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Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)

Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua),10.1186/1471-2164-11-191,BMC Genomics,Sophie Hubert,Brent Higg

Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)   (Citations: 8)
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BACKGROUND: Atlantic cod (Gadus morhua) is a species with increasing economic significance for the aquaculture industry. The genetic improvement of cod will play a critical role in achieving successful large-scale aquaculture. While many microsatellite markers have been developed in cod, the number of single nucleotide polymorphisms (SNPs) is currently limited. Here we report the identification of SNPs from sequence data generated by a large-scale expressed sequence tag (EST) program, focusing on fish originating from Canadian waters. RESULTS: A total of 97976 ESTs were assembled to generate 13448 contigs. We detected 4753 SNPs that met our selection criteria (depth of coverage ≥ 4 reads; minor allele frequency > 25%). 3072 SNPs were selected for testing. The percentage of successful assays was 75%, with 2291 SNPs amplifying correctly. Of these, 607 (26%) SNPs were monomorphic for all populations tested. In total, 64 (4%) of SNPs are likely to represent duplicated genes or highly similar members of gene families, rather than alternative alleles of the same gene, since they showed a high frequency of heterozygosity. The remaining polymorphic SNPs (1620) were categorised as validated SNPs. The mean minor allele frequency of the validated loci was 0.258 (± 0.141). Of the 1514 contigs from which validated SNPs were selected, 31% have a significant blast hit. For the SNPs predicted to occur in coding regions (141), we determined that 36% (51) are non-synonymous. Many loci (1033 SNPs; 64%) are polymorphic in all populations tested. However a small number of SNPs (184) that are polymorphic in the Western Atlantic were monomorphic in fish tested from three European populations. A preliminary linkage map has been constructed with 23 major linkage groups and 924 mapped SNPs. CONCLUSIONS: These SNPs represent powerful tools to accelerate the genetic improvement of cod aquaculture. They have been used to build a genetic linkage map that can be applied to quantitative trait locus (QTL) discovery. Since these SNPs were generated from ESTs, they are linked to specific genes. Genes that map within QTL intervals can be prioritized for testing to determine whether they contribute to observed phenotypes.
Journal: BMC Genomics , vol. 11, no. 1, pp. 191-14, 2010
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    • ...Likewise, gene-associated SNPs derived from ESTs have been identified in several fish species, including Atlantic salmon [12], Atlantic cod [13] and catfish [14-16]...

    Shikai Liuet al. Generation of genome-scale gene-associated SNPs in catfish for the con...

    • ...Recently, a large number of single nucleotide polymorphisms (SNPs) have been identified [11-13] and two independent genetic linkage maps have been generated [12,14]...
    • ...Recently, a large number of single nucleotide polymorphisms (SNPs) have been identified [11-13] and two independent genetic linkage maps have been generated [12,14]...
    • ...Mapping the haemoglobin genes We used a curated Illumina GoldenGate panel containing 1536 SNPs [12], including three SNPs identified in the Hb b1 gene, two SNPs specific to the Hb b 3g ene and one characteristic for the Hb b4 gene (details in Additional file 1). These SNPs were derived from...
    • ...The 23 linkage groups obtained for family B30 were compared to the linkage groups previously reported by Hubert et al. 2010 [12]; a 1:1 correspondence between linkage groups (LGs) was confirmed and the corresponding LGs were merged (Figures 1, 2, 3; more details about mapping can be found in Hubert et al. 2010 and Additional file 1). The 23 linkage groups observed for family B30 (and those described in Hubert et al. 2010) matches the ...
    • ...iants [17]. Family B87, one of the two families used in the generation of the initial map [12] was determined to be polymorphic for Pan I A G767A and the Pan I locus...
    • ...The addition of family B30 allowed new SNPs to be mapped onto the CGP map The new map, resulted from the addition of family B30, and of Pan I and Hb loci, contains 1046 mapped SNPs, an increase of 122 SNPs when compared to the genetic linkage map reported earlier by Hubert et al. 2010 [12]...
    • ...Linkage group correspondence between maps produced by independent research groups Finally, we aimed to merge the CGP genetic linkage map data (this paper and Hubert et al. [12]) with the genetic linkage map data produced by ad ifferent group [14]...
    • ...To identify sequences that were mapped by both, CGP (this paper and Hubert et al. [12]) and Moen et al. [14] we performed a Blastn search of an in-house made database containing the ESTs listed by Moen et al. [14] using 124 nucleotides long CGP SNP-containing sequences...
    • ...Using this approach we identified 29 shared SNPs distributed on 10 different linkage groups (Additional file 4). The minimal overlap between the linkage map produced in the present study and that of Moen et al. [14] might result from ascertainment bias caused by different frequencies of SNPs in NE and NW Atlantic populations of cod and/or because CGP sequenced the 3’ ends of ESTs to identify SNPs [11,12] whereas Moen et al. [13,14] ...

    Tudor Borzaet al. Integrating the markers Pan I and haemoglobin with the genetic linkage...

    • ...Together with the recently constructed SNP platform and linkage map (Hubert et al. 2010), and an ongoing effort to sequence the full Atlantic cod genome (Johansen et al. 2009), they form an important set of tools for marker-assisted selection to improve Atlantic cod...

    Marije Boomanet al. Development and Experimental Validation of a 20K Atlantic Cod ( Gadus ...

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