Abstract
BackgroundLinkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. However, a high density SSCX linkage map has not been reported up to date. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping.ResultsA female-specific high density linkage map was built for SSCX using Sscrofa10.2 annotation. The total length of this chromosome was 84.61 cM; although the average recombination rate was 0.60 cM/Mb, both cold and hot recombination regions were identified. A Bayesian probabilistic to genetic groups and revealed that the animals used in the current study for linkage map construction were likely to be carriers of X chromosomes of European origin. Finally, the newly generated linkage map was used to fine-map a QTL at 16 cM for intramuscular fat content (IMF) measured on longissimus dorsi. The sulfatase isozyme S gene constitutes a functional and positional candidate gene underlying the QTL effect.ConclusionsThe current study presents for the first time a high density linkage map for SSCX and supports the presence of cold and hot recombination intervals along this chromosome. The large cold recombination region in the central segment of the chromosome is not likely to be due to structural differences between X chromosomes of European and Asian origin. In addition, the newly generated linkage map has allowed us to fine-map a QTL on SSCX for fat deposition.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0148-x) contains supplementary material, which is available to authorized users.
Highlights
Linkage maps are essential tools for the study of several topics in genome biology
The high-quality Single nucleotide polymorphism (SNP) mapped on SSCX following Sscrofa10.2 genome assembly [9] were retained, giving a total of 426 SNPs that were used for further analyses
An admixed ancestry model was assumed, and K values equal to 2 and 3 were considered according to the results reported in the quoted study concerning worldwide genetic relationships between pigs based on SSCX SNPs [12]
Summary
Linkage maps are essential tools for the study of several topics in genome biology. High density linkage maps for the porcine autosomes have been constructed exploiting the high density data provided by the PorcineSNP60 BeadChip. The aim of the current study was to build an accurate linkage map of SSCX to provide precise estimates of recombination rates along this chromosome and creating a new tool for QTL fine mapping. Previous studies have reported larger recombination rate variations across and within chromosomes from swine species than those observed in other mammals [2] These and other results, such as the construction of the most recent porcine linkage maps, have been enabled by the high density of markers provided by the PorcineSNP60 BeadChip [3,4]. The aim of the current study was to construct a high density linkage map of the SSCX, obtaining precise estimates of the recombination rate along this chromosome. We have employed the new dense marker linkage map to identify possible QTL for several production and meat quality traits in an experimental Iberian x Landrace cross
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