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

Abstract

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).

Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

“…These individual differences could not be due to environmental variation because we sampled the animals from one natural population. Rather, this inter-individual variation could be due to the age of the individuals sampled, as gene expression profiles can change rapidly at different stages of development (e.g., Xu et al, 2011). The three individuals we sampled were all young of the year, but they differed by up to 20 mm in the SVL and thus may have been at slightly different stages of development.…”

The influence of parental effects on transcriptomic landscape during early development in brook charr (Salvelinus fontinalis, Mitchill)

“…For example, genes involved in the cell cycle and nucleotide and nucleic acid metabolism functional categories were found to be differentially expressed between two ecotypes of lake whitefish at the embryonic stage, suggesting their importance in transcription regulation and development of the embryos (Nolte et al, 2009). In addition, genes involved in these two functional categories were also found to be overexpressed in fast developing rainbow trout individuals (Xu et al, 2010). Thus, the higher length of L~R# relative to R~L# hybrids at the yolk sac resorption stage, and faster development rate from hatching to yolk Parental effects on transcriptomic profiles B Bougas et al sac resorption, could be associated with the great number of genes that were differentially expressed at this stage.…”

“…In particular, Gibson et al (2004) showed that 2% of the 12 559 analyzed genes in F1 heterozygotes presented parental effects (that is, a resemblance to either paternal or maternal expression). In fishes, previous studies mostly emphasized differences in gene expression during embryogenesis to detect maternal-effect genes across developmental transitions or to detect differences in development rate in embryos (Mathavan et al, 2005;Bai et al, 2007;Nolte et al, 2009;Xu et al, 2010;Renaut et al, 2011). To our knowledge, however, no study has yet systematically focused on investigating the dynamics of parental effects on the transcriptome across different development stages.…”

Linking transcriptomic and genomic variation to growth in brook charr hybrids (Salvelinus fontinalis, Mitchill)

“…Microarrays and, more recently, RNA-seq by means of NGS technologies have been used to compare the transcriptomes of phenotypically distinct individuals, namely in salmonid fishes St-Cyr et al, 2008;Goetz et al, 2010;Jeukens et al, 2010;Xu et al, 2010). Typically, many transcriptomic differences involved genes with functions related to energy production, muscular activity, immunity and cell cycle regulation processes.…”