PAG-X  Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA


Poster: SNP
            


DEVELOPMENT AND TYPING OF SINGLE NUCLEOTIDE POLYMORPHISM (SNP) MARKERS IN A QTL REGION FOR FATNESS TRAITS ON PORCINE CHROMOSOME 2

Bart Jungerius1 , Annemieke Rattink1 , Barbara Harlizius2 , Bernard van Oost3 , Marinus te Pas4 , Martien Groenen1

1 Animal Breeding and Genetics Group, Wageningen Institute of Animal Sciences, Wageningen University, The Netherlands
2 Animal Breeding and Genetics Group, Wageningen Institute of Animal Sciences, Wageningen University, The Netherlands
   present adress: Institute for Pig Genetics, Beuningen, The Netherlands
3 Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht university, The Netherlands
4 Institute for Animal Science and Health (ID-Lelystad), The Netherlands

A maternally imprinted quantative trait locus (QTL) for backfat thickness (BFT) has been identified on the p-arm of porcine chromosome 2 (SSC2p)(Rattink et al., 2000). To reduce the size of the interval of the QTL and eventually be able to identify the underlying genes responsible for the observed effects additional DNA markers are needed. In order to increase the marker density on SSC2 single nucleotide polymorphism (SNP) markers were developed by sequencing PCR products amplified from genomic DNA of 8 individuals from different breeds. PCR primers were designed on genes that map to SSC2 and on sequences derived from BAC clones isolated from the QTL region. In addition, primers were based on porcine cDNA homologous to genes on human chromosomes 11p and 19p (HSA11p and HSA19p). These human chromosomal regions show homology in gene order when compared to SSC2 (Rattink et al., 2001). Until now 169 SNPs were identified in 28 sequence tagged sites (STS) covering 80 cM of SSC2 which corresponds to the P-arm of this chromosome. Currently these SNP markers are being used for detailed haplotyping of animals from the experimental QTL mapping cross. The SNPs are assayed in multiplex single base extension reactions using the ABI Prism SNaPshot kit and analysed on an automated sequencer (ABI377). The genotypes can be assigned in a (semi-) automated way using the Genescan (v3.1.2) and Genotyper (v2.0) software and are prepared for integration in Markbase (an ORACLE based database) and CRIMAP (linkage analysis) via a MS Excel spreadsheet.


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