Original Article

Marine Biotechnology

, Volume 13, Issue 2, pp 215-231

First online:

Transcriptome Profiling of Embryonic Development Rate in Rainbow Trout Advanced Backcross Introgression Lines

  • Peng XuAffiliated withDepartment of Biological Sciences, Purdue UniversityApplied Aquatic Genomics Center, Chinese Academy of Fishery Sciences
  • , Lauren M. McIntyreAffiliated withDepartment of Molecular Genetics and Microbiology, University of Florida
  • , Julie ScardinaAffiliated withDepartment of Biological Sciences, Purdue University
  • , Paul A. WheelerAffiliated withSchool of Biological Sciences and Center for Reproductive Biology, Washington State University
  • , Gary H. ThorgaardAffiliated withSchool of Biological Sciences and Center for Reproductive Biology, Washington State University
  • , Krista M. NicholsAffiliated withDepartment of Biological Sciences, Purdue UniversityDepartment of Forestry and National Resources, Purdue University Email author 

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In rainbow trout (Oncorhynchus mykiss) and other fishes, embryonic development rate is an ecologically and evolutionarily important trait that is closely associated with survival and physiological performance later in life. To identify genes differentially regulated in fast and slow-developing embryos of rainbow trout, we examined gene expression across developmental time points in rainbow trout embryos possessing alleles linked to a major quantitative trait loci (QTL) for fast versus slow embryonic development rate. Whole genome expression microarray analyses were conducted using embryos from a fourth generation backcross family, whereby each backcross generation involved the introgression of the fast-developing alleles for a major development rate QTL into a slow-developing clonal line of rainbow trout. Embryos were collected at 15, 19, and 28 days post-fertilization; sex and QTL genotype were determined using molecular markers, and cDNA from 48 embryos were used for microarray analysis. A total of 183 features were identified with significant differences between embryonic development rate genotypes. Genes associated with cell cycle growth, muscle contraction and protein synthesis were expressed significantly higher in embryos with the fast-developing allele (Clearwater) than those with the slow-developing allele (Oregon State University), which may associate with fast growth and early body mass construction in embryo development. Across time points, individuals with the fast-developing QTL allele appeared to have earlier onset of these developmental processes when compared to individuals with the slow development alleles, even as early as 15 days post-fertilization. Differentially expressed candidate genes chosen for linkage mapping were localized primarily to regions outside of the major embryonic development rate QTL, with the exception of a single gene (very low-density lipoprotein receptor precursor).


Rainbow trout Gene expression QTL Embryonic development rate Microarray