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The OryzaSNP Project-SNP Discovery in Diverse Rice

分子植物育种 2007年第2期5卷 246-247页

作者： K. McNally R. Bruskiewich D. Mackill D. Weigel K. Frazer K. Childs R. Buell J. Leach H. Leung International Rice Research Institute DAPO Box 7777 Metro Manila Philippines Max Planck Institute for Developmental Biology D-72076 Tübingen Germany perlegen sciences Inc. 2021 Stierlin Court Mountain View CA 94043 USA The Institute for Genomic Research 9712 Medical Center Dr. Rockville MD 20850 USA Bioagricultural sciences and Pest Management Colorado State UniversityFt. Collins CO 80523 USA

The OryzaSNP project (http://***) is undertaking SNP discovery across the entire rice genome for 20 diverse varieties (McNally et al., 2006). These varieties include representatives from the indica, tropical

关键词：低聚物序列稻子单倍体种植技术

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Deletions in the genomes of fifteen inbred mouse lines and their possible implications for fat accumulation

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2007年第11期8卷 777-781页

作者： SCHMITT Armin O. DEMPFLE Astrid BROCKMANN Gudrun A. Institute for Animal sciences Humboldt-Universitt zu Berlin Invalidenstraβe 42 10115 Berlin Germany Institute for Medical Biometry and Epidemiology Phillips-Universitt Marburg Bunsenstraβe 3 35037 Marburg Germany

Copy number variants (CNVs) are pieces of genomic DNA of 1000 base pairs or longer which occur in a given genome at a different frequency than in a reference genome. Their importance as a source for phenotypic variability has been recognized only in the last couple of years. Chromosomal deletions can be seen as a special case of CNVs where stretches of DNA are missing in certain lines when compared to the reference genome of the mouse line C57BL/6, for example. Based upon more than 8 million single nucleotide polymorphisms (SNPs) in the fifteen inbred mouse lines which were determined in a whole genome chip based resequencing project by perlegen sciences, we detected 20166 such long chromosomal deletions. They cover altogether between 4.4 million and 8.8 million base pairs, depending on the mouse line. Thus, their extent is comparable to that of SNPs. The chromosomal deletions were found by searching for clusters of missing values in the genotyping data by applying bioinformatics and biostatistical methods. In contrast to isolated missing values, clusters are likely the consequence of missing DNA probe rather than of a failed hybridization or deficient oligos. We analyzed these deletion sites in various ways. Twenty-two percent of these deletion sites overlap with exons; they could therefore affect a gene's functioning. The corresponding genes seem to exist in alternative forms, a phenomenon that reminds of the alternative forms of mRNA generated during gene splicing. We furthermore detected statistically significant association between hundreds of deletion sites and fat weight at the age of eight weeks.

关键词： Copy number variants (CNVs) Chromosomal deletions Single nucleotide polymorphisms (SNPs) Resequencing Cluster analysis Association between genotype and phenotype

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