3,498 research outputs found

    In-silico single nucleotide polymorphisms (SNP) mining of Sorghum bicolor genome

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    Single nucleotide polymorphisms (SNPs) may be considered the ultimate genetic markers as they represent the finest resolution of a DNA sequence (a single nucleotide), and are generally abundant in populations with a low mutation rate. SNPs are important tools in studying complex genetic traits and genome evolution. SNP mining can be done by experimental and computational methods. Computational strategies for SNP discovery make use of a large number of sequences present in public databases [in most cases as expressed sequence tags (ESTs)] and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only. In the present study, online SNP and allele detection tool HaploSNPer (based on QualitySNP pipeline) and Sorghum bicolor genome was used. As a result, 77094 potential SNPs and 40589 reliable SNPs were detected in S. bicolor. In the 77094 potential SNPs detectedtransitions, transversions and indels were 34398, 35871 and 6825, respectively. In the 40589 reliable SNPs detected transitions, transversions and indels were 17042, 20500 and 3047, respectively.Key words: Single nucleotide polymorphisms (SNP), expressed sequence tags (EST), HaploSNPer

    Single nucleotide polymorphisms from Theobroma cacao expressed sequence tags associated with witches' broom disease in cacao

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    In order to increase the efficiency of cacao tree resistance to witches¿ broom disease, which is caused by Moniliophthora perniciosa (Tricholomataceae), we looked for molecular markers that could help in the selection of resistant cacao genotypes. Among the different markers useful for developing marker-assisted selection, single nucleotide polymorphisms (SNPs) constitute the most common type of sequence difference between alleles and can be easily detected by in silico analysis from expressed sequence tag libraries. We report the first detection and analysis of SNPs from cacao-M. perniciosa interaction expressed sequence tags, using bioinformatics. Selection based on analysis of these SNPs should be useful for developing cacao varieties resistant to this devastating disease. (Résumé d'auteur

    Comprehensive Functional Analyses of Expressed Sequence Tags in Common Wheat (Triticum aestivum)

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    About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37 138 contigs and 215 199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics

    Bioinformatics tools for development of fast and cost effective simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs)

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    The development of current molecular biology techniques has led to the generation of huge amount of gene sequence information under the expressed sequence tag (EST) sequencing projects on a large number of plant species. This has opened a new era in crop molecular breeding with identification and/or development of a new class of useful DNA markers called genic molecular markers (GMMs). These markers represent the functional component of the genome in contrast to all other random DNA markers (RMMs). Many recent studies have demonstrated that GMMs may be superior to RMMs for use in the marker assisted selection, comparative mapping and exploration of functional genetic diversity in the germplasms adapted to different environment. Therefore, identification of DNA sequences which can be used as markers remains fundamental to the development of GMMs. Amongst others; bioinformatics approaches are very useful for development of molecular markers, making their development much faster and cheaper. Already, a number of computer programs have been implemented that aim at identifying molecular markers from sequence data. A revision of current bioinformatics tools for development of genic molecular markers is, therefore, crucial in this phase. This mini-review mainly provides an overview of different bioinformatics tools available and its use in marker development with particular reference to SNP and SSR markers.Keywords: Genic molecular marker, simple sequence repeat (SSR), and single nucleotide polymorphisms (SNP) markers from expressed sequence tags (ESTs).African Journal of Biotechnology Vol. 12(30), pp. 4713-472

    Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_

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    Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and Indel(4.1/kbp) frequency was higher in _E. oleifera_ than _E. guineensis_ species (16.8/kbp, 1.6/kbp). _E. oleifera_ showed higher transition to transversion ratio (1.40) than in _E. guineensis_ (1.02). The ratio of Ts vs Tv showed, the genetic divergence is occurring in this crops in different fashion and _E. guineensis_ had diverged more than _E. oleifera_. We provide the results of the study as online database ("http://riju.byethost31.com/oilpalm/":http://riju.byethost31.com/oilpalm/) for use by oil palm breeders

    review marcatori genetici acquacoltura

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    Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags

