A robust linkage map of the porcine autosomes based on gene-associated SNPs

Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting in an average SNP spacing of 3.94 cM. The female and male maps were estimated to 2,336.1 and 1,441.5 cM, respectively. The gene order was validated through comparisons to the cytogenetic and/or physical location of 203 genes, linkage to evenly spaced microsatellite markers as well as previously reported conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations.The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic events provide good reliability and make this map suitable for QTL and association studies. In addition, the linkage to the RH-map of microsatellites makes it suitable for comparison to other QTL studies.Genetic linkage maps are essential tools for locating genes and quantitative trait loci (QTLs) that control important traits. The first linkage map covering all 18 autosomes of the pig was published in 1995 [1], followed by a large map containing approximately 1,200 markers [2]. These maps were primarily constructed on the basis of anonymous microsatellites and restriction fragment length polymorphism (RFLP) markers [1-3]. Other marker types including amplified fragment length polymorphisms (AFLP) and single nucleotide polymorphisms (SNPs) have been added to online versions of the maps [4].SNP-based genetic variation is found with high density throughout the genome. Efficient technologies have been developed, which allow for highly parallel and cost efficient genotyping, SNPs have therefore become the markers of choice for genetic mapping. This makes SNP maps highly suitable for association studies, fine mapping of QTLs as well as haplotype determination. Moreover, to i