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 372464
Title High throughput SNP discovery and validation in the Pig: towards the development of a high density swine SNP chip
Author(s) Ramos, A.; Amaral, A.J.; Kerstens, H.H.D.; Bendixen, C.; Hedegaard, J.; Rohrer, G.; Smith, T.; Tassell, C.; Taylor, J.F.; Groenen, M.A.M.
Event 31st Conference of the International Society of Animal Genetics, 2008-07-20/2008-07-24
Department(s) Animal Breeding and Genetics
WIAS
Publication type Abstract in scientific journal or proceedings
Publication year 2008
Abstract Recent developments in sequencing technology have allowed the generation of millions of short read sequences in a fast and inexpensive way. This enables the cost effective large scale identification of hundreds of thousands of SNPs needed for the development of high density SNP arrays. Currently, a high density swine SNP chip is being developed as part of an integrated effort of several European and American institutions involved in swine genomics research. The future pig SNP chip will include already validated SNPs as well as SNPs identified de novo using second generation sequencing on the Illumina 1 G analyzer (Solexa) and the Roche 454 sequencer. Towards this end, a total of 15 DNA libraries were prepared using pooled DNA samples from five breeds (Duroc, Landrace, Large White, Pietrain and Wild Boar) digested with three restriction enzymes (AluI, HaeIII, MspI). Fragments in the size range of 150-200 bp were selected for sequencing. The ends of these fragments (35 bp) will be sequenced at 30X coverage complemented with 2X sequencing of the complete fragment using 454 sequence technology. The Solexa short sequence reads will be filtered using several quality criteria to produce the dataset used for SNP discovery. Additional criteria for the selection of the 60K SNPs include the estimated minor allele frequency and genome position of the SNPs. The high density 60K SNP chip will be an extremely valuable tool for the pig genomics community for a variety of applications including QTL and LD mapping, association studies and genomic selection.
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