An Integrated Approach to Gene Discovery and Marker Development in Atlantic Cod (Gadus morhua)

Abstract

Atlantic cod is a species that has been overexploited by the capture fishery. Programs to domesticate this species are underway in several countries, including Canada, to provide an alternative route for production. Selective breeding programs have been successfully applied in the domestication of other species, with genomics-based approaches used to augment conventional methods of animal production in recent years. Genomics tools, such as gene sequences and sets of variable markers, also have the potential to enhance and accelerate selective breeding programs in aquaculture, and to provide better monitoring tools to ensure that wild cod populations are well managed. We describe the generation of significant genomics resources for Atlantic cod through an integrated genomics/selective breeding approach. These include 158,877 expressed sequence tags (ESTs), a set of annotated putative transcripts and several thousand single nucleotide polymorphism markers that were developed from, and have been shown to be highly variable in, fish enrolled in two selective breeding programs. Our EST collection was generated from various tissues and life cycle stages. In some cases, tissues from which libraries were generated were isolated from fish exposed to stressors, including elevated temperature, or antigen stimulation (bacterial and viral) to enrich for transcripts that are involved in these response pathways. The genomics resources described here support the developing aquaculture industry, enabling the application of molecular markers within selective breeding programs. Marker sets should also find widespread application in fisheries management.Electronic supplementary materialThe online version of this article (doi:10.1007/s10126-010-9285-z) contains supplementary material, which is available to authorized users.

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

“…74%) were selected following screening, of which 1641 were informative (53%). Further details regarding SNP development, genotyping and linkage mapping are contained in the electronic supplementary material and available in Hubert et al (2009Hubert et al ( , 2010 and Bowman et al (2007Bowman et al ( , 2010. To ensure that our samples were representative and to estimate the frequency of rare alleles, two (temperature-associated, see below) SNPs (cgpGmo-S866 and cgpGmo-S419) were genotyped in an additional 500 individuals (adults and juveniles) from southern Newfoundland, using the KASpar genotyping system (KBiosciences).…”

Identification and molecular cloning of Atlantic cod (Gadus morhua) activating transcription factor 3 (ATF3) transcript and its induction in spleen following intraperitoneal polyriboinosinic polyribocytidylic acid injection

“…BLASTn analysis of the putative cod ATF3 cDNA against the CGP EST database identified a total of 38 ATF3-representing clones, all of which were identified in cDNA libraries enriched for transcripts that were induced by pIC stimulation ( Table 2, see Supplemental Table S1 for EST accession numbers) [13,15]. In addition, 35 of the 38 ATF3-representing clones were generated from the spleen pIC forward SSH library that was described in Rise et al [15] (Table 2).…”

“…To verify this assembly, a PCR using primers designed near the 5 0 and 3 0 ends of the cDNA [15]. Normalized cDNA libraries were constructed to normalize the abundance of transcripts in order to maximize gene discovery [13]. b The identifiers of the SSH or normalized libraries in the CGP EST database:…”

A moderate increase in ambient temperature modulates the Atlantic cod (Gadus morhua) spleen transcriptome response to intraperitoneal viral mimic injection

“…Rise et al [18]; Milev-Milovanovic et al [19]; Workenhe et al [20]; Booman et al [21]). In this study we used the 20,000 element (20K) oligonucleotide microarray platform (GEO accession # GPL10532 [21]), which includes sequences from both suppression subtractive hybridization (SSH) and normalized libraries enriched for immune and heat-stress responsive transcripts [22-26] (as well as sequences from several other normalized libraries), and reverse transcription – quantitative polymerase chain reaction (QPCR), to investigate the effects of an increasing temperature regime (gradually from 10°C to 16°C – Figures 1 and 2) on the Atlantic cod spleen response to the intra-peritoneal (IP) injection of the viral mimic polyriboinosinic polyribocytidylic acid (pIC). A better understanding of how moderately increased ambient temperature affects the genes and pathways involved in the cod’s anti-viral response may shed light on the potential mechanisms of temperature-induced immune suppression [14,17,27-29].…”