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 420163
Title Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof
Author(s) Esteve-Codina, A.; Kofler, R.; Himmelbauer, H.; Ferretti, L.; Vivancos, P.; Groenen, M.A.M.
Source Heredity 107 (2011)3. - ISSN 0018-067X - p. 256 - 264.
DOI http://dx.doi.org/10.1038/hdy.2011.13
Department(s) Animal Breeding and Genetics
WIAS
Publication type Refereed Article in a scientific journal
Publication year 2011
Keyword(s) snp discovery - recombination rates - whole-genome - qtl - diversity - mutation
Abstract Despite dramatic reduction in sequencing costs with the advent of next generation sequencing technologies, obtaining a complete mammalian genome sequence at sufficient depth is still costly. An alternative is partial sequencing. Here, we have sequenced a reduced representation library of an Iberian sow from the Guadyerbas strain, a highly inbred strain that has been used in numerous QTL studies because of its extreme phenotypic characteristics. Using the Illumina Genome Analyzer II (San Diego, CA, USA), we resequenced ~1% of the genome with average 4 × depth, identifying 68¿778 polymorphisms. Of these, 55¿457 were putative fixed differences with respect to the assembly, based on the genome of a Duroc pig, and 13¿321 were heterozygous positions within Guadyerbas. Despite being highly inbred, the estimate of heterozygosity within Guadyerbas was ~0.78¿kb-1 in autosomes, after correcting for low depth. Nucleotide variability was consistently higher at the telomeric regions than on the rest of the chromosome, likely a result of increased recombination rates. Further, variability was 50% lower in the X-chromosome than in autosomes, which may be explained by a recent bottleneck or by selection. We divided the whole genome in 500¿kb windows and we analyzed overrepresented gene ontology terms in regions of low and high variability. Multi organism process, pigmentation and cell killing were overrepresented in high variability regions and metabolic process ontology, within low variability regions. Further, a genome wide Hudson–Kreitman–Aguadé test was carried out per window; overall, variability was in agreement with neutral expectations
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