Abstract
BackgroundGenetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived from expressed sequence tags (ESTs) and genomic shotgun sequences.ResultsLinkage 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.ConclusionThe 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.
Highlights
Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs)
A total of 709 single nucleotide polymorphism (SNP) were initially detected in sequence alignments of the gene associated amplicons derived from expressed sequence tags (ESTs) and shotgun sequences
Six SNPs (Additional file 1) were not similar to any known gene or EST in the human genome and were mapped as porcine EST-based SNPs
Summary
Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on geneassociated single nucleotide polymorphism (SNP) markers is highly valuable. Efficient technologies have been developed, which allow for highly parallel and cost efficient genotyping, SNPs have 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. To identify the genes underlying monogenic and quantitative traits, it is an advantage if the maps are based on gene-associated markers, such as genic SNPs. Genic SNPs, whether they are located in coding or in 5' and 3' untranslated regions are more likely to cause a functional change than those that occur outside genes [5]. More than one million porcine expressed sequence tags (ESTs) are available [7], and tools to evaluate and select candidate SNPs in coding regions for application as genetic markers have been developed [8]
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