Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection

<p>Abstract</p> <p>Background</p> <p>The Atlantic cod (<it>Gadus morhua</it>) is a groundfish of great economic value in fisheries and an emerging species in aquaculture. Genetic markers are needed to identify wild stocks in order to ensure sustainable management, and for marker-assisted selection and pedigree determination in aquaculture. Here, we report on the development and evaluation of a large number of Single Nucleotide Polymorphism (SNP) markers from the alignment of Expressed Sequence Tag (EST) sequences in Atlantic cod. We also present basic population parameters of the SNPs in samples of North-East Arctic cod and Norwegian coastal cod obtained from three different localities, and test for SNPs that may have been targeted by natural selection.</p> <p>Results</p> <p>A total of 17,056 EST sequences were used to find 724 putative SNPs, from which 318 segregating SNPs were isolated. The SNPs were tested on Atlantic cod from four different sites, comprising both North-East Arctic cod (NEAC) and Norwegian coastal cod (NCC). The average heterozygosity of the SNPs was 0.25 and the average minor allele frequency was 0.18. <it>F</it>_{<it>ST </it>}values were highly variable, with the majority of SNPs displaying very little differentiation while others had <it>F</it>_{<it>ST </it>}values as high as 0.83. The <it>F</it>_{<it>ST </it>}values of 29 SNPs were found to be larger than expected under a strictly neutral model, suggesting that these loci are, or have been, influenced by natural selection. For the majority of these outlier SNPs, allele frequencies in a northern sample of NCC were intermediate between allele frequencies in a southern sample of NCC and a sample of NEAC, indicating a cline in allele frequencies similar to that found at the Pantophysin I locus.</p> <p>Conclusion</p> <p>The SNP markers presented here are powerful tools for future genetics work related to management and aquaculture. In particular, some SNPs exhibiting high levels of population divergence have potential to significantly enhance studies on the population structure of Atlantic cod.</p

Population genetic structure of grey seals (Halichoerus grypus) : Diversity, differentiation and prospects for genetic population assignment with special reference to Norwegian waters

Population structure of grey seal breeding colonies in Norway (n=300), Northwest Russia (n=40) and Scotland (n=100) is currently being investigated based on Mt-DNA control region sequencing and fragment analysis (8 microsatellite primers) applied to biopsies from live sampled pups. In addition, mixed adult/pup samples from Iceland (n=80), the Baltic Sea (n=50) and Canada (n=50) are included in the study, which thus spans the distributional limits of the main grey seal concentrations worldwide. In line with previous observations of a high degree of female philopatry in grey seals, preliminary results from Mt-DNA analyses show highly significant differentiation of 3 breeding populations along the Norwegian coastline. Both juvenile and adult grey seals are, however, capable of undertaking long distance migrations and mixing of non breeding animals from different populations has been documented by tagging studies. We analyse the grey seal sequence and microsatellite data with respect to genetic diversity and population differentiation and evaluate the potential for genetic assignment of native population to grey seals sampled out of the breeding season with particular focus on Norwegian waters. Depending on geographical resolution, assignment tests may be a valuable tool for assessing degrees of population intermixing in grey seals and for estimating population specific parameters such as huntig and bycatch mortality

Analysis of the parental contribution to a group of fry from a single day of spawning from a commercial Atlantic cod (Gadus morhua) breeding tank

The parentage of 300 Atlantic cod (Gadus morhua) fry from eggs collected on a single day in a commercial mass spawning breeding tank was analysed by DNA profiling. Employing eight polymorphic microsatellite DNA markers, exclusion-based parentage analysis unambiguously assigned 81% of fry to a single pair of parents each (or 84.6% of the fry successfully genotyped). Of 99 adult fish present in the broodstock tank, 26 were found to have contributed to the assigned offspring. The spawning pattern was highly skewed. One parental pair contributed to 25% of the sample, while nine parents contributed to 90% of the assigned individuals. Among these highly represented individuals, both multiple paternity and multiple maternity was common. There was no evidence for size assortative mating being a factor in the spawning outcomes, though the dataset was not ideal for such an analysis. The genetic data were backed up by observations of cod mating behaviour, in a breeding tank, using infrared cameras. The video recordings gathered showed the occurrence of ventral mountings and suggested a mechanism for multiple paternity of egg batches

Novel polymorphic microsatellite markers for Panulirus ornatus and their cross-species primer amplification in Panulirus homarus

