26 research outputs found

    Chromosomal localization of echidna MHC BAC clones in male meiotic metaphase I preparations

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    BAC 48g5 (green) on Y3X3. DAPI inverted picture. The elements of the chain are indicated by the bold lines; the elements containing MHC genes are shown in green. Hybridization of BAC 268a21 on the meiotic chain. Chromosome telomeres are highlighted by hybridization of a telomere repeat (red). In DAPI inverted picture. The elements at the end of the chain are indicated by the bold lines.<p><b>Copyright information:</b></p><p>Taken from "Disruption and pseudoautosomal localization of the major histocompatibility complex in monotremes"</p><p>http://genomebiology.com/2007/8/8/R175</p><p>Genome Biology 2007;8(8):R175-R175.</p><p>Published online 29 Aug 2007</p><p>PMCID:PMC2375005.</p><p></p

    Genome-environment associations along elevation gradients in two snowbed species of the North-Eastern Calcareous Alps

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    In this pilot study we assessed the suitability of two alpine species,  Achillea clusiana and Campanula pulla, to serve as models for genetic  monitoring of climate change adaptation along an altitudinal gradient.  We identified loci under selection and correlated them with  environmental factors relevant in a climate change context. The data available with this figshare link: de novo assembled loci for Achillea clusiana and Campanula pulla, called variants, keyfile and a Supplemental Information file with detailed code used for analysing the data as well as a list of software and versions used in the study.</p

    Scoring of polymorphisms.

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    <p>Polymorphic sites were categorised according to three criteria as described in the methods section. Test A: Neighbourhood Quality Standard, average score of polymorphic bases> = 20, average score of 5 bases up-/downstream> = 15; test B: minimal distance to border> = 80 bp; test C: polymorphism length < = 3 bp.</p><p>Scoring of polymorphisms.</p

    Detailed results of the marker generation.

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    <p>All tests comprises test A: Neighbourhood Quality Standard; test B: minimal distance to border and test C: polymorphism length. Neighbourhood Quality Standard (NQS) is a possible criterion to evaluate the reliability. More details can be found in Materials and Methods and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110113#pone-0110113-t002" target="_blank">Table 2</a>.</p><p>Detailed results of the marker generation.</p

    Workflow of data processing for polymorphic site detection.

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    <p>The analysis steps (marked <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110113#pone.0110113-Magana1" target="_blank">[1]</a> to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110113#pone.0110113-Syvanen1" target="_blank">[9]</a>) executed from the two starting data sets to the polymorphic alignments are summarised.</p

    Reliable <i>In Silico</i> Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (<i>Beta vulgaris</i>)

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    <div><p>Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (<i>Beta vulgaris</i> L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the <i>in silico</i> detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers.</p></div

    Display of chromosome 1 comparing the current and former genetic map derived from the KWS1 mapping population.

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    <p>The new map designated BeetMap-3 is shown on the left, the former BeetMap on the right. Names of markers added by this study are highlighted in green, excluded markers are marked in red. Terminal marker were named by using the prefix “KWS_”. Cosegregating markers are indicated by identical map positions.</p

    Evaluation of alignments for polymorphic site detection.

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    <p>*Excluding 19 cases with uncertain mismatch typing due to lower sequence quality.</p><p>Alignments between Sanger sequence reads (K1P1) and either K1P2-singlets or K1P2-contigs were created and evaluated with regard to the presence and type of polymorphic sites. Numbers in brackets reflect successive analysis steps.</p><p>Evaluation of alignments for polymorphic site detection.</p