Sharifi, Ahmad Reza

[["dc.bibliographiccitation.firstpage","377"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Animal Genetics"],["dc.bibliographiccitation.lastpage","389"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Qanbari, Saber"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Lichtner, Peter"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:40:33Z"],["dc.date.available","2018-11-07T08:40:33Z"],["dc.date.issued","2010"],["dc.description.abstract","P>The data from the newly available 50 K SNP chip was used for tagging the genome-wide footprints of positive selection in Holstein-Friesian cattle. For this purpose, we employed the recently described Extended Haplotype Homozygosity test, which detects selection by measuring the characteristics of haplotypes within a single population. To assess formally the significance of these results, we compared the combination of frequency and the Relative Extended Haplotype Homozygosity value of each core haplotype with equally frequent haplotypes across the genome. A subset of the putative regions showing the highest significance in the genome-wide EHH tests was mapped. We annotated genes to identify possible influence they have in beneficial traits by using the Gene Ontology database. A panel of genes, including FABP3, CLPN3, SPERT, HTR2A5, ABCE1, BMP4 and PTGER2, was detected, which overlapped with the most extreme P-values. This panel comprises some interesting candidate genes and QTL, representing a broad range of economically important traits such as milk yield and composition, as well as reproductive and behavioural traits. We also report high values of linkage disequilibrium and a slower decay of haplotype homozygosity for some candidate regions harbouring major genes related to dairy quality. The results of this study provide a genome-wide map of selection footprints in the Holstein genome, and can be used to better understand the mechanisms of selection in dairy cattle breeding."],["dc.identifier.doi","10.1111/j.1365-2052.2009.02016.x"],["dc.identifier.isi","000279717800005"],["dc.identifier.pmid","20096028"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19260"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0268-9146"],["dc.title","A genome-wide scan for signatures of recent selection in Holstein cattle"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Journal of Animal Breeding and Genetics"],["dc.bibliographiccitation.lastpage","14"],["dc.bibliographiccitation.volume","128"],["dc.contributor.author","Erbe, Malena"],["dc.contributor.author","Ytournel, Florence"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:59:29Z"],["dc.date.available","2018-11-07T08:59:29Z"],["dc.date.issued","2011"],["dc.description.abstract","P>Selection is known to influence the linkage disequilibrium (LD) pattern in livestock populations. Spurious LD may lead to a higher number of false-positive signals in whole genome association mapping experiments. We compared three approaches for whole genome association mapping in a simulation study: single marker regression (SMR), a two-step approach, which analyses residuals corrected for family effects with an SMR (GRAMMAR), and a combined linkage and LD approach, which applies the quantitative transmission disequilibrium test to the Mendelian sampling term (MTDT). Three different scenarios were simulated: idealized random mating, limited number of parents and directional selection. The number of false-positive associations increased when the number of parents was limited. Mapping accuracy was the worst in the scenario with directional selection for all approaches. As SMR produced a high number of false-positive signals in small populations, results of whole genome scans in livestock analysed with SMR should be considered with caution. GRAMMAR was the most accurate approach, but also the least powerful one. The Bonferroni-corrected significance threshold seemed to be too stringent for this approach. Results obtained with MTDT changed only slightly with selected populations. MTDT combined sufficient power with a manageable number of false-positive associations in all scenarios."],["dc.identifier.doi","10.1111/j.1439-0388.2010.00885.x"],["dc.identifier.isi","000285967900002"],["dc.identifier.pmid","21214639"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/23911"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0931-2668"],["dc.title","Power and robustness of three whole genome association mapping approaches in selected populations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","77"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Züchtungskunde"],["dc.bibliographiccitation.lastpage","87"],["dc.bibliographiccitation.volume","82"],["dc.contributor.author","Erbe, Malena"],["dc.contributor.author","Ytournel, Florence"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:48:44Z"],["dc.date.available","2018-11-07T08:48:44Z"],["dc.date.issued","2010"],["dc.description.abstract","Selection is known to influence the linkage disequilibrium (LD) pattern in livestock populations. Spurious LD may lead to a higher number of false positive signals in whole genome association mapping experiments. We compared three approaches for whole genome association mapping in a simulation study: single marker regression (SMR), a two-step approach, which