Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss GARRETT J. MCKINNEY,* † MATTHEW C. HALE,* GILES GOETZ, ‡ MICHAEL GRIBSKOV,* FRANK P. THROWER § and KRISTA M. NICHOLS* ‡ *Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA, †School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195-5020, USA, ‡Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA, §Ted Stevens Marine Research Institute, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, AK 99801, USA Abstract Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behav- iours. We sampled offspring produced from migrant and resident parents, collecting whole embryos prior to the beginning of first feeding, and brain tissue at three addi- tional time points over the first year of development. RNA sequencing for 32 individu- als generated a reference transcriptome of 30 177 genes that passed count thresholds. Differential gene expression between migrant and resident offspring was observed for 1982 genes. The greatest number of differentially expressed genes occurred at 8 months of age, in the spring a full year before the obvious physiological transformation from stream-dwelling parr to sea water-adaptable smolts begins for migrant individuals. Sex and age exhibited considerable effects on differential gene expression between migrants and resident offspring. Differential gene expression was observed in genes previously associated with migration, but also in genes previously unassociated with early life history divergence. Pathway analysis revealed coordinated differential expression in genes related to phototransduction, which could modulate photoperiod responsiveness and variation in circadian rhythms. The role for early differentiation in light sensitivity and biological rhythms is particularly intriguing in understanding early brain processes involved in differentiation of migratory and resident life history types. Keywords: migration, RNAseq, transcriptome Received 7 January 2015; revision received 27 February 2015; accepted 2 March 2015 Introduction Migration is a common theme across taxa whether it is to take advantage of periodic fluctuations in resources at a seasonal or even daily level, or to move between habitats that are suitable for different developmental stages of an organism (Dingle 1996; Pulido 2007; Wysu- jack et al. 2009). Migration often occurs at a critical sea- sonal period (Dingle 1996), and the ultimate success of an individual may be greatly affected by the timing of migration which is modulated by environmental signals such as photoperiod and temperature (Thorstad et al. Correspondence: Krista M. Nichols, Fax: 206-860-3335; E-mail: krista.nichols@noaa.gov and Garrett J. McKinney, Fax: 206-685-7471; E-mail: gjmckinn@u.washington.edu © 2015 John Wiley & Sons Ltd Molecular Ecology (2015) 24, 1792–1809 doi: 10.1111/mec.13143