Development of a SNP Resource and a Genetic Linkage Map for Atlantic Cod (Gadus Morhua)

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2010 Mar 24

PMID 20307277

Citations 45

Authors

Sophie Hubert

Brent Higgins

Tudor Borza

Sharen Bowman

Affiliations

Soon will be listed here.

Abstract

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 > or = 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.

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References

Delghandi M, Mortensen A, Westgaard J . Simultaneous analysis of six microsatellite markers in Atlantic cod ( Gadus morhua): a novel multiplex assay system for use in selective breeding studies. Mar Biotechnol (NY). 2003; 5(2):141-8. DOI: 10.1007/s10126-002-0086-x. View

Rise M, Hall J, Rise M, Hori T, Gamperl A, Kimball J . Functional genomic analysis of the response of Atlantic cod (Gadus morhua) spleen to the viral mimic polyriboinosinic polyribocytidylic acid (pIC). Dev Comp Immunol. 2008; 32(8):916-31. DOI: 10.1016/j.dci.2008.01.002. View

Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad K, Fevolden S . Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genet. 2008; 9:18. PMC: 2288615. DOI: 10.1186/1471-2156-9-18. View

Wang S, Sha Z, Sonstegard T, Liu H, Xu P, Somridhivej B . Quality assessment parameters for EST-derived SNPs from catfish. BMC Genomics. 2008; 9:450. PMC: 2570692. DOI: 10.1186/1471-2164-9-450. View

Koski L, Gray M, Lang B, Burger G . AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics. 2005; 6:151. PMC: 1182349. DOI: 10.1186/1471-2105-6-151. View

Spigler R, Lewers K, Main D, Ashman T . Genetic mapping of sex determination in a wild strawberry, Fragaria virginiana, reveals earliest form of sex chromosome. Heredity (Edinb). 2008; 101(6):507-17. DOI: 10.1038/hdy.2008.100. View

Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P . Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010; 11(1):R8. PMC: 2847720. DOI: 10.1186/gb-2010-11-1-r8. View

Pogson G, Mesa K, Boutilier R . Genetic population structure and gene flow in the Atlantic cod Gadus morhua: a comparison of allozyme and nuclear RFLP loci. Genetics. 1995; 139(1):375-85. PMC: 1206334. DOI: 10.1093/genetics/139.1.375. View

Wondji C, Hemingway J, Ranson H . Identification and analysis of single nucleotide polymorphisms (SNPs) in the mosquito Anopheles funestus, malaria vector. BMC Genomics. 2007; 8:5. PMC: 1781065. DOI: 10.1186/1471-2164-8-5. View

10.

Guryev V, Berezikov E, Malik R, Plasterk R, Cuppen E . Single nucleotide polymorphisms associated with rat expressed sequences. Genome Res. 2004; 14(7):1438-43. PMC: 442160. DOI: 10.1101/gr.2154304. View

11.

Rohrer G, Freking B, Nonneman D . Single nucleotide polymorphisms for pig identification and parentage exclusion. Anim Genet. 2007; 38(3):253-8. DOI: 10.1111/j.1365-2052.2007.01593.x. View

12.

Simoes M, Bahia D, Zerlotini A, Torres K, Artiguenave F, Neshich G . Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni. Mol Biochem Parasitol. 2007; 154(2):134-40. PMC: 1986741. DOI: 10.1016/j.molbiopara.2007.04.003. View

13.

Feng C, Johnson S, Hori T, Rise M, Hall J, Gamperl A . Identification and analysis of differentially expressed genes in immune tissues of Atlantic cod stimulated with formalin-killed, atypical Aeromonas salmonicida. Physiol Genomics. 2009; 37(3):149-63. DOI: 10.1152/physiolgenomics.90373.2008. View

14.

Kim H, Schmidt C, Decker K, Emara M . A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data. Anim Genet. 2003; 34(4):249-54. DOI: 10.1046/j.1365-2052.2003.01003.x. View

15.

Palermo M, Marazzi M, Hughes B, Stewart P, Clayton P, Shackleton C . Human Delta4-3-oxosteroid 5beta-reductase (AKR1D1) deficiency and steroid metabolism. Steroids. 2008; 73(4):417-23. DOI: 10.1016/j.steroids.2007.12.001. View

16.

Stickney H, Schmutz J, Woods I, Holtzer C, Dickson M, Kelly P . Rapid mapping of zebrafish mutations with SNPs and oligonucleotide microarrays. Genome Res. 2002; 12(12):1929-34. PMC: 187572. DOI: 10.1101/gr.777302. View

17.

Bonaldo M, Lennon G, Soares M . Normalization and subtraction: two approaches to facilitate gene discovery. Genome Res. 1996; 6(9):791-806. DOI: 10.1101/gr.6.9.791. View

18.

Bowman S, Hubert S, Higgins B, Stone C, Kimball J, Borza T . An integrated approach to gene discovery and marker development in Atlantic cod (Gadus morhua). Mar Biotechnol (NY). 2010; 13(2):242-55. PMC: 3084941. DOI: 10.1007/s10126-010-9285-z. View

19.

Rousset F . genepop'007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour. 2011; 8(1):103-6. DOI: 10.1111/j.1471-8286.2007.01931.x. View

20.

Ryynanen H, Primmer C . Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes. BMC Genomics. 2006; 7:192. PMC: 1557852. DOI: 10.1186/1471-2164-7-192. View