Marine Biotechnology

, Volume 13, Issue 2, pp 215–231

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


  • Peng Xu
    • Department of Biological SciencesPurdue University
    • Applied Aquatic Genomics CenterChinese Academy of Fishery Sciences
  • Lauren M. McIntyre
    • Department of Molecular Genetics and MicrobiologyUniversity of Florida
  • Julie Scardina
    • Department of Biological SciencesPurdue University
  • Paul A. Wheeler
    • School of Biological Sciences and Center for Reproductive BiologyWashington State University
  • Gary H. Thorgaard
    • School of Biological Sciences and Center for Reproductive BiologyWashington State University
    • Department of Biological SciencesPurdue University
    • Department of Forestry and National ResourcesPurdue University
Original Article

DOI: 10.1007/s10126-010-9283-1

Cite this article as:
Xu, P., McIntyre, L.M., Scardina, J. et al. Mar Biotechnol (2011) 13: 215. doi:10.1007/s10126-010-9283-1


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 troutGene expressionQTLEmbryonic development rateMicroarray

Supplementary material

10126_2010_9283_MOESM1_ESM.doc (54 kb)
Supplemental Table 1Primer sequences used for marker-assisted selection and qRT-PCR (DOC 54 kb)
10126_2010_9283_MOESM2_ESM.doc (56 kb)
Supplemental Table 2Primer sequences and details for genes successfully amplified for linkage mapping (DOC 56 kb)
10126_2010_9283_MOESM3_ESM.doc (44 kb)
Supplemental Figure 1Comparison of gene expression results from qRT-PCR analysis and microarray analysis. On the y-axis, the positive values indicate the genes have higher expression in CW embryos, and the negative values indicate the genes have higher expression in OSU embryos. Ten genes examined in the qRT-PCR analysis are presented as subunit of the THO complex (THO differentially expressed at 28 dpf), transforming growth factor-beta-induced protein ig-h3 precursor (TGFBI differentially expressed at 19 dpf), high choriolytic enzyme 1 precursor (HCE1 differentially expressed at 28 dpf ), myosin light chain 1, skeletal muscle isoform (MYL1differentially expressed at 19 dpf), myosin regulatory light chain 2 (MYL2 differentially expressed at 19 dpf), myosin light chain 3, skeletal muscle isoform (MYL3 differentially expressed at 19 dpf), thiosulfate sulfurtransferase KAT (KAT, differentially expressed at 15 dpf), ceruloplasmin precursor (CP differentially expressed at 19 dpf), parvalbumin beta 1 (pvalb1 differentially expressed at 15 dpf and 19 dpf), parvalbumin beta 2 (pvalb2 differentially expressed at 19 dpf). The asterisk is used to indicate the statistical significance in the qRT-PCR at the p < 0.05 level (DOC 44 kb)

Copyright information

© Springer Science+Business Media, LLC 2010