Dataset Information

Quality assessment parameters for EST-derived SNPs from catfish.

ABSTRACT:

Background

SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large resource of ESTs is to become available in catfish allowing identification of large number of SNPs, but reliability of EST-derived SNPs are relatively low because of sequencing errors. This project was designed to answer some of the questions relevant to quality assessment of EST-derived SNPs.

Results

wo factors were found to be most significant for validation of EST-derived SNPs: the contig size (number of sequences in the contig) and the minor allele sequence frequency. The larger the contigs were, the greater the validation rate although the validation rate was reasonably high when the contigs contain four or more EST sequences with the minor allele sequence being represented at least twice in the contigs. Sequence quality surrounding the SNP under test is also crucially important. PCR extension appeared to be limited to a very short distance, prohibiting successful genotyping when an intron was present, a surprising finding.

Conclusion

Stringent quality assessment measures should be used when working with EST-derived SNPs. In particular, contigs containing four or more ESTs should be used and the minor allele sequence should be represented at least twice. Genotyping primers should be designed from a single exon, completely avoiding introns. Application of such quality assessment measures, along with large resources of ESTs, should provide effective means for SNP identification in species where genome sequence resources are lacking.

SUBMITTER: Wang S

PROVIDER: S-EPMC2570692 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature

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Publications

Quality assessment parameters for EST-derived SNPs from catfish.

Wang Shaolin S Sha Zhenxia Z Sonstegard Tad S TS Liu Hong H Xu Peng P Somridhivej Benjaporn B Peatman Eric E Kucuktas Huseyin H Liu Zhanjiang Z

BMC genomics 20080930

<h4>Background</h4>SNPs are abundant, codominantly inherited, and sequence-tagged markers. They are highly adaptable to large-scale automated genotyping, and therefore, are most suitable for association studies and applicable to comparative genome analysis. However, discovery of SNPs requires genome sequencing efforts through whole genome sequencing or deep sequencing of reduced representation libraries. Such genome resources are not yet available for many species including catfish. A large reso ...[more]

PMID: 18826589

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Project description: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.

Project description:BackgroundThere are few genomic tools available in melon (Cucumis melo L.), a member of the Cucurbitaceae, despite its importance as a crop. Among these tools, genetic maps have been constructed mainly using marker types such as simple sequence repeats (SSR), restriction fragment length polymorphisms (RFLP) and amplified fragment length polymorphisms (AFLP) in different mapping populations. There is a growing need for saturating the genetic map with single nucleotide polymorphisms (SNP), more amenable for high throughput analysis, especially if these markers are located in gene coding regions, to provide functional markers. Expressed sequence tags (ESTs) from melon are available in public databases, and resequencing ESTs or validating SNPs detected in silico are excellent ways to discover SNPs.ResultsEST-based SNPs were discovered after resequencing ESTs between the parental lines of the PI 161375 (SC) x 'Piel de sapo' (PS) genetic map or using in silico SNP information from EST databases. In total 200 EST-based SNPs were mapped in the melon genetic map using a bin-mapping strategy, increasing the map density to 2.35 cM/marker. A subset of 45 SNPs was used to study variation in a panel of 48 melon accessions covering a wide range of the genetic diversity of the species. SNP analysis correctly reflected the genetic relationships compared with other marker systems, being able to distinguish all the accessions and cultivars.ConclusionThis is the first example of a genetic map in a cucurbit species that includes a major set of SNP markers discovered using ESTs. The PI 161375 x 'Piel de sapo' melon genetic map has around 700 markers, of which more than 500 are gene-based markers (SNP, RFLP and SSR). This genetic map will be a central tool for the construction of the melon physical map, the step prior to sequencing the complete genome. Using the set of SNP markers, it was possible to define the genetic relationships within a collection of forty-eight melon accessions as efficiently as with SSR markers, and these markers may also be useful for cultivar identification in Occidental melon varieties.

Project description:OBJECTIVE::To evaluate the exposure parameters, radiation protection, absorbed dose and radiographic image quality of the DIOX® intraoral portable radiography device. METHODS::The exposure parameters were measured using the Xi UNFORS detector. Operator exposure to secondary radiation was measured using the 1800cc ionization chamber coupled to the electrometer. The absorbed dose (D) in the patient was calculated using TLD-100H positioned in the Alderson RANDO anthropomorphic simulator. The quality of the radiographic digital image was assessed by comparing radiographic images obtained from two conventional devices (CS 2200®, Carestream Health; Heliodent plus®, Sirona Dental Systems GMbH) with the radiological simulator of the upper molar region RMI (Radiation Measurements Instruments), using three acquisition sensors: Kodak RVG 5000® and Kodak PSP®, Eastman Kodak Company, Rochester, NY; EVO Micro Image®, Brazil. RESULTS::The DIOX intraoral portable radiographic device demonstrated reliability in relation to the performance of the standard evaluated parameters, except for the diameter of the radiation field (5.8 ?mm) less or greater. No evidence of device head radiation was detected. The Pb lead protection of the apparatus attenuates the secondary radiation, thus protecting the operator. However, it was observed that the region of the operator's gonads was the most exposed during the measurements. In the Alderson RANDO anthropomorphic simulator, the highest value of D was in the region corresponding to the submandibular and lingual glands of the left side (0.568 mGy). The image quality of the DIOX portable radiographic apparatus presented quality standards equivalent to those produced by the two conventional radiographic devices. CONCLUSION::The DIOX intraoral portable radiography device demonstrated reliability in relation to the quality control and radioprotection criteria, according to international standards. Results obtained demonstrated the safe use of the DIOX intraoral portable radiography device and indicated the need for debate and change in international sanitary oversight standards regarding the use of portable XR devices in dentistry.

Dataset Information

Quality assessment parameters for EST-derived SNPs from catfish.

Background

Results

Conclusion

Publications

Quality assessment parameters for EST-derived SNPs from catfish.

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