analyzes residuals corrected for family effects with an SMR (GRAMMAR), and a combined linkage and LD approach, which applies the quantitative transmission disequilibrium test to the Mendelian sampling term (MTDT). Three different scenarios were simulated: idealized random mating, limited number of parents and directional selection. The number of false positive associations increased when the number of parents was limited. Since SMR produced a high number of false positive signals in small populations, results of whole genome scans in livestock analyzed with SMR should be considered with caution. GRAMMAR was the most accurate, but also the least powerful approach. The Bonferroni corrected significance threshold seemed to be too stringent for this approach. Results obtained with MTDT changed only slightly with selected populations. MTDT combined sufficient power with a manageable number of false positive associations in all scenarios."],["dc.identifier.isi","000274913300011"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/21293"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Eugen Ulmer Gmbh Co"],["dc.relation.issn","0044-5401"],["dc.title","Comparison of three whole genome association mapping approaches in selected populations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","346"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Animal Genetics"],["dc.bibliographiccitation.lastpage","356"],["dc.bibliographiccitation.volume","41"],["dc.contributor.author","Qanbari, Saber"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Tetens, Jens"],["dc.contributor.author","Thaller, Georg"],["dc.contributor.author","Lichtner, Peter"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T08:40:32Z"],["dc.date.available","2018-11-07T08:40:32Z"],["dc.date.issued","2010"],["dc.description.abstract","P>This study presents a second generation of linkage disequilibrium (LD) map statistics for the whole genome of the Holstein-Friesian population, which has a four times higher resolution compared with that of the maps available so far. We used DNA samples of 810 German Holstein-Friesian cattle genotyped by the Illumina Bovine SNP50K BeadChip to analyse LD structure. A panel of 40 854 (75.6%) markers was included in the final analysis. The pairwise r2 statistic of SNPs up to 5 Mb apart across the genome was estimated. A mean value of r2 = 0.30 +/- 0.32 was observed in pairwise distances of < 25 kb and it dropped to 0.20 +/- 0.24 at 50-75 kb, which is nearly the average inter-marker space in this study. The proportion of SNPs in useful LD (r2 >= 0.25) was 26% for the distance of 50 and 75 kb between SNPs. We found a lower level of LD for SNP pairs at the distance < 100 kb than previously thought. Analysis revealed 712 haplo-blocks spanning 4.7% of the genome and containing 8.0% of all SNPs. Mean and median block length were estimated as 164 +/- 117 kb and 144 kb respectively. Allele frequencies of the SNPs have a considerable and systematic impact on the estimate of r2. It is shown that minimizing the allele frequency difference between SNPs reduces the influence of frequency on r2 estimates. Analysis of past effective population size based on the direct estimates of recombination rates from SNP data showed a decline in effective population size to N(e) = 103 up to similar to 4 generations ago. Systematic effects of marker density and effective population size on observed LD and haplotype structure are discussed."],["dc.identifier.doi","10.1111/j.1365-2052.2009.02011.x"],["dc.identifier.isi","000279717800002"],["dc.identifier.pmid","20055813"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19259"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","0268-9146"],["dc.title","The pattern of linkage disequilibrium in German Holstein cattle"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","381"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Animal Genetics"],["dc.bibliographiccitation.lastpage","391"],["dc.bibliographiccitation.volume","45"],["dc.contributor.author","Gaerke, Christian"],["dc.contributor.author","Ytournel, Florence"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Pimentel, E. C. G."],["dc.contributor.author","Ludwig, A."],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2018-11-07T09:39:54Z"],["dc.date.available","2018-11-07T09:39:54Z"],["dc.date.issued","2014"],["dc.description.abstract","The Gottingen Minipig (GMP) developed at the University of Gottingen is a synthetic breed that is widely used in medical research and toxicology. It combines the high fertility of the Vietnamese potbellied pig, the low body weight of the Minnesota Minipig and the white coat colour of the German Landrace pig. The aim of this study was to find genomic regions that may have undergone selection since the creation of the breed in the 1960s. Therefore, the whole genome was screened for footprints of recent selection based on single nucleotide polymorphism (SNP) genotypes from the Illumina Porcine SNP60 BeadChip using two methods: the extended haplotype homozygosity (EHH) test and the estimation of the genomic proportion of the three original breeds at each SNP using a Bayesian approach. Local deviations from the average genome-wide breed composition were tested with a permutation-based empirical test. Results for a comprehensive whