ESTIMATION OF THE EXTENT OF LINKAGE DISEQUILIBRIUM IN SEVEN REGIONS OF THE PORCINE GENOME

ABSTRACT

Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting non-random patterns of association between alleles at (nearby) loci. A better understanding of LD in the porcine genome is of direct relevance for identification of genes and mutations with a certain effect on the traits of interest.

Here, 215 SNPs in seven genomic regions were genotyped in individuals of three breeds. Pairwise linkage disequilibrium was calculated for all marker pairs. To estimate the extent of LD, all pairwise LD values were plotted against the distance between the markers. Based on SNP markers in four genomic regions analyzed in three panels from populations of Large White, Dutch Landrace, and Meishan origin, useful LD is estimated to extend for approximately 40 to 60 kb in the porcine genome.

Keywords:

• Linkage disequilibrium
• single nucleotide polymorphism
• pig

ACKNOWLEDGMENTS

We thank Jan Aerts and Cleopatra del Prado for their comments and suggestions and Anita Grootemaat for technical assistance.

Notes

¹BACs E, F, C and G are part of a BAC contig generated by the NIH Intramural Sequencing Center (www.nisc.nih.gov).

¹SNPs were discovered from a panel of 63 individuals.