Dataset Information

Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2.

ABSTRACT: Domestic species allow us to study dramatic evolutionary changes at an accelerated rate due to the effectiveness of modern breeding techniques and the availability of breeds that have undergone distinct selection pressures. We present a worldwide survey of haplotype variability around a known causative mutation in porcine gene IGF2, which increases lean content. We genotyped 34 SNPs spanning 27 kb in 237 domestic pigs and 162 wild boars. Although the selective process had wiped out variability for at least 27 kb in the haplotypes carrying the mutation, there was no indication of an overall reduction in genetic variability of international vs. European local breeds; there was also no evidence of a reduction in variability caused by domestication. The haplotype structure and a plot of Tajima's D against the frequency of the causative mutation across breeds suggested a temporal pattern, where each breed corresponded to a different selective stage. This was observed comparing the haplotype neighbor-joining (NJ) trees of breeds that have undergone increasing selection pressures for leanness, e.g., European local breeds vs. Pietrain. These results anticipate that comparing current domestic breeds will decisively help to recover the genetic history of domestication and contemporary selective processes.

SUBMITTER: Ojeda A

PROVIDER: S-EPMC2278092 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature

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Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2.

Ojeda A A Huang L-S LS Ren J J Angiolillo A A Cho I-C IC Soto H H Lemús-Flores C C Makuza S M SM Folch J M JM Pérez-Enciso M M

Genetics 20080203 3

Domestic species allow us to study dramatic evolutionary changes at an accelerated rate due to the effectiveness of modern breeding techniques and the availability of breeds that have undergone distinct selection pressures. We present a worldwide survey of haplotype variability around a known causative mutation in porcine gene IGF2, which increases lean content. We genotyped 34 SNPs spanning 27 kb in 237 domestic pigs and 162 wild boars. Although the selective process had wiped out variability f ...[more]

PMID: 18245828

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Project description:BackgroundPorcine IGF2 and the H19 genes are imprinted. The IGF2 is paternally expressed, while the H19 gene is maternally expressed. Extensive studies in mice established a boundary model indicating that the H19 differentially methylated domain (DMD) controls, upon binding with the CTCF protein, reciprocal imprinting of the IGF2 and the H19 genes. IGF2 transcription is tissue and development specific involving the use of 4 promoters. In the liver of adult Large White boars IGF2 is expressed from both parental alleles, whereas in skeletal muscle and kidney tissues we observed variable relaxation of IGF2 imprinting. We hypothesized that IGF2 expression from both paternal alleles and relaxation of IGF2 imprinting is reflected in differences in DNA methylation patterns at the H19 DMD and IGF2 differentially methylated regions 1 and 2 (DMR1 and DMR2).ResultsBisulfite sequencing analysis did not show any differences in DNA methylation at the three porcine CTCF binding sites in the H19 DMD between liver, muscle and kidney tissues of adult pigs. A DNA methylation analysis using methyl-sensitive restriction endonuclease SacII and 'hot-stop' PCR gave consistent results with those from the bisulfite sequencing analysis. We found that porcine H19 DMD is distinctly differentially methylated, at least for the region formally confirmed by two SNPs, in liver, skeletal muscle and kidney of foetal, newborn and adult pigs, independent of the combined imprinting status of all IGF2 expressed transcripts. DNA methylation at CpG sites in DMR1 of foetal liver was significantly lower than in the adult liver due to the presence of hypomethylated molecules. An allele specific analysis was performed for IGF2 DMR2 using a SNP in the IGF2 3'-UTR. The maternal IGF2 DMR2 of foetal and newborn liver revealed a higher DNA methylation content compared to the respective paternal allele.ConclusionsOur results indicate that the IGF2 imprinting status is transcript-specific. Biallelic IGF2 expression in adult porcine liver and relaxation of IGF2 imprinting in porcine muscle were a common feature. These results were consistent with the IGF2 promoter P1 usage in adult liver and IGF2 promoter P2, P3 and P4 usages in muscle. The results showed further that bialellic IGF2 expression in liver and relaxation of imprinting in muscle and kidney were not associated with DNA methylation variation at and around at least one CTCF binding site in H19 DMD. The imprinting status in adult liver, muscle and kidney tissues were also not reflected in the methylation patterns of IGF2 DMRs 1 and 2.

Project description:PurposeTrauma team activation (TTA) is thought to be essential for advanced and specialized care of very severely injured patients. However, non-specific TTA criteria may result in overtriage that consumes valuable resources or endanger patients in need of TTA secondary to undertriage. Consequently, criterion standard definitions to calculate the accuracy of the various TTA protocols are required for research and quality assurance purposes. Recently, several groups suggested a list of conditions when a trauma team is considered to be essential in the initial care in the emergency room. The objective of the survey was to post hoc identify trauma-related conditions that are thought to require a specialized trauma team that may be widely accepted, independent from the country's income level.MethodsA set of questions was developed, centered around the level of agreement with the proposed post hoc criteria to define adequate trauma team activation. The participants gave feedback before they answered the survey to improve the quality of the questions. The finalized survey was conducted using an online tool and a word form. The income per capita of a country was rated according to the World Bank Country and Lending groups.ResultsThe return rate was 76% with a total of 37 countries participating. The agreement with the proposed criteria to define post hoc correct requirements for trauma team activation was more than 75% for 12 of the 20 criteria. The rate of disagreement was low and varied between zero and 13%. The level of agreement was independent from the country's level of income.ConclusionsThe agreement on criteria to post hoc define correct requirements for trauma team activation appears high and it may be concluded that the proposed criteria could be useful for most countries, independent from their level of income. Nevertheless, more discussions on an international level appear to be warranted to achieve a full consensus to define a universal set of criteria that will allow for quality assessment of over- and undertriage of trauma team activation as well as for the validation of field triage criteria for the most severely injured patients worldwide.

Dataset Information

Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2.

Publications

Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2.

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