Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 387557
Title Genome wide SNP detection in the great tit Parus major using high throughput sequencing
Author(s) Bers, N.E.M. van; Oers, K. van; Kerstens, H.H.D.; Dibbits, B.W.; Crooijmans, R.P.M.A.; Visser, C.; Groenen, M.A.M.
Event Plant & Animal Genomes XVIII Conference, 2010-01-09/2010-01-13
Department(s) Animal Breeding and Genetics
WIAS
Publication type Abstract in scientific journal or proceedings
Publication year 2010
Abstract Next generation sequencing technologies have dramatically lowered the costs to obtain genomic sequence information. This has opened exiting possibilities for (partial) de novo assembly of genomes, and for genome-wide SNP detection in organisms currently lacking a sequenced genome. We have combined high throughput sequencing (Illumina GA) with de novo assembly of the resulting short reads into small contigs. These contigs function as a reference sequence for mapping of the original short sequence reads, allowing the detection of high quality SNPs. The contig sequence provides the flanking sequence essential for use in a genotyping assay. This strategy has resulted in the detection of more than 7,000 novel SNPs in turkey (Meleagris gallopavo), 3,500 SNPs in tilapia (Oreochromis niloticus), and over 20,000 SNPs for the ecological model species Parus major, the great tit. Mapping of the contig sequences against the genome sequence of a related species, e.g. chicken in case of turkey and the zebra finch in case of the great tit, allows the selection of genome-wide distributed SNPs. Additionally, the availability of the genome sequence of a related species can be employed for the merging of adjacent contigs, which increases the number of SNPs usable in a genotyping assay.
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