In situ hybridization in Vitis vinifera L.

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Extensive Chromosome Homoeology among Brassiceae Species Were Revealed by Comparative Genetic Mapping with High-Density EST-Based SNP Markers in Radish (Raphanus sativus L.)‡

A linkage map of expressed sequence tag (EST)-based markers in radish (Raphanus sativus L.) was constructed using a low-cost and high-efficiency single-nucleotide polymorphism (SNP) genotyping method named multiplex polymerase chain reaction–mixed probe dot-blot analysis developed in this study. Seven hundred and forty-six SNP markers derived from EST sequences of R. sativus were assigned to nine linkage groups with a total length of 806.7 cM. By BLASTN, 726 markers were found to have homologous genes in Arabidopsis thaliana, and 72 syntenic regions, which have great potential for utilizing genomic information of the model species A. thaliana in basic and applied genetics of R. sativus, were identified. By construction and analysis of the genome structures of R. sativus based on the 24 genomic blocks within the Brassicaceae ancestral karyotype, 23 of the 24 genomic blocks were detected in the genome of R. sativus, and half of them were found to be triplicated. Comparison of the genome structure of R. sativus with those of the A, B, and C genomes of Brassica species and that of Sinapis alba L. revealed extensive chromosome homoeology among Brassiceae species, which would facilitate transfer of the genomic information from one Brassiceae species to another

An EST-SSR Linkage Map of Raphanus sativus and Comparative Genomics of the Brassicaceae†

Raphanus sativus (2n = 2x = 18) is a widely cultivated member of the family Brassicaceae, for which genomic resources are available only to a limited extent in comparison to many other members of the family. To promote more genetic and genomic studies and to enhance breeding programmes of R. sativus, we have prepared genetic resources such as complementary DNA libraries, expressed sequences tags (ESTs), simple sequence repeat (SSR) markers and a genetic linkage map. A total of 26 606 ESTs have been collected from seedlings, roots, leaves, and flowers, and clustered into 10 381 unigenes. Similarities were observed between the expression patterns of transcripts from R. sativus and those from representative members of the genera Arabidopsis and Brassica, indicating their functional relatedness. The EST sequence data were used to design 3800 SSR markers and consequently 630 polymorphic SSR loci and 213 reported marker loci have been mapped onto nine linkage groups, covering 1129.2 cM with an average distance of 1.3 cM between loci. Comparison of the mapped EST-SSR marker positions in R. sativus with the genome sequence of A. thaliana indicated that the Brassicaceae members have evolved from a common ancestor. It appears that genomic fragments corresponding to those of A. thaliana have been doubled and tripled in R. sativus. The genetic map developed here is expected to provide a standard map for the genetics, genomics, and molecular breeding of R. sativus as well as of related species. The resources are available at http://marker.kazusa.or.jp/Daikon

Association mapping of agronomically important traits in Brassica rapa L.

An association mapping approach was used to find marker-phenotype associations in the VIR core collection of 96 Brassica rapa accessions representing various morphotypes of different geographical origin. Genetic distances of accessions were determined using a set of SSR and S-SAP (CACTA) markers and NTSYSpc program. The same program was used to determine marker-marker and marker-phenotype correlations. Significant associations to molecular markers were found for bolting and flowering time, growth related traits, lamina and petiole morphological characters connected with quality, as well as for biochemical and resistance features.</p

Werkzeugunterstuetzte Parallelisierung von Finite-Element Anwendungen (PARFEM) Abschlussbericht

Goal of the PARFEM project was the development of software tools and methods to support the efficient treatment of large sparse matrices on parallel computers. Also new algorithms for the solution of such systems should be investigated. Portability of all components was an important aspect. Finally, the algorithms and methods should be integrated in the well-known FE software package PERMAS. The parallelization concept for PERMAS is based on the exploitation of task parallelism and not on the usual mesh partitioning (or domain decomposition) technique. The solution of the sparse system leads to the execution on many tasks which operate on independent data and which can be executed in parallel. A task graph controls the data dependency. A scheduler maps those tasks to processors and tries to achieve load balance. As an alternative to the standard direct Cholesky solver parallel preconditioned cg-solvers and parallel multifrontal solvers were implemented and investigated: - Several variants of preconditioners were tested as well as different storage schemes. The optimal variants showed very good speed-up results and the execution time was shorter than the time of the standard direct solver for a large number of processors. The integration into the PERMAS code, however, lead to some loss of scalability. - A parallel multifrontal solver was integrated and parallelized using the tools developed in the project. Speedup figures on an IBM SP2 system were satisfactory. The PARFEM project was very important for the development of the PERMAS code. The tools in PARFEM made it possible to maintain one version of the code for sequential and parallel platforms. Users can use the parallel code without additional training since the user interface was not changed at all. Since portability was very important the project used PARMACS and later MPI as portability platform. The parallel approach could even be executed on workstation clusters although, due to weak communication performance, not very efficiently. (orig.)SIGLEAvailable from TIB Hannover: F98B607+a / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekBundesministerium fuer Bildung, Wissenschaft, Forschung und Technologie, Bonn (Germany)DEGerman