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    Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially ‘A/T’ repeats in Oil palm. Flanking primers were designed using primer3, SSR primers. The results of the study are given as an online database ‘MEMCO’ to help Oil palm researchers

    Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach

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    <p>Abstract</p> <p>Background</p> <p>Single nucleotide polymorphisms (SNPs) represent the most widespread type of DNA variation in vertebrates and may be used as genetic markers for a range of applications. This has led to an increased interest in identification of SNP markers in non-model species and farmed animals. The <it>in silico </it>SNP mining method used for discovery of most known SNPs in Atlantic salmon (<it>Salmo salar</it>) has applied a global (genome-wide) approach. In this study we present a targeted 3'UTR-primed SNP discovery strategy that utilizes sequence data from <it>Salmo salar </it>full length sequenced cDNAs (FLIcs). We compare the efficiency of this new strategy to the <it>in silico </it>SNP mining method when using both methods for targeted SNP discovery.</p> <p>Results</p> <p>The SNP discovery efficiency of the two methods was tested in a set of FLIc target genes. The 3'UTR-primed SNP discovery method detected novel SNPs in 35% of the target genes while the <it>in silico </it>SNP mining method detected novel SNPs in 15% of the target genes. Furthermore, the 3'UTR-primed SNP discovery strategy was the less labor intensive one and revealed a higher success rate than the <it>in silico </it>SNP mining method in the initial amplification step. When testing the methods we discovered 112 novel bi-allelic polymorphisms (type I markers) in 88 salmon genes [dbSNP: ss179319972-179320081, ss250608647-250608648], and three of the SNPs discovered were missense substitutions.</p> <p>Conclusions</p> <p>Full length insert cDNAs (FLIcs) are important genomic resources that have been developed in many farmed animals. The 3'UTR-primed SNP discovery strategy successfully utilized FLIc data to detect novel SNPs in the partially tetraploid Atlantic salmon. This strategy may therefore be useful for targeted SNP discovery in several species, and particularly useful in species that, like salmonids, have duplicated genomes.</p

    A fast and cost-effective approach to develop and map EST-SSR markers: oak as a case study

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    Background: Expressed Sequence Tags (ESTs) are a source of simple sequence repeats (SSRs) that can be used to develop molecular markers for genetic studies. The availability of ESTs for Quercus robur and Quercus petraea provided a unique opportunity to develop microsatellite markers to accelerate research aimed at studying adaptation of these long-lived species to their environment. As a first step toward the construction of a SSR-based linkage map of oak for quantitative trait locus (QTL) mapping, we describe the mining and survey of EST-SSRs as well as a fast and cost-effective approach (bin mapping) to assign these markers to an approximate map position. We also compared the level of polymorphism between genomic and EST-derived SSRs and address the transferability of EST-SSRs in Castanea sativa (chestnut). Results: A catalogue of 103,000 Sanger ESTs was assembled into 28,024 unigenes from which 18.6% presented one or more SSR motifs. More than 42% of these SSRs corresponded to trinucleotides. Primer pairs were designed for 748 putative unigenes. Overall 37.7% (283) were found to amplify a single polymorphic locus in a reference fullsib pedigree of Quercus robur. The usefulness of these loci for establishing a genetic map was assessed using a bin mapping approach. Bin maps were constructed for the male and female parental tree for which framework linkage maps based on AFLP markers were available. The bin set consisting of 14 highly informative offspring selected based on the number and position of crossover sites. The female and male maps comprised 44 and 37 bins, with an average bin length of 16.5 cM and 20.99 cM, respectively. A total of 256 EST-SSRs were assigned to bins and their map position was further validated by linkage mapping. EST-SSRs were found to be less polymorphic than genomic SSRs, but their transferability rate to chestnut, a phylogenetically related species to oak, was higher. Conclusion: We have generated a bin map for oak comprising 256 EST-SSRs. This resource constitutes a first step toward the establishment of a gene-based map for this genus that will facilitate the dissection of QTLs affecting complex traits of ecological importance
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