Worldwide genetic relationships of pigs as inferred from X chromosome <scp>SNP</scp>s

Burgos-Paz, William; Souza, Carla A.; Castelló, Anna; Mercadé, A.; Okumura, Naohiko; Шереметьева, И. Н.; Huang, Lusheng; Cho, I. C.; Paiva, Samuel Rezende; Ramos-Onsins, Sebastián E.; Pérez‐Enciso, Miguel

doi:10.1111/j.1365-2052.2012.02374.x

Cited by 9 publications

(7 citation statements)

References 33 publications

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“…2 C and D ). A similar pattern of lower mean F ST in the PAR than the X-linked regions has also been observed among worldwide pig populations and between domestic pigs and wild boar ( Burgos-Paz et al. 2013 ).…”

Section: Resultssupporting

confidence: 74%

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

Chen

Zhang

et al. 2018

Genome Biology and Evolution

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Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world’s sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05–79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep’s recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

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Section: Resultssupporting

confidence: 74%

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

Chen

Zhang

et al. 2018

Genome Biology and Evolution

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“…The SNPs contained within the pseudoautosomal (PAR) and non-pseudoautosomal (NPAR) regions of X chromosome were differentiated following Burgos-Paz et al [ 12 ] criteria. The first 37 SNPs (from 0 to 6.54 Mb) fall within PAR and the remaining 389 (from 7.18 to 143.48 Mb) within NPAR, and each one of these chromosome regions was independently analyzed.…”

Section: Methodsmentioning

confidence: 99%

“…A Bayesian clustering method in STRUCTURE software [ 13 ] was used to assign individuals to one of the K clusters representing ancestral populations, or jointly to two or more populations if their genotypes indicated that they were admixed. In this analysis, 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 ]. For each analysis performed, a burn-in period of 50,000 iterations was followed by 500,000 iterations.…”

Section: Methodsmentioning

confidence: 99%

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

Fernández¹,

Muñoz

Alves³

et al. 2014

BMC Genet

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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.

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“…The SSCX PAR occupies the first 6.7 Mb and the last 400 kb of SSCX, approximately. Although assembly 10.2 separates two telomeric PARs, linkage analyses using genotyping data from the 60k SNP chip in an Iberian x Landrace cross and results from Burgos-Paz [45] suggest that a single PAR exists – as in most mammals. We therefore pooled the results from the two annotated PARs in the analyses reported here.…”

Section: Methodsmentioning

confidence: 99%

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

et al. 2013

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BackgroundIn contrast to international pig breeds, the Iberian breed has not been admixed with Asian germplasm. This makes it an important model to study both domestication and relevance of Asian genes in the pig. Besides, Iberian pigs exhibit high meat quality as well as appetite and propensity to obesity. Here we provide a genome wide analysis of nucleotide and structural diversity in a reduced representation library from a pool (n=9 sows) and shotgun genomic sequence from a single sow of the highly inbred Guadyerbas strain. In the pool, we applied newly developed tools to account for the peculiarities of these data.ResultsA total of 254,106 SNPs in the pool (79.6 Mb covered) and 643,783 in the Guadyerbas sow (1.47 Gb covered) were called. The nucleotide diversity (1.31x10-3 per bp in autosomes) is very similar to that reported in wild boar. A much lower than expected diversity in the X chromosome was confirmed (1.79x10-4 per bp in the individual and 5.83x10-4 per bp in the pool). A strong (0.70) correlation between recombination and variability was observed, but not with gene density or GC content. Multicopy regions affected about 4% of annotated pig genes in their entirety, and 2% of the genes partially. Genes within the lowest variability windows comprised interferon genes and, in chromosome X, genes involved in behavior like HTR2C or MCEP2. A modified Hudson-Kreitman-Aguadé test for pools also indicated an accelerated evolution in genes involved in behavior, as well as in spermatogenesis and in lipid metabolism.ConclusionsThis work illustrates the strength of current sequencing technologies to picture a comprehensive landscape of variability in livestock species, and to pinpoint regions containing genes potentially under selection. Among those genes, we report genes involved in behavior, including feeding behavior, and lipid metabolism. The pig X chromosome is an outlier in terms of nucleotide diversity, which suggests selective constraints. Our data further confirm the importance of structural variation in the species, including Iberian pigs, and allowed us to identify new paralogs for known gene families.

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Worldwide genetic relationships of pigs as inferred from X chromosome SNPs

Cited by 9 publications

References 33 publications

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species

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

Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs

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