7 Genomic Approaches in Aquaculture and Fisheries
227
in the mRNA expression of different myogenic factors (Levesque et al. 2008).
However, until very recently, global transcriptional changes in muscle of GH transgenic salmon had not been evaluated using high-throughput approaches. A recent
study has reported on the effects of exogenous bovine GH administration on the
rainbow trout muscle transcriptome using the GRASP 16 K cDNA microarray (Gahr
et al. 2008). In this study, GH was injected in fish from two different rainbow trout
families, selected for low- and high- growth rates, and different sets of genes up- and
down-regulated were identified in white muscle mediating cellular processes such as
cell cycle, immune response, metabolism or protein degradation. Also recently, the
muscle transcriptome was investigated in another growth model (fasting and refeeding) using a custom cDNA microarray generated in the INRA-GADIE Resource
Center containing 9,023 gene sequences (Rescan et al. 2007). In the early phases of
muscle growth recovery, an induction of genes involved in RNA processing, translation, cell proliferation followed by a later phase involved in Golgi and endoplasmic
reticulum dynamics and muscle remodeling was observed.
To date, no studies on gene expression related to muscle growth using microarrays have been performed in model organisms like zebrafish and fugu, with fully
sequenced genomes. In fugu, subtractive hybridization and quantitative PCR were
used to identify differentially expressed transcripts in skeletal muscle from young
versus adult individuals (Fernandes et al. 2005). The adult skeletal muscle stops
muscle fiber formation, inhibiting the recruitment of muscle fibers, whereas the
young skeletal muscle has an active fiber formation. Fernandes et al. identified
four novel genes that were expressed at higher levels in fast muscle of adult fugu
(Fernandes et al. 2005). These novel genes probably act as growth inhibitors but
they do not have significant homology with any known gene. This study provided
the initial tools to develop high-throughput strategies to study growth in fugu since
they have generated different ESTs libraries that could be used to create cDNA or
oligonucleotide microarrays. It is surprising the absence of microarray studies in the
growing muscle of zebrafish (hypertrophic growth), since there are oligonucleotides
microarrays commercially available (i.e. Agilent) and its genome is fully sequenced
and partially annotated.
7.4.3 Transcriptomic Changes in Skeletal Muscle Related
to External Factors
External factors such as temperature or infectious pathogens may have an effect on
different physiological processes that directly could affect muscle growth. Using
high-throughput technologies, the skeletal muscle transcriptome has been studied
in response to changes in ambient temperature (Cossins et al. 2006, Gracey et al.
2004, Malek et al. 2004), vitellogenesis-induced atrophy of skeletal muscle (Salem
et al. 2006) and vaccination (Purcell et al. 2006). The effects of temperature changes
on the skeletal muscle transcriptome were initially studied in zebrafish (Malek
et al. 2004). A temperature shift of 10 ◦ C provoked an increase in the expression
227
in the mRNA expression of different myogenic factors (Levesque et al. 2008).
However, until very recently, global transcriptional changes in muscle of GH transgenic salmon had not been evaluated using high-throughput approaches. A recent
study has reported on the effects of exogenous bovine GH administration on the
rainbow trout muscle transcriptome using the GRASP 16 K cDNA microarray (Gahr
et al. 2008). In this study, GH was injected in fish from two different rainbow trout
families, selected for low- and high- growth rates, and different sets of genes up- and
down-regulated were identified in white muscle mediating cellular processes such as
cell cycle, immune response, metabolism or protein degradation. Also recently, the
muscle transcriptome was investigated in another growth model (fasting and refeeding) using a custom cDNA microarray generated in the INRA-GADIE Resource
Center containing 9,023 gene sequences (Rescan et al. 2007). In the early phases of
muscle growth recovery, an induction of genes involved in RNA processing, translation, cell proliferation followed by a later phase involved in Golgi and endoplasmic
reticulum dynamics and muscle remodeling was observed.
To date, no studies on gene expression related to muscle growth using microarrays have been performed in model organisms like zebrafish and fugu, with fully
sequenced genomes. In fugu, subtractive hybridization and quantitative PCR were
used to identify differentially expressed transcripts in skeletal muscle from young
versus adult individuals (Fernandes et al. 2005). The adult skeletal muscle stops
muscle fiber formation, inhibiting the recruitment of muscle fibers, whereas the
young skeletal muscle has an active fiber formation. Fernandes et al. identified
four novel genes that were expressed at higher levels in fast muscle of adult fugu
(Fernandes et al. 2005). These novel genes probably act as growth inhibitors but
they do not have significant homology with any known gene. This study provided
the initial tools to develop high-throughput strategies to study growth in fugu since
they have generated different ESTs libraries that could be used to create cDNA or
oligonucleotide microarrays. It is surprising the absence of microarray studies in the
growing muscle of zebrafish (hypertrophic growth), since there are oligonucleotides
microarrays commercially available (i.e. Agilent) and its genome is fully sequenced
and partially annotated.
7.4.3 Transcriptomic Changes in Skeletal Muscle Related
to External Factors
External factors such as temperature or infectious pathogens may have an effect on
different physiological processes that directly could affect muscle growth. Using
high-throughput technologies, the skeletal muscle transcriptome has been studied
in response to changes in ambient temperature (Cossins et al. 2006, Gracey et al.
2004, Malek et al. 2004), vitellogenesis-induced atrophy of skeletal muscle (Salem
et al. 2006) and vaccination (Purcell et al. 2006). The effects of temperature changes
on the skeletal muscle transcriptome were initially studied in zebrafish (Malek
et al. 2004). A temperature shift of 10 ◦ C provoked an increase in the expression