISE is managed by ORAU under DOE contract number DE-AC05-06OR23100. The authors acknowledge Jim Everson, Mark Hostuttler, Josh Kretzer, Kyle Jenkins, Jenea McGowan, and Dave Payne (NCCCWA) for animal care and phenotyping; Jill Birkett and Lisa Radler (NCCCWA) for phenotyping and sample collection; Roseanna Long, Kristy Shewbridge, and Bryce Williams (NCCCWA) for DNA preparation; and Aunchalee Aussanasuwannakul, Hao Ma, Meghan Manor, Johnni-Ann Sims, and Susan Slider (West Virginia University) for phenotyping and sample collection. The use of trade, firm, or corporation names in this publication is for the information and convenience of the reader. Such use does not constitute an official endorsement or approval by the USDA or the ARS of any product or service to the exclusion of others that may be suitable. USDA is an equal opportunity provider and employer. Supplementary material The Supplementary Material for this article can be found online at: http://journal.frontiersin.org/article/10.3389/fgene.2016.00203/full#supplementary-material Table S1 The rainbow trout genetic linkage map. Click here for additional data file. Table S2 The 40 SNP markers from the two windows that explained the largest proportion of variance for FY and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014). Click here for additional data file. Table S3 The 40 SNP markers from the two windows that explained the largest proportion of variance for FW and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014). Click here for additional data file. Table S4 The 20 SNP markers from the one window that explained the largest proportion of variance for BW10 and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014). Click here for additional data file. Table S5 The 20 SNP markers from the one window that explained the largest proportion of variance for BW13 and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014). Click here for additional data file. Table S6 The 60 SNP markers from the three windows that explained the largest proportion of variance for CAR and harboring or neighboring genes from the same genome scaffold (Berthelot et al., 2014). Click here for additional data file.