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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Use of RADs to identify canidate genes for response to crowding stress in rainbow trout

Authors
item Rexroad, Caird
item Liu, Sixin
item Vallejo, Roger
item Gao, Guangtu
item Palti, Yniv
item Weber, Gregory

Submitted to: Aquaculture America Conference
Publication Type: Abstract Only
Publication Acceptance Date: November 26, 2013
Publication Date: February 9, 2014
Citation: Rexroad III, C.E., Liu, S., Vallejo, R.L., Gao, G., Palti, Y., Weber, G.M. 2014. Use of RADs to identify canidate genes for response to crowding stress in rainbow trout. Aquaculture America Conference. 168.

Technical Abstract: 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 that aim to improve animal welfare and aquaculture production efficiency. Previously, we have reported microsatellite markers associated with QTL for 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 query the reference genome to identify positional candidate genes. One hundred and twenty fish identified as low or high responders were selected from family 2008052 for RAD genotyping; 55 RAD markers were associated with crowding stress QTL. Both the sequences of microsatellite and RAD markers associated with stress QTL were used as queries for BLAST search against the BAC sequences of the rainbow trout genome reference sequence. Based on the BAC physical maps of rainbow trout, additional BAC clones in the QTL regions were identified. The sequences of those BAC clones were used for BLAST searching the RAD markers mapped in families 2008052, 2009070 and 2009196. Based on the map positions of RAD markers, BAC clones which might be located on the non-targeted chromosomes were excluded from further analysis. BAC sequences mapped to the QTL regions were searched for putative genes using online tool FGENESH. In total, we identified 980 putative genes in the stress QTL regions. Among the 316 DETs (differentially expressed transcripts) in response to handling and confinement stress previously identified in the liver RNA-seq experiment, four were mapped to the stress QTL region on chromosome 12, and two 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.

Last Modified: 9/22/2014
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