Recombination of the porcine X chromosome: a high density linkage map

Fernández et al. BMC Genetics 2014, 15:148 http://www.biomedcentral.com/1471-2156/15/148 RESEARCH ARTICLE Open Access Recombination of the porcine X chromosome: a high density linkage map Ana I Fernández1*, María Muñoz1,2, Estefânia Alves1, Josep María Folch3,4, Jose Luis Noguera5, Miguel Pérez Enciso3,4,6, Maria del Carmen Rodríguez1 and Luis Silió1 Abstract Background: 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. 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. Results: A 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. Conclusions: The 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. Keywords: Porcine linkage maps, Recombination, X chromosome, European and Asian X chromosome Background Linkage maps are key tools to genetically map and dissect complex traits, as well as for the study of several topics in genome biology such as the molecular basis of recombination and evolutionary genomics [1]. Interestingly, 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 X chromosome plays an important role in the evolution of human and animals [5], and experiences higher * Correspondence: 1 Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid 28040, Spain Full list of author information is available at the end of the article selection pressure than autosomes due to the sex-specific dosage compensation [6]. Moreover, the X chromosome of pigs carries many interesting genes involved in development, fertility, reproduction and diseases such as the inactive X specific transcripts (XIST), androgen receptor (AR) and thyroid-binding globulin (TGB), and over 370 QTLs for productive and reproductive related traits have been reported on this chromosome (www.animalgenome.org/ cgi-bin/QTLdb). However, the location of these QTL is not precise, due to the low density of the available linkage map. In spite of its relevance, the highest density linkage map for the porcine X chromosome to date includes only 60 markers [7]. None of the above mentioned high density linkage maps include this chromosome. High density genetic linkage maps are not only essential for QTL fine-mapping, they are also needed to successfully identify functional and positional candidate genes © 2014 Fernandez et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Fernández et al. BMC Genetics 2014, 15:148 http://www.biomedcentral.com/1471-2156/15/148 that may carry causal mutations. Therefore, 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. Furthermore, 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. Methods Linkage map construction The animals used in the current study belong to three generations of an experimental Iberian x Landrace cross, the so-called IBMAP pedigree [3]. Briefly, there were a total of 416 pigs of the IBMAP experimental cross, comprising 147 males and 269 females organized in 62 families. There were 86 F3 animals from the cross of three F2 boars with 15 F2 sows, 79 backcrossed animals (BC2) from the cross of four F2 boars with 22 Landrace sows, and 160 backcrossed animals (BC1) from the cross of five F1 boars with 25 Landrace sows. In addition, F1 and F0 sires and dams of the F2 and F1 animals described were also genotyped. A total of 329 meiotic events were available for further analyses. Animal manipulations were performed according to the Spanish Policy for Animal Protection RD1201/05, which meets the European Union Directive 86/609 about the protection of animals used in experimentation. The animals were genotyped with the PorcineSNP60 BeadChip [8] using the Infinium HD Assay Ultra protocol (Illumina, Inc.). Raw individual data had high-genotyping quality (call rate >0.99). The clustering of the genotype data obtained with the Illumina BeadStudio software was checked, and markers with poor clustering performance (GenScore <0.85) were excluded from the analysis. The high-quality SNPs mapped on SSCX following Sscrofa10.2 genome assembly [9] were retained, giving a total of 426 SNPs that were used for further analyses. The linkage map was built employing exclusively the female genotypes and using those high-quality SNPs with a minor allele frequency higher than 0.15 (a total of 200 SNPs) (Additional file 1: Table S1). The Fixed option of the updated CRI-MAP v2.503 (provided by JF Maddox, http:// www.animalgenome.org/bioinfo/tools/share/crimap/) was used for linkage map construction. The order given to the SNPs followed the physical order of the Sscrofa10.2 assembly. Note that possible errors in the Xq tail assembly (from 125 Mb in Sscrofa9 version corresponding to 144 Mb in Sscrofa10.2 (...truncated)