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Volume 56 • Number 10 • October 2013

Special commemorative issue marking the one-year anniversary of “Genomics: The Power and the Promise”

Title Page


Vol. 56No. 10pp. v


Vol. 56No. 10pp. 540–541


Vol. 56No. 10pp. 556–566
The emergence of the middle class in countries such as Brazil, Russia, India, and China is resulting in increasing global demand for animal-based food products. This increase represents a unique opportunity for Canadian livestock producers to export their products to new markets and expand Canada’s reputation as a global provider of safe and highest quality food items. This article has two major themes. First, current Canadian contributions to livestock genomics in the cattle and swine industries are outlined. Second, important future opportunities are discussed, including the high throughput collection of phenotypic data, development of environmentally friendly livestock, emergence of decision support software, and the use of Web 2.0. Through the use of genomic technologies, livestock producers can not only ensure that the nutritional demands of Canada are secured, but also play a pivotal role in ensuring the rest of the world is fed as well. Furthermore, investment through initiatives led by Genome Canada has ensured that Canada is favorably positioned to contribute cutting-edge solutions to meet this global challenge. Ultimately, genomic-based innovations will enable producers to increase efficiency, lower production costs, decrease the use of prophylactics, and limit the expenditure of resources.


Vol. 56No. 10pp. 567–576
Exposure to elevated temperature is an inherent feature of Atlantic cod (Gadus morhua) sea-cage culture in some regions (e.g., Newfoundland) and may also become an increasingly prevalent challenge for wild fish populations because of accelerated climate change. Therefore, understanding how elevated temperatures impacts the immune response of this commercially important species may help to reduce the potential negative impacts of such challenges. Previously, we investigated the impacts of moderately elevated temperature on the antiviral responses of Atlantic cod (Hori et al. 2012) and reported that elevated temperature modulated the spleen transcriptome response to polyriboinosinic polyribocytidylic acid (pIC, a viral mimic). Herein, we report a complementary microarray study that investigated the impact of the same elevated temperature regime on the Atlantic cod spleen transcriptome response to intraperitoneal (IP) injection of formalin-killed Aeromonas salmonicida (ASAL). Fish were held at two different temperatures (10 °C and 16 °C) prior to immune stimulation and sampled 6 and 24 h post-injection (HPI). In this experiment, we identified 711 and 666 nonredundant ASAL-responsive genes at 6HPI and 24HPI, respectively. These included several known antibacterial genes, including hepcidin, cathelicidin, ferritin heavy subunit, and interleukin 8. However, we only identified 15 differentially expressed genes at 6HPI and 2 at 24HPI (FDR 1%) when comparing ASAL-injected fish held at 10 °C versus 16 °C. In contrast, the same comparisons with pIC-injected fish yielded 290 and 339 differentially expressed genes (FDR 1%) at 6HPI and 24HPI, respectively. These results suggest that moderately elevated temperature has a lesser effect on the Atlantic cod spleen transcriptome response to ASAL (i.e., the antibacterial response) than to pIC (i.e., antiviral response). Thus, the impacts of high temperatures on the cod’s immune response may be pathogen dependent.
Vol. 56No. 10pp. 577–585
Forest trees exhibit a remarkable range of adaptations to their environment, but as a result of frequent and long-distance gene flow, populations are often only weakly differentiated. Lodgepole and jack pine hybridize in western Canada, which adds the opportunity for introgression through hybridization to contribute to population structure and (or) adaptive variation. Access to large sample size, high density SNP datasets for these species would improve our ability to resolve population structure, parameterize introgression, and separate the influence of demography from adaptation. To accomplish this, 454 transcriptome reads for lodgepole and jack pine were assembled using Newbler and MIRA, the assemblies mined for SNPs, and 1536 SNPs were selected for typing on lodgepole pine, jack pine, and their hybrids (N = 536). We identified population structure using both Bayesian clustering and discriminate analysis of principle components. Introgressed SNP loci were identified and their influence on observed population structure was assessed. We found that introgressed loci resulted in increased differentiation both within lodgepole and jack pine populations. These findings are timely given the recent mountain pine beetle population expansion in the hybrid zone, and will facilitate future studies of adaptive traits in these ecologically important species.
Vol. 56No. 10pp. 586–591
This study reports a genome wide scan for chromosome regions and their haplotypes that significantly associated with average daily gain (ADG), dry matter intake (DMI), and residual feed intake (RFI) in beef cattle. The study used data from 597 Angus, 450 Charolais, and 616 crossbred beef cattle, and the Illumina Bovine SNP50 beadchip. Extended haplotype homozygosity was used to identify chromosome regions that had been recently selected for in the three groups of animals. Such regions in the crossbreds were tested for association with ADG, DMI, and RFI. At false discovery rates of 5% and 10%, there were six and eight chromosome regions showing significant associations with the traits, respectively. At nominal significance levels (at least P < 0.05), 23 regions with a total number of 31 haplotypes were found significantly associated with at least one of the three traits. The proportion of phenotypic variance explained by these 23 regions varied depending on the trait; the highest proportion for ADG, DMI, and RFI was 13.50%, 9.92%, and 2.64%, respectively. Most of the haplotypes affected single traits, except for GAA (BTA4), GCG (BTA7), and TAGT (BTA12) that affected multiple traits. Thirty-six quantitative trait loci for 16 production traits, from the current literature, covered fully or in part the 23 chromosome regions. The findings from this study might be an important contribution to the current knowledge of the beef cattle genome and to the effective identification of causative genes associated with important traits in cattle.
Vol. 56No. 10pp. 592–598
