SNP discovery in swine by reduced representation and high throughput pyrosequencing

Wiedmann, Ralph T.; Smith, Timothy P. L.; Nonneman, Dan

doi:10.1186/1471-2156-9-81

Cited by 88 publications

(90 citation statements)

References 14 publications

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“…Likewise, we found a strong correspondence between the predicted allele frequencies based on the pooled samples and those obtained from Sanger sequencing of a different sample of crickets. This result is similar to those reported in other SNP discovery experiments with comparable coverage (Van Tassell et al 2008;Wiedmann et al 2008).…”

Section: Discussionsupporting

confidence: 82%

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

et al. 2013

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One of the central questions in evolutionary genetics is how much of the genome is involved in the early stages of divergence between populations, causing them to be reproductively isolated. In this article, we investigate genomic differentiation in a pair of closely related field crickets (Gryllus firmus and G. pennsylvanicus). These two species are the result of allopatric divergence and now interact along an extensive hybrid zone in eastern North America. Genes encoding seminal fluid proteins (SFPs) are often divergent between species, and it has been hypothesized that these proteins may play a key role in the origin and maintenance of reproductive isolation between diverging lineages. Hence, we chose to scan the accessory gland transcriptome to enable direct comparisons of differentiation for genes known to encode SFPs with differentiation in a much larger set of genes expressed in the same tissue. We have characterized differences in allele frequency between two populations for .6000 SNPs and .26,000 contigs. About 10% of all SNPs showed nearly fixed differences between the two species. Genes encoding SFPs did not have significantly elevated numbers of fixed SNPs per contig, nor did they seem to show larger differences than expected in their average allele frequencies. The distribution of allele frequency differences across the transcriptome is distinctly bimodal, but the relatively high proportion of fixed SNPs does not necessarily imply "ancient" divergence between these two lineages. Further studies of linkage disequilibrium and introgression across the hybrid zone are needed to direct our attention to those genome regions that are important for reproductive isolation.T HE study of speciation, defined as the origin of intrinsic barriers to gene exchange (Mayr 1942;Harrison 1998;Coyne and Orr 2004), relies on comparisons of phenotypes and genotypes among diverging populations, strains, subspecies, or closely related species. In recently diverged taxa, observed differences in genotypes or phenotypes are likely to be associated with the origin of reproductive barriers and less likely to be differences that have accumulated subsequent to initial divergence. As Templeton (1981) emphasized, our ultimate goal is to understand the genetics of speciation, not simply the genetics of species differences.It is now widely recognized that the amount of divergence between populations or species will vary across the genome due to selective and random lineage sorting from polymorphic ancestral populations and differential introgression when diverging taxa hybridize where their distributions overlap (Harrison 1991;Wu 2001;Turner et al. 2005;Nosil et al. 2009). Barton and Hewitt (1981) explicitly argued that gene exchange between hybridizing taxa will depend on genome region. Differential introgression has been widely discussed and documented in the hybrid zone literature (Harrison 1990;Rieseberg et al. 1999;Payseur 2010), where species boundaries have been described as semipermeable. Chromosome regions that harbo...

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Section: Discussionsupporting

confidence: 82%

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

et al. 2013

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“…Wiedmann et al (2008) reported that the SNP density in pigs was higher than 1:370 bp. Here the SNP frequency of the pDRD2 gene is one per 80 bp, similar to previous results before correction for sample size (Jungerius et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Molecular cloning, expression and variation analyses of the dopamine D2 receptor gene in pig breeds in China

Hp¹,

Xm²,

Mx³

et al. 2011

Genet. Mol. Res.

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ABSTRACT. The dopamine D2 receptor (DRD2) is a crucial mediator for normal physiological processes. We cloned the pig DRD2 gene, investigated its distribution in tissues and identified polymorphisms by RT-PCR, quantitative real-time PCR and direct sequencing. Two Yorkshire pigs from Guangdong Academy of Agricultural Sciences (Guangzhou, China) were selected to clone the gene and investigate its expression; 16 individuals from four pig breeds (Yorkshire, Landrace, small-ear spotted, and Xinchang) were used to scan the variations. comprises five miRNA targeting sites, based on bioinformatics predictions. The pig DRD2 gene expresses predominantly in the pituitary gland, and then in oviducts and the hypothalamus. Both DRD2L and DRD2S mRNA were detected in cerebrum, cerebellum, hypothalamus, pituitary gland, back muscle, oviduct, uterus, and testis tissues; DRD2L was more abundant than DRD2S. The DRD2 gene is located on chromosome 9 and contains seven exons. Sixty-one different sequences were identified in this gene; among seven in the coding region, only one altered the encoded amino acid. These findings will help us understand the functions of the DRD2 gene in pigs.

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“…One of the first drastic changes comes from the ease with which a large number of markers are now produced, either as by-products of completed or ongoing genome sequencing projects or generated using parallel sequencing technologies and reduced representation libraries aimed at producing SNP [Van Tassell et al, 2008;Wiedmann et al, 2008]. These markers are genotyped by using the new genotyping technologies that were developed for SNP.…”

Section: Rh Mapping Todaymentioning

confidence: 99%

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

Faraut

Givry²,

Hitte³

et al. 2009

Cytogenet Genome Res

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Radiation hybrid mapping has emerged in the end of the 1990s as a successful and complementary approach to map genomes, essentially because of its ability to bridge the gaps between genetic and clone-based physical maps, but also using comparative mapping approaches, between ‘gene-rich’ and ‘gene-poor’ maps. Since its early development in human, radiation hybrid mapping played a pivotal role in the process of mapping animal genomes, especially mammalian ones. We review here all the different steps involved in radiation hybrid mapping from the constitution of panels to the construction of maps. A description of its contribution to whole genome maps with a special emphasis on domestic animals will also be presented. Finally, current applications of radiation hybrid mapping in the context of whole genome assemblies will be described.

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SNP discovery in swine by reduced representation and high throughput pyrosequencing

Cited by 88 publications

References 14 publications

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets

Molecular cloning, expression and variation analyses of the dopamine D2 receptor gene in pig breeds in China

Contribution of Radiation Hybrids to Genome Mapping in Domestic Animals

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