Gene expression profiling of genetically determined growth variation in bivalve larvae (Crassostrea gigas)

Abstract

Bayne, 2004b). For bivalve larvae, Pace and colleagues have shown that a complex set of physiological processes regulate differences in genetically determined growth rates, including differential feeding rates and protein metabolism. These comparisons between fast-and slowgrowing families of larvae provide clear experimental advantages for understanding the mechanisms of growth heterosis during development. Accepted 27 November 2009 SUMMARY Growth rates in animals are governed by a wide range of biological factors, many of which remain poorly understood. To identify the genes that establish growth differences in bivalve larvae, we compared expression patterns in contrasting phenotypes (slowand fast-growth) that were experimentally produced by genetic crosses of the Pacific oyster Crassostrea gigas. Based on transcriptomic profiling of 4.5 million cDNA sequence tags, we sequenced and annotated 181 cDNA clones identified by statistical analysis as candidates for differential growth. Significant matches were found in GenBank for 43% of clones (N78), including 34 known genes. These sequences included genes involved in protein metabolism, energy metabolism and regulation of feeding activity. Ribosomal protein genes were predominant, comprising half of the 34 genes identified. Expression of ribosomal protein genes showed non-additive inheritance -i.e. expression in fast-growing hybrid larvae was different from average levels in inbred larvae from these parental families. The expression profiles of four ribosomal protein genes (RPL18, RPL31, RPL35 and RPS3) were validated by RNA blots using additional, independent crosses from the same families. Expression of RPL35 was monitored throughout early larval development, revealing that these expression patterns were established early in development (in 2-day-old larvae). Our findings (i) provide new insights into the mechanistic bases of growth and highlight genes not previously considered in growth regulation, (ii) support the general conclusion that genes involved in protein metabolism and feeding regulation are key regulators of growth, and (iii) provide a set of candidate biomarkers for predicting differential growth rates during animal development. Supplementary material available online at

Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation

“…Genes exhibiting expression patterns unique to particular taxa or phenotypes are more likely to have evolved to enable novel life histories (Whitehead, 2012;Whitehead et al, 2011). The comparative approach can be further improved by integrating phylogeny (Whitehead, 2012) or genetic background (Meyer and Manahan, 2010) into downstream analyses. For example, if three or more species or populations are being compared and a robust phylogeny is available, one may test whether the transcriptomic response across species is consistent with neutral expectations or rejects neutral expectations.…”

“…Within the field of environmental physiology, transcriptomics has been used successfully to address a broad range of questions concerning how or whether organisms can acclimate or adapt to the abiotic conditions associated with life in specific habitats (Evans and Hofmann, 2012). These investigations have demonstrated the complexity of responses to the environment (Chapman et al, 2011;Evans et al, 2011), isolated cellular and physiological processes that are robust or sensitive to environmental change (Logan and Somero, 2010), provided clues as to how organisms cope with life in challenging habitats (Podrabsky and Somero, 2004;Bilyk and Cheng, 2013), helped to predict vulnerabilities or resistance toward climate change (Barshis et al, 2013;Palumbi et al, 2014) and highlighted potentially important genes for future study (Meyer and Manahan, 2010;Whitehead et al, 2013), as well as leading to many other valuable scientific discoveries. However, like any other experimental approach, transcriptomics is associated with a set of limitations, and some have questioned the adequacy of transcriptomics to address particular questions of interest to environmental physiologists (Feder and Walser, 2005;Suarez and Moyes, 2012).…”

The effect of food conditioning on feeding and growth responses to variable rations in fast and slow growing spat of the Manila clam (Ruditapes philippinarum)

“…Constitutive (i.e., genetic) differences between fast and slow growing bivalves have long been related to variable degrees of multi-locus heterozygosity (Bayne and Hawkins, 1997;Garton et al, 1984;Hawkins, 1995;Hawkins et al, 1986;Holey and Foltz, 1987;Meyer and Manahan, 2010;Pace et al, 2006;Toro and Vergara, 1998). It seems to be well established that increasing heterozygosity causes the reduction of the metabolic costs associated to protein deposition (Bayne and Hawkins, 1997;Hawkins et al, 1986Hawkins et al, , 1989 this being a physiological factor contributing to the maximization of energy budget in fast growing individuals.…”

Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway

“…Peterson et al studied the differential mRNA expression of IGF-I and IGF-II in slow and fast-growth catfish [14]. Studies examining the differential gene expression in a FG phenotype in Pacific oyster Crassostrea gigas [15, 16] identified genes overrepresented in screens of growth heterosis, 50% of which were ribosomal proteins, indicating the importance of translational regulation in fast growth [17]. Several of these studies were on single growth factors, but Pace et al [18] showed that a range of environmental and metabolic variables can affect growth heterosis and that these interactions are very complex.…”