Polymorphic microsatellite loci were isolated for Panulirus ornatus using 454 GS-FLX Titanium pyrosequencing. Fifteen markers containing perfect di-, tri-, tetra-, and penta-nucleotide motifs were consistently co-amplified in five multiplexes in a panel of 91 randomly selected samples. Observed number of alleles varied from 2 to 14 per locus. Observed and expected heterozygosity ranged from 0.090 to 0.79 and 0.08 to 0.87, respectively. Ten loci deviated from Hardy-Weinberg equilibrium after sequential Bonferroni correction. Genetic linkage disequilibrium analysis between all pairs of the loci showed significant departure from the null hypothesis between 11 loci. The microsatellite markers were also amplified successfully in related Panulirus homarus species with adequate level of polymorphism. The successful cross-species primer amplification of the 15 microsatellites indicates the potential of the developed markers to be transferred to other Panulirus species. The 15 novel microsatellite markers reported in this work add to the previously characterized markers by our group, exhibit adequate levels of polymorphism for wide range of future studies investigating population structure, genetic diversity, and evolutionary relationships among Panulirus species

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

Abstract Background The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. Results After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise F ST estimates revealed low differentiation among populations (pairwise F ST range = − 0.0008 - 0.0021). Analysis of genetic variation using putatively directional F ST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise F ST range = 0.0288–0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. Conclusions Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes

Genome-wide SNP analyses reveal high gene flow and signatures of local adaptation among the scalloped spiny lobster (Panulirus homarus) along the Omani coastline

Background: The scalloped spiny lobster (Panulirus homarus) is a popular seafood commodity worldwide and an important export item from Oman. Annual catches in commercial fisheries are in serious decline, which has resulted in calls for the development of an integrated stock management approach. In Oman, the scalloped spiny lobster is currently treated as a single management unit (MU) or stock and there is an absence of information on the genetic population structure of the species that can inform management decisions, particularly at a fine-scale level. This work is the first to identify genome-wide single nucleotide polymorphisms (SNPs) for P. homarus using Diversity Arrays Technology sequencing (DArT-seq) and to elucidate any stock structure in the species. Results: After stringent filtering, 7988 high utility SNPs were discovered and used to assess the genetic diversity, connectivity and structure of P. homarus populations from Al Ashkharah, Masirah Island, Duqm, Ras Madrakah, Haitam, Ashuwaymiyah, Mirbat and Dhalkut landing sites. Pairwise F-ST estimates revealed low differentiation among populations (pairwise F-ST range = - 0.0008 - 0.0021). Analysis of genetic variation using putatively directional F-ST outliers (504 SNPs) revealed higher and significant pairwise differentiation (p < 0.01) for all locations, with Ashuwaymiyah being the most diverged population (Ashuwaymiyah pairwise FST range = 0.0288-0.0736). Analysis of population structure using Discriminant Analysis of Principal Components (DAPC) revealed a broad admixture among P. homarus, however, Ashuwaymiyah stock appeared to be potentially under local adaptive pressures. Fine scale analysis using Netview R provided further support for the general admixture of P. homarus. Conclusions: Findings here suggested that stocks of P. homarus along the Omani coastline are admixed. Yet, fishery managers need to treat the lobster stock from Ashuwaymiyah with caution as it might be subject to local adaptive pressures. We emphasize further study with larger number of samples to confirm the genetic status of the Ashuwaymiyah stock. The approach utilised in this study has high transferability in conservation and management of other marine stocks with similar biological and ecological attributes

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection-2

Norwegian coastal cod north (NCC-N), and Norwegian coastal cod south (NCC-S)). Blue columns = outlier loci according to the Beaumont and Nichols [29] test (Figure 4); red columns = non-outlier SNPs with values significantly different from zero; green columns = SNPs with values not significantly different from zero.<p><b>Copyright information:</b></p><p>Taken from "Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection"</p><p>http://www.biomedcentral.com/1471-2156/9/18</p><p>BMC Genetics 2008;9():18-18.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2288615.</p><p></p

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection-1

<p><b>Copyright information:</b></p><p>Taken from "Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection"</p><p>http://www.biomedcentral.com/1471-2156/9/18</p><p>BMC Genetics 2008;9():18-18.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2288615.</p><p></p

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection-0

<p><b>Copyright information:</b></p><p>Taken from "Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection"</p><p>http://www.biomedcentral.com/1471-2156/9/18</p><p>BMC Genetics 2008;9():18-18.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2288615.</p><p></p

Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection-3

Nder a neutral model. SNPs that had values above the 0.975 quantile were considered outlier loci.<p><b>Copyright information:</b></p><p>Taken from "Identification and characterisation of novel SNP markers in Atlantic cod: Evidence for directional selection"</p><p>http://www.biomedcentral.com/1471-2156/9/18</p><p>BMC Genetics 2008;9():18-18.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2288615.</p><p></p