<i>In Silico</i>Identification and Mapping of Microsatellite Markers on<i>Sus Scrofa</i>Chromosome 4

Wijk, H.J. van; Harlizius, B.; Liefers, S.C.; Buschbell, H.; Dibbits, Bert; Groenen, Martien A. M.

doi:10.1080/10495390701399368

Animal Biotechnology

2007

DOI: 10.1080/10495390701399368

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In SilicoIdentification and Mapping of Microsatellite Markers onSus ScrofaChromosome 4

H.J. van Wijk¹,

B. Harlizius²,

S.C. Liefers³

et al.

Abstract: Marker density of a QTL region on pig chromosome 4 was increased. New microsatellites were identified by in silico mining of BAC-end and genomic shotgun sequences. Among 8,784 BAC-end sequences predicted within the region, 148 microsatellites were identified. In addition, 27,450 CA/TG repeats were identified within the genomic shotgun sequences, of which 157 were most likely located on SSC4q. A selection of 61 new microsatellites was mapped, together with previously mapped markers. The results showed that the … Show more

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Cited by 2 publications

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Simple Sequence Repeats for Genetic Studies of Alpaca

Reed¹,

Chaves²

2008

Animal Biotechnology

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Trace sequences from the 2X alpaca genome sequencing effort were examined to identify simple sequence repeats (microsatellites) for genetic studies. A total of 6,685 repeat-containing sequences were downloaded from GenBank, processed, and assembled into contigs representing an estimated 4,278 distinct sequences. This sequence set contained 2,290 sequences of length > 100 nucleotides that contained microsatellites of length > or = 14 dinucleotide or 10 trinucleotide repeats with purity equal to 100%. An additional 13 sequences contained a GC microsatellite of length > or = 12 repeats (purity = 100%) were also obtained. Primer pairs for amplification of 1,516 putative loci are presented. Amplification of genomic DNA from alpaca and llama by PCR was demonstrated for 14 primer sets including one from each of the microsatellite repeat types. Comparative chromosomal location for the alpaca markers was predicted in the bovine genome by BLAT searches against assembly 4.0 of the bovine whole genome sequence. A total of 634 markers (41.8%) returned BLAT hits with score > 100 and Identity > 85%, with the majority assignable to unique locations. We show that microsatellites are abundant and easily identified within the alpaca genome sequence. These markers will provide a valuable resource for further genetic studies of the alpaca and related species.

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Simple Sequence Repeats for Genetic Studies of Alpaca

Reed¹,

Chaves²

2008

Animal Biotechnology

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Validation of the QTL on SSC4 for meat and carcass quality traits in a commercial crossbred pig population

Sławińska

Siwek

Knol³

et al. 2009

J Animal Breeding Genetics

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Porcine chromosome 4 harbours many quantitative trait loci (QTL) affecting meat quality, fatness and carcass composition traits, detected in resource pig populations previously. However, prior to selection in commercial breeds, QTL identified in an intercross between divergent breeds require confirmation, so that they can be segregated. Consequently, the objective of this study was to validate several QTL on porcine chromosome 4 responsible for meat and carcass quality traits. The experimental population consisted of 14 crossbred paternal half-sib families. The region of investigation was the q arm of SSC4 flanked by the markers S0073 and S0813. Regression analysis resulted in the validation of three QTL within the interval: Minolta a* loin, back fat thickness and the weight of trimmed ham. The results were additionally confirmed by factor analysis. Candidate genes were proposed for meat colour, which was the most evident QTL validated in this study.

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In SilicoIdentification and Mapping of Microsatellite Markers onSus ScrofaChromosome 4

Cited by 2 publications

References 14 publications

Simple Sequence Repeats for Genetic Studies of Alpaca

Simple Sequence Repeats for Genetic Studies of Alpaca

Validation of the QTL on SSC4 for meat and carcass quality traits in a commercial crossbred pig population

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