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

Ryynänen, Heikki J.; Primmer, Craig R.

doi:10.1186/1471-2164-7-192

Cited by 43 publications

(35 citation statements)

References 72 publications

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“…PSVs are sequence differences between two paralogous loci but the substitution does not segregate within either locus and were considered false positive SNPs. Similar observations were obtained with Atlantic salmon [10,12,13]. …”

Section: Resultssupporting

confidence: 87%

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Boussaha

Guyomard

Cabau³

et al. 2012

BMC Genomics

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BackgroundThere is considerable interest in developing high-throughput genotyping with single nucleotide polymorphisms (SNPs) for the identification of genes affecting important ecological or economical traits. SNPs are evenly distributed throughout the genome and are likely to be functionally relevant. In rainbow trout, in silico screening of EST databases represents an attractive approach for de novo SNP identification. Nevertheless, EST sequencing errors and assembly of EST paralogous sequences can lead to the identification of false positive SNPs which renders the reliability of EST-derived SNPs relatively low. Further validation of EST-derived SNPs is therefore required. The objective of this work was to assess the quality of and to validate a large number of rainbow trout EST-derived SNPs.ResultsA panel of 1,152 EST-derived SNPs was selected from the INRA Sigenae SNP database and was genotyped in standard and double haploid individuals from several populations using the Illumina GoldenGate BeadXpress assay. High-quality genotyping data were obtained for 958 SNPs representing a genotyping success rate of 83.2 %, out of which, 350 SNPs (36.5 %) were polymorphic in at least one population and were designated as true SNPs. They also proved to be a potential tool to investigate genetic diversity of the species, as the set of SNP successfully sorted individuals into three main groups using STRUCTURE software. Functional annotations revealed 28 non-synonymous SNPs, out of which four substitutions were predicted to affect protein functions. A subset of 223 true SNPs were polymorphic in the two INRA mapping reference families and were integrated into the INRA microsatellite-based linkage map.ConclusionsOur results represent the first study of EST-derived SNPs validation in rainbow trout, a species whose genome sequences is not yet available. We designed several specific filters in order to improve the genotyping yield. Nevertheless, our selection criteria should be further improved in order to reduce the observed high rate of false positive SNPs which results from the occurrence of whole genome duplications.

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Section: Resultssupporting

confidence: 87%

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Boussaha

Guyomard

Cabau³

et al. 2012

BMC Genomics

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“…Thus, these results suggest that false discovery problems owing to gene duplications could be limited in Atlantic cod compared to other species, such as salmonids (see e.g. Smith et al 2005 and discussion in Ryynänen & Primmer 2006).…”

Section: Discussionmentioning

confidence: 89%

Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua

Hemmer‐Hansen

Nielsen

Meldrup

et al. 2011

Molecular Ecology Resources

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Recent technological developments have facilitated intensified searches for genetic markers under selection in nonmodel species. Here, we present an approach for the identification of candidate gene variation in nonmodel organisms. We report on the characterization of 82 single nucleotide polymorphisms (SNPs) and on the development of a specific genotyping assay for 30 SNPs in 18 candidate genes for growth and reproduction in Atlantic cod (Gadus morhua). These markers can be used for scanning natural populations for signatures of selection in both contemporary and archived historical samples, for example in retrospective studies assessing the effects of environmental changes, such as increasing temperatures, and selection imposed by high fishing pressure. Furthermore, these gene markers may be of interest to aquaculture, serving as a starting point for linking phenotypic traits important for productivity with genotypes and potentially be of use for marker-assisted selection in the future. This study demonstrates that the candidate gene approach is a valuable and targeted complement to the more random approach for discovering genetic variation in the genome and transcriptome applied through high throughput methods in nonmodel species.

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“…However, when using EST data for SNP identification, the salmonid pseudo-tetraploid genome [28] can lead to assemblies of paralogous sequences and false positive SNP identification [24,26,27]. Initially, we attempted an SNP discovery approach based on alignments of ESTs.…”

Section: Introductionmentioning

confidence: 99%

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

et al. 2009

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BackgroundTo enhance capabilities for genomic analyses in rainbow trout, such as genomic selection, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be identified. Expressed Sequence Tags (ESTs) have been used for single nucleotide polymorphism (SNP) discovery in salmonids. In those strategies, the salmonid semi-tetraploid genomes often led to assemblies of paralogous sequences and therefore resulted in a high rate of false positive SNP identification. Sequencing genomic DNA using primers identified from ESTs proved to be an effective but time consuming methodology of SNP identification in rainbow trout, therefore not suitable for high throughput SNP discovery. In this study, we employed a high-throughput strategy that used pyrosequencing technology to generate data from a reduced representation library constructed with genomic DNA pooled from 96 unrelated rainbow trout that represent the National Center for Cool and Cold Water Aquaculture (NCCCWA) broodstock population.ResultsThe reduced representation library consisted of 440 bp fragments resulting from complete digestion with the restriction enzyme HaeIII; sequencing produced 2,000,000 reads providing an average 6 fold coverage of the estimated 150,000 unique genomic restriction fragments (300,000 fragment ends). Three independent data analyses identified 22,022 to 47,128 putative SNPs on 13,140 to 24,627 independent contigs. A set of 384 putative SNPs, randomly selected from the sets produced by the three analyses were genotyped on individual fish to determine the validation rate of putative SNPs among analyses, distinguish apparent SNPs that actually represent paralogous loci in the tetraploid genome, examine Mendelian segregation, and place the validated SNPs on the rainbow trout linkage map. Approximately 48% (183) of the putative SNPs were validated; 167 markers were successfully incorporated into the rainbow trout linkage map. In addition, 2% of the sequences from the validated markers were associated with rainbow trout transcripts.ConclusionThe use of reduced representation libraries and pyrosequencing technology proved to be an effective strategy for the discovery of a high number of putative SNPs in rainbow trout; however, modifications to the technique to decrease the false discovery rate resulting from the evolutionary recent genome duplication would be desirable.

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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

Cited by 43 publications

References 72 publications

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Development and characterisation of an expressed sequence tags (EST)-derived single nucleotide polymorphisms (SNPs) resource in rainbow trout

Identification of single nucleotide polymorphisms in candidate genes for growth and reproduction in a nonmodel organism; the Atlantic cod, Gadus morhua

Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library

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