Quality assessment parameters for EST-derived SNPs from catfish

Wang, Shaolin; Sha, Zhenxia; Sonstegard, Tad S.; Liu, Hong; Xu, Peng; Somridhivej, Benjaporn; Peatman, Eric; Kucuktas, Huseyin; Liu, Zhanjiang

doi:10.1186/1471-2164-9-450

Cited by 103 publications

(126 citation statements)

References 44 publications

(44 reference statements)

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“…EST-derived SNP markers: Wang et al (2008) described the factors that are significant for validation of EST-derived SNPs. One hundred eighteen of 384 SNP markers failed, and 125 were polymorphic in the mapping family.…”

Section: Resultsmentioning

confidence: 99%

“…SNP markers: A total of 384 EST-derived SNP markers were genotyped as described in Wang et al (2008) using the F 1 -2 3 channel catfish-6 hybrid catfish.…”

Section: Methodsmentioning

confidence: 99%

“…Because gene-associated markers are conserved through a wide evolutionary spectrum of species, they have become the most desirable type of marker for comparative mapping (Martin et al 2005;Moretzsohn et al 2005;Smith et al 2005;Snelling et al 2005;Casasoli et al 2006;Kim et al 2006;Sasazaki et al 2006;Sawera et al 2006). We have previously reported the identification of a large number of ESTassociated microsatellites and SNPs (He et al 2003;Serapion et al 2004a;Wang et al 2008). Here we present a gene-based linkage map of the catfish genome constructed with EST-associated microsatellites and SNPs.…”

mentioning

confidence: 95%

“…A gene-based linkage map would provide a start for such a platform. In addition to these traditional genome resources, the use of single nucleotide polymorphism (SNP) markers is gaining significant momentum in aquacultured species (Hayes et al 2007;Moen et al 2008;Wang et al 2008).…”

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confidence: 99%

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Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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A genetic linkage map of the channel catfish genome (N ¼ 29) was constructed using EST-based microsatellite and single nucleotide polymorphism (SNP) markers in an interspecific reference family. A total of 413 microsatellites and 125 SNP markers were polymorphic in the reference family. Linkage analysis using JoinMap 4.0 allowed mapping of 331 markers (259 microsatellites and 72 SNPs) to 29 linkage groups. Each linkage group contained 3-18 markers. The largest linkage group contained 18 markers and spanned 131.2 cM, while the smallest linkage group contained 14 markers and spanned only 7.9 cM. The linkage map covered a genetic distance of 1811 cM with an average marker interval of 6.0 cM. Sex-specific maps were also constructed; the recombination rate for females was 1.6 times higher than that for males. Putative conserved syntenies between catfish and zebrafish, medaka, and Tetraodon were established, but the overall levels of genome rearrangements were high among the teleost genomes. This study represents a first-generation linkage map constructed by using EST-derived microsatellites and SNPs, laying a framework for large-scale comparative genome analysis in catfish. The conserved syntenies identified here between the catfish and the three model fish species should facilitate structural genome analysis and evolutionary studies, but more importantly should facilitate functional inference of catfish genes. Given that determination of gene functions is difficult in nonmodel species such as catfish, functional genome analysis will have to rely heavily on the establishment of orthologies from model species.

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Section: Resultsmentioning

confidence: 99%

“…SNP markers: A total of 384 EST-derived SNP markers were genotyped as described in Wang et al (2008) using the F 1 -2 3 channel catfish-6 hybrid catfish.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 95%

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confidence: 99%

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Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

et al. 2009

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“…Because of their high frequency, codominant inheritance, amenability to high-throughout genotyping analysis, and lower mutation rate compared to microsatellites (Wang et al 2008), SNPs have become mark-ers of choice for population genetics and genomic mapping studies (Rafalski 2002, Li et al 2010a, Zhang & Guo 2010. Generally, locus discovery and genotyping are involved in the development of SNP markers.…”

Section: Introductionmentioning

confidence: 99%

Characterization of single nucleotide polymorphisms from expressed sequence tags of Chinese mitten crab Eriocheir sinensis

Li¹,

He²,

Yang³

et al. 2010

Aquat. Biol.

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The Chinese mitten crab Eriocheir sinensis is an important aquaculture species in Asia and causes considerable economic and ecological damage as an invasive species in North America and Europe. Until recently, molecular markers available for genetic analysis in this species were limited to a few microsatellite sequences used in population studies. Here we describe the discovery of 3191 single nucleotide polymorphisms (SNPs) from the alignment of expressed sequence tags (ESTs) in E. sinensis. The observed frequency of SNPs was estimated at 0.78 per 100 bp of contig sequences. C/T substitutions were frequent and accounted for 32.2% of all SNPs. A subset of these SNPs (n = 38) was selected for validation by allele-specific PCR with melting temperature (T m )-shift primers based on their observed frequency in sequence data; 12 (31.6%) of these were polymorphic in a panel of 40 wild-caught crabs. Eight (21.1%) did not amplify any product, and 18 (47.4%) failed due to amplification failure of 1 allele-specific primer. A table of optimal codons was deduced from the analysis of the E. sinensis EST dataset, and the results implied that the gene expression levels and GC-content might play important roles in codon usage bias. Sixteen codons ending with a G or C base were defined as 'optimal codons,' which may provide useful information for predicting gene expression in crabs. These are the first SNPs developed for the Chinese mitten crab and will provide a useful complement to currently available genetic markers.

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Genomic Selection in Aquaculture: Methods and Practical Considerations

Ragavendran

Muir

2010

Next Generation Sequencing and Whole Genome Selection in Aquaculture

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Quality assessment parameters for EST-derived SNPs from catfish

Cited by 103 publications

References 44 publications

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Construction of Genetic Linkage Maps and Comparative Genome Analysis of Catfish Using Gene-Associated Markers

Characterization of single nucleotide polymorphisms from expressed sequence tags of Chinese mitten crab Eriocheir sinensis

Genomic Selection in Aquaculture: Methods and Practical Considerations

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