Genetic variation in Gir cattle (Bos indicus) has so far not been well characterized. In this study, we used whole genome sequencing of three Gir bulls and a pooled sample from another 11 bulls to identify polymorphisms and loci under selection. A total of 9 990 733 single nucleotide polymorphisms (SNPs) and 604 308 insertion/deletions (indels) were discovered in Gir samples, of which 62.34% and 83.62%, respectively, are previously unknown. Moreover, we detected 79 putative selective sweeps using the sequence data of the pooled sample. One of the most striking sweeps harbours several genes belonging to the cathelicidin gene family, such as CAMP, CATHL1, CATHL2, and CATHL3, which are related to pathogen- and parasite-resistance. Another interesting region harbours genes encoding mitogen-activated protein kinases, which are involved in directing cellular responses to a variety of stimuli, such as osmotic stress and heat shock. These findings are particularly interesting because Gir is resistant to hot temperatures and tropical diseases. This initial selective sweep analysis of Gir cattle has revealed a number of loci that could be important for their adaptation to tropical climates.
Vol. 56No. 10pp. 599–611
A microbial community (short-chain alkane-degrading culture, SCADC) enriched from an oil sands tailings pond was shown to degrade C6–C10 alkanes under methanogenic conditions. Total genomic DNA from SCADC was subjected to 454 pyrosequencing, Illumina paired-end sequencing, and 16S rRNA amplicon pyrotag sequencing; the latter revealed 320 operational taxonomic units at 5% distance. Metagenomic sequences were subjected to in-house quality control and co-assembly, yielding 984 086 contigs, and annotation using MG-Rast and IMG. Substantial nucleotide and protein recruitment to Methanosaeta concilii, Syntrophus aciditrophicus, and Desulfobulbus propionicus reference genomes suggested the presence of closely related strains in SCADC; other genomes were not well mapped, reflecting the paucity of suitable reference sequences for such communities. Nonetheless, we detected numerous homologues of putative hydrocarbon succinate synthase genes (e.g., assA, bssA, and nmsA) implicated in anaerobic hydrocarbon degradation, suggesting the ability of the SCADC microbial community to initiate methanogenic alkane degradation by addition to fumarate. Annotation of a large contig revealed analogues of the ass operon 1 in the alkane-degrading sulphate-reducing bacterium Desulfatibacillum alkenivorans AK-01. Despite being enriched under methanogenic–fermentative conditions, additional metabolic functions inferred by COG profiling indicated multiple CO2 fixation pathways, organic acid utilization, hydrogenase activity, and sulphate reduction.
Vol. 56No. 10pp. 612–618
Oil sands tailings ponds harbor large amounts of tailings resulting from surface mining of bitumen and consist of water, sand, clays, residual bitumen, and hydrocarbon diluent. Oxygen ingress in these ponds is limited to the surface layers, causing most hydrocarbon degradation to be catalyzed by anaerobic, methanogenic microbial communities. This causes the evolution of large volumes of methane of up to 104 m3/day. A pyrosequencing survey of 16S rRNA amplicons from 10 samples obtained from different depths indicated the presence of a wide variety of taxa involved in anaerobic hydrocarbon degradation and methanogenesis, including the phyla Proteobacteria, Euryarchaeota, Firmicutes, Actinobacteria, Chloroflexi, and Bacteroidetes. Metagenomic sequencing of DNA isolated from one of these samples indicated a more diverse community than indicated by the 16S rRNA amplicon survey. Both methods indicated the same major phyla to be present. The metagenomic dataset indicated the presence of genes involved in the three stages of anaerobic aromatic hydrocarbon degradation, including genes for enzymes of the peripheral (upper), the central (lower), and the methanogenesis pathways. Upper pathway genes showed broad phylogenetic affiliation (Proteobacteria, Firmicutes, and Actinobacteria), whereas lower pathway genes were mostly affiliated with the Deltaproteobacteria. Genes for both hydrogenotrophic and acetotrophic methanogenesis were also found. The wide variety of taxa involved in initial hydrocarbon degradation through upper pathways may reflect the variety of residual bitumen and diluent components present in the tailings pond.
Vol. 56No. 10pp. 619–625
Neuregulins (NRGs) are signaling molecules involved in various cellular and developmental processes. Abnormal expression and (or) genomic variations of some of these molecules, such as NRG1, have been associated with disease conditions such as cancer and schizophrenia. To gain a comprehensive molecular insight into possible pathways/networks regulated by NRG1-alpha, we performed a global expression profiling analysis on lymphoblastoid cell lines exposed to NRG1-alpha. Our data show that this signaling molecule mainly regulates coordinated expression of genes involved in three processes: phosphorylation, acetylation, and alternative splicing. These processes have fundamental roles in proper development and function of various tissues including the central nervous system (CNS)—a fact that may explain conditions associated with NRG1 dysregulations such as schizophrenia. The data also suggest NRG1-alpha regulates genes (FBXO41) and miRNAs (miR-33) involved in cholesterol metabolism. Moreover, RPN2, a gene already shown to be dysregulated in breast cancer cells, is also differentially regulated by NRG1-alpha treatment.
Vol. 56No. 10pp. 626–633
Including low penetrance genomic variants in population-based screening might enable personalization of screening intensity and follow up. The application of genomics in this way requires formal evaluation. Even if clinically beneficial, uptake would still depend on the attitudes of target populations. We developed a deliberative workshop on two hypothetical applications (in colorectal cancer and newborn screening) in which we applied stepped, neutrally-framed, information sets. Data were collected using nonparticipant observation, free-text comments by individual participants, and a structured survey. Qualitative data were transcribed and analyzed using thematic content analysis. Eight workshops were conducted with 170 individuals (120 colorectal cancer screening and 50 newborn screening for type 1 diabetes). The use of information sets promoted informed deliberation. In both contexts, attitudes appeared to be heavily informed by assessments of the likely validity of the test results and its personal and health care utility. Perceived benefits included the potential for early intervention, prevention, and closer monitoring while concerns related to costs, education needs regarding the probabilistic nature of risk, the potential for worry, and control of access to personal genomic information. Differences between the colorectal cancer and newborn screening groups appeared to reflect different assessments of potential personal utility, particularly regarding prevention.


