Identification of Positional Candidate Genes for Response to Crowding Stress in Rainbow Trout

Fish under intensive rearing conditions experience various stressors which have negative impacts on survival, growth, reproduction and fillet quality. Identifying and characterizing the molecular mechanisms underlying stress responses will facilitate the development of strategies for improving animal welfare and aquaculture production efficiency. Previously, we have reported microsatellite markers associated with QTL for response to crowding stress in rainbow trout. The objectives of this study were to identify RAD (restriction-site associated DNA) markers associated with the plasma cortisol response to crowding stress and to query the draft reference genome to identify candidate genes. One hundred and twenty offspring with low or high EBV values were selected from the mapping family 2008052 for RAD genotyping, and 55 RAD markers associated with response to crowding stress were identified. The sequences of microsatellite and RAD markers associated with stress QTL were used as queries for BLAST search against the BAC sequences of rainbow trout. Based on the BAC physical map of rainbow trout, additional BAC clones in the QTL regions were identified. In total, 980 putative genes in the stress QTL regions were identified using the online program FGENESH. Among the 316 DETs (differentially expressed transcripts) in response to handling and confinement stress previously identified in our liver RNA-seq study, four DETs were mapped to the stress QTL region on chromosome 12, and two DETs were mapped to the stress QTL region on chromosome 20. Additional candidate genes were identified by pathway analysis and gene annotation based on BLAST search of the NCBI NR database.