The Sino-Danish Pig Genome Project



  • A data resource of 838 porcine microsatellite sequences with repeat motifs of three to six bases.
    P. Karlskov-Mortensen, Z.L. Hu,  J. M. Reecy and M. Fredholm
    Animal Genetics, 39:85-86, 2008.

  • Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences.
    P. Karlskov-Mortensen, Z.L. Hu, J. Gorodkin, J. M. Reecy and M. Fredholm
    Animal Genetics, 38:401-405, 2007


The 3.8 million genomic shotgun reads from the Sino-Danish Pig Genome Sequencing Consortium (Wernersson et al. 2005) have been scanned to identify microsatellite containing sequences with repeat motifs of two to six bases. Only sequences with at least ten perfect repeats are included, as these will be the best suited for use as genetic markers. More than 10,000 new dinucleotide repeat sequences are identified. Of the longer repeats, 190 are trinucleotide repeats, 584 are tetranucleotide repeats, 57 are pentanucleotide repeats and 7 are hexanucleotide repeats.

Of the new microsatellite sequences, 4,528 dinucleotide repeats and 296 longer repeats have been virtually mapped onto pig-human comparative maps and hereby assigned a putative position in the porcine genome. For easy accessibility all marker sequences can be downloaded from the links below, or in silico mapped markers can be browsed and selected based on position via the comparative maps at On these maps, one can browse or search to get to a chromosome view for QTL, then click on a QTL vertical bar, and choose "To New Pig Microsatellites Map" from the popup menu. Due to the limited space on the chromosome map, the number of markers displayed is limited. To overcome this problem a "regional chromosome view" is implemented where all markers within 5 Mb of a chromosome region, and the details of the marker in query is displayed. This set of microsatellite markers is one of the resources developed based on data from the Sino-Danish Pig Genome Sequencing Consortium.

Processed data

Marker info (Dinucleotide repeat sequences) markerinfo.txt
MS virtually mapped (Dinucleotide repeat sequences) MS_virtually_mapped.fasta
MS without map positions (Dinucleotide repeat sequences) MS_without_mapposition.fasta
Marker info (Longer repeat sequences)
MS without map positions (Longer repeat sequence) 838_longMS.fasta


This resource was supported by

  • The National Committee of Pig Breeding, Health and Production.
  • The Danish Research Councils: SJVF and STVF (now FTP).
  • USDA National Animal Genome Research Program (NRSP-8).

Contact: Peter Karlskov-Mortensen.

Comments, questions, etc., email

Last updated March 27th, 2007 by Jan Gorodkin