Vol. 56No. 10pp. 634–640
Bipolar disorder (BD) is a psychiatric condition characterized by the occurrence of at least two episodes of clinically disturbed mood including mania and depression. A vast literature describing BD studies suggests that a strong genetic contribution likely underlies this condition; heritability is estimated to be as high as 80%. Many studies have identified BD susceptibility loci, but because of the genetic and phenotypic heterogeneity observed across individuals, very few loci were subsequently replicated. Research in BD genetics to date has consisted of classical linkage or genome-wide association studies, which have identified candidate genes hypothesized to present common susceptibility variants. Although the observation of such common variants is informative, they can only explain a small fraction of the predicted BD heritability, suggesting a considerable contribution would come from rare and highly penetrant variants. We are seeking to identify such rare variants, and to increase the likelihood of being successful, we aimed to reduce the phenotypic heterogeneity factor by focusing on a well-defined subphenotype of BD: excellent response to lithium monotherapy. Our group has previously shown positive response to lithium therapy clusters in families and has a consistent clinical presentation with minimal comorbidity. To identify such rare variants, we are using a targeted exome capture and high-throughput DNA sequencing approach, and analyzing the entire coding sequences of BD affected individuals from multigenerational families. We are prioritizing rare variants with a frequency of less than 1% in the population that segregate with affected status within each family, as well as being potentially highly penetrant (e.g., protein truncating, missense, or frameshift) or functionally relevant (e.g., 3′UTR, 5′UTR, or splicing). By focusing on rare variants in a familial cohort, we hope to explain a significant portion of the missing heritability in BD, as well as to narrow our current insight on the key biochemical pathways implicated in this complex disorder.
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Volume 66
Issue 12
December 2023
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November 2023
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Issue 10
October 2023
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Issue 9
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Issue 7
July 2023