Strategies to detect genetic diversity in plants

Next-generation sequencing can provide access to the genomic sequence of even large and complex plant genomes. Three major strategies exist to assess the genomic information of a species at different scales and complexity levels: transcriptome, target capture and whole-genome shotgun sequencing. The scope of this thesis was to evaluate each concept, ascertain its potential for the discovery of genetic diversity, and develop methods for their improvement. With these objectives, the economically important crops rye, maize and barley were investigated to reveal novel insights into their genetic diversity. The study constructed the first rye transcriptome reference that was utilized for variant discovery revealing ~18,000 single nucleotide variants (SNVs) in coding regions. Subsequently, this resource was converted into a genotyping assay (RYE5k) for application e.g. in breeding programs. The identification of genomic variants requires a high degree of accuracy. Two methods were developed to increase the accuracy in the process of variant discovery: the ‘combinatorial variant calling’ and the approach of ‘k-mer repeat investigation’. With the first method, the reliability of variant calling was increased by the interlaced support and analysis of multiple detection procedures. The approach was successfully applied to determine the diversity in biomass-related genes of maize. Hereby, the applied capture sequencing approach revealed 86,875 SNVs in coding regions. The second method was motivated by the complexity of the large and repetitive barley genome. Therefore, k-mer analyses were used to gain knowledge of repetitive features and this resulted in greater precision in variant calling. The positive effect was shown in a genome-wide diversity study of barley. As a result, more than 15 million high-quality SNVs were identified in five cultivars and a wild progenitor of cultivated barley. The study successfully revealed novel insights into the genetic diversity of barley

Sequencing of BAC pools by different next generation sequencing platforms and strategies

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing of BACs is a viable option for deciphering the sequence of even large and highly repetitive genomes. In order to optimize this strategy, we examined the influence of read length on the quality of Roche/454 sequence assemblies, to what extent Illumina/Solexa mate pairs (MPs) improve the assemblies by scaffolding and whether barcoding of BACs is dispensable.</p> <p>Results</p> <p>Sequencing four BACs with both FLX and Titanium technologies revealed similar sequencing accuracy, but showed that the longer Titanium reads produce considerably less misassemblies and gaps. The 454 assemblies of 96 barcoded BACs were improved by scaffolding 79% of the total contig length with MPs from a non-barcoded library.</p> <p>Assembly of the unmasked 454 sequences without separation by barcodes revealed chimeric contig formation to be a major problem, encompassing 47% of the total contig length. Masking the sequences reduced this fraction to 24%.</p> <p>Conclusion</p> <p>Optimal BAC pool sequencing should be based on the longest available reads, with barcoding essential for a comprehensive assessment of both repetitive and non-repetitive sequence information. When interest is restricted to non-repetitive regions and repeats are masked prior to assembly, barcoding is non-essential. In any case, the assemblies can be improved considerably by scaffolding with non-barcoded BAC pool MPs.</p

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. `Morex' was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).Peer reviewe

A chromosome conformation capture ordered sequence of the barley genome

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Wollhandel im Hundertjährigen Krieg unter Edward III. (1337-1377)

Die Diplomarbeit behandelt den Hundertjährigen Krieg zwischen England und Frankreich im Zeitraum von 1335-1377. Untersucht wird, welche Rolle der Wollhandel für die Staatsfinanzen und die Kriegskasse des englischen Königs spielte. Einleitend wird ein Überblick über die Vorgeschichte des Krieges, die Wirtschaft Englands und den Wollhandel vor dem Krieg sowie vorhandene Steuersysteme des englischen Königreichs gegeben. Im Hauptteil wird chronologisch jedes Jahr (1335-1377) hinsichtlich der historischen Vorkommnisse und dem dadurch eventuell beeinflussten Staatseinkommen wie auch den Woll- & Tuchexporten behandelt. Nachdem England in den Anfangsjahren den Krieg hauptsächlich durch Kredite aus dem Ausland finanzierte, wird anhand von ermittelten Daten dargelegt, dass England die Kosten in den späteren Jahren durch Zolleinnahmen aus dem Wollhandel tragen konnte. Dabei waren nicht gestiegene Exportzahlen, sondern höhere Zollabgaben ausschlaggebend sowie zusätzliche Steuerabgaben durch die Kirche und den Laienstand.The diploma thesis covers the hundred year’s war between England and France in the interval of 1335-1377. It is examined which role the wool trade played for the state finances and the war chest for the English King. Preliminary there is an overview of the background for the war, the economy in England and the wool trade before the war and the existing fiscal systems of the English realm. The main part is a chronological analysis of every year (1335-1377) regarding the historical events and the possible influenced state finances plus the wool & cloth trade. In the early years, England financed the war with foreign money, but based on calculated data it is proven that England was able to finance itself with the money from the custom duty on the wool. Thereby not increased exports, but higher custom duties and additional clerical and laity grants were the main reason for that