Animal QTL database: Development and Release Notes

This work has been published

P. Karlskov-Mortensen, et al. Identification of 10,882 porcine microsatellite sequences and virtual mapping of 4,528 of these sequences Animal Genetics, Volume38, Issue4, August 2007, Pages 401-405. DOI: https://doi.org/10.1111/j.1365-2052.2007.01609.x

Identification of 10,882 new porcine microsatellites with in silico mapping of 4,528 markers to aid positional QTL mining

Peter Karlskov-Mortensen ¹, Zhi-Liang Hu ², Jan Gorodkin ¹, James Reecy ² and Merete Fredholm ¹

1: Department of Animal- and Veterinary Basic Sciences, Division of Genetics. The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.

2: Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011-3150, USA

(Animal Genetics, 38(4),401-405)

ABSTRACT: 10,882 new porcine microsatellite markers have been identified in genomic shot gun sequences from the Sino-Danish Pig Genome Sequencing Consortium (Wernersson et al. 2005). 4,528 of these were placed on the pig-human comparative map by BLAST of porcine sequences against the human genome (BLAST cut-off threshold = 1E-5). Markers placed on the comparative map are grouped into three categories depending on length of the sequence flanking the microsatellite repeat and they are available on the PigQTLdb.

Updates:

Feb. 5, 2007: See http://piggenome.dk/ms/ for more recent updates information.
Aug. 15, 2007: Annitional 838 microsatellites are added to this pool.

Reference:

Wernersson R., Schierup M.H., Jorgensen F.G., Gorodkin J., Panitz F., Staerfeldt H.H., Christensen O.F., Mailund T., Hornshoj H., Klein A., Wang J., Liu B., Hu S.N., Dong W., Li W., Wong G.K.S., Yu J., Wang J., Bendixen C., Fredholm M., Brunak S., Yang H.M., and Bolund L. (2005) "Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing". BMC Genomics, 2005 May 10; 6(1):70.

A data resource of 838 porcine microsatellite sequences with repeat motifs of three to six bases.

Peter Karlskov-Mortensen ¹, Zhi-Liang Hu ², James Reecy ² and Merete Fredholm ¹

1: Department of Animal- and Veterinary Basic Sciences, Division of Genetics. The Royal Veterinary and Agricultural University, Frederiksberg, Denmark.

2: Department of Animal Science, Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, Iowa 50011-3150, USA

(Animal Genetics, 39(1),85-86)

(Brief Note; No abstract)