Characterization of 20 single nucleotide polymorphism markers in the Pacific oyster (<i>Crassostrea gigas</i>)

Bai, Jie; Li, Q.; Kong, Lingfeng; Li, R. H.

doi:10.1111/j.1365-2052.2009.01949.x

Cited by 9 publications

(7 citation statements)

References 5 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Adding the five SNPs from Bai et al . (), this gave a total of 77 in vitro SNPs to be included in the array, representing 70 different gene fragments. A total of 307 in silico SNPs completed the array, which corresponded to 148 different contigs.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Development of SNP‐genotyping arrays in two shellfish species

Lapègue¹,

Harrang²,

Heurtebise³

et al. 2014

Molecular Ecology Resources

View full text Add to dashboard Cite

Use of SNPs has been favoured due to their abundance in plant and animal genomes, accompanied by the falling cost and rising throughput capacity for detection and genotyping. Here, we present in vitro (obtained from targeted sequencing) and in silico discovery of SNPs, and the design of medium-throughput genotyping arrays for two oyster species, the Pacific oyster, Crassostrea gigas, and European flat oyster, Ostrea edulis. Two sets of 384 SNP markers were designed for two Illumina GoldenGate arrays and genotyped on more than 1000 samples for each species. In each case, oyster samples were obtained from wild and selected populations and from three-generation families segregating for traits of interest in aquaculture. The rate of successfully genotyped polymorphic SNPs was about 60% for each species. Effects of SNP origin and quality on genotyping success (Illumina functionality Score) were analysed and compared with other model and nonmodel species. Furthermore, a simulation was made based on a subset of the C. gigas SNP array with a minor allele frequency of 0.3 and typical crosses used in shellfish hatcheries. This simulation indicated that at least 150 markers were needed to perform an accurate parental assignment. Such panels might provide valuable tools to improve our understanding of the connectivity between wild (and selected) populations and could contribute to future selective breeding programmes.

show abstract

Section: Resultsmentioning

confidence: 99%

“…(), together with a third set of five SNPs from the 20 developed by Bai et al . (). Sequence alignment was performed with ClustalW via the BioEdit interface (Hall ) and DNAMAN version 4.1 (http://www.lynnon.com).…”

Section: Methodsmentioning

confidence: 97%

Development of SNP‐genotyping arrays in two shellfish species

Lapègue¹,

Harrang²,

Heurtebise³

et al. 2014

Molecular Ecology Resources

View full text Add to dashboard Cite

show abstract

“…Genetic mapping of important traits, gene characterization and molecular breeding require genetic markers (Davey et al 2011). In the past few years, several studies have discovered traditional DNA markers for C. gigas (Sekino et al 2003;Li et al 2003;Yu & Li 2007Bai et al 2009;Qi et al 2009;Sauvage et al 2009;Yu et al 2010;Li et al 2011;Zhong et al 2013), and linkage maps with different purposes have been constructed (Hubert & Hedgecock 2004;Li & Guo 2004;Sauvage et al 2010;Plough & Hedgecock 2011;Guo et al 2012). Additionally, the whole genome sequencing of C. gigas was completed, deepening our understanding of the mechanisms of stress adaptation and shell formation of oysters (Zhang et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas

Wang

et al. 2014

Molecular Ecology Resources

View full text Add to dashboard Cite

The economic and ecological importance of the oyster necessitates further research on the molecular mechanisms, which both regulate the commercially important traits of the oyster and help it to survive in the variable marine environment. Single nucleotide polymorphisms (SNPs) have been widely used to assess genetic variation and identify genes underlying target traits. In addition, high-resolution melting (HRM) analysis is a potentially powerful method for validating candidate SNPs. In this study, we adopted a rapid and efficient pipeline for the screening and validation of SNPs in the genic region of Crassostrea gigas based on transcriptome sequencing and HRM analysis. Transcriptomes of three wild oyster populations were sequenced using Illumina sequencing technology. In total, 50-60 million short reads, corresponding to 4.5-5.4 Gbp, from each population were aligned to the oyster genome, and 5.8 × 10(5) SNPs were putatively identified, resulting in a predicted SNP every 47 nucleotides on average. The putative SNPs were unevenly distributed in the genome and high-density (≥2%), nonsynonymous coding SNPs were enriched in genes related to apoptosis and responses to biotic stimuli. Subsequently, 1,671 loci were detected by HRM analysis, accounting for 64.7% of the total selected candidate primers, and finally, 1,301 polymorphic SNP markers were developed based on HRM analysis. All of the validated SNPs were distributed into 897 genes and located in 672 scaffolds, and 275 of these genes were stress inducible under unfavourable salinity, temperature, and exposure to air and heavy metals. The validated SNPs in this study provide valuable molecular markers for genetic mapping and characterization of important traits in oysters.

show abstract

“…They offer a wide range of applications such as association studies, high‐density linkage maps, traceability of genealogies, and MAS (Liu and Cordes ). However, the number of available SNP markers is still limited for C. gigas (Sauvage et al ; Bai et al ). The rapid increase in the availability of EST collection provides abundant resources for obtaining SNP markers for the species (Cunningham et al ; Jenny et al ; Tanguy et al ; Fleury et al ).…”

mentioning

confidence: 99%

Development and Validation of Single‐nucleotide Polymorphism Markers in the Pacific Oyster, Crassostrea gigas, Using High‐resolution Melting Analysis

Zhong

et al. 2013

J World Aquaculture Soc

View full text Add to dashboard Cite

High-resolution melting (HRM) has been considered as a fast and simple single-nucleotide polymorphism (SNP) scanning and genotyping method for identifying differences in the shapes of melting curves between different genotypes. Fifty-six SNPs were developed in the Pacific oyster, Crassostrea gigas by mining expressed sequence tags database, using the HRM method. The frequency of the SNPs was estimated at 1 per 113 bp of contig sequences. Analysis of segregation in a full-sib family showed that 28 SNPs were polymorphic, with 15 in accordance to expected Mendelian ratios. Linkage grouping of the 28 markers resulted in six linkage groups. The combined power of exclusion of the 42 SNPs, which conformed to Hardy-Weinberg equilibrium, was greater than 99.98%, while the average polymorphic information content was 0.2223. The simulation results showed that the success rate of parentage analysis could be 97% with the 42 SNPs. These SNPs will be useful for pedigree analysis, association studies, and marker-associated selection of this species.

show abstract

Characterization of 20 single nucleotide polymorphism markers in the Pacific oyster (Crassostrea gigas)

Cited by 9 publications

References 5 publications

Development of SNP‐genotyping arrays in two shellfish species

Development of SNP‐genotyping arrays in two shellfish species

Discovery and validation of genic single nucleotide polymorphisms in the Pacific oyster Crassostrea gigas

Development and Validation of Single‐nucleotide Polymorphism Markers in the Pacific Oyster, Crassostrea gigas, Using High‐resolution Melting Analysis

Contact Info

Product

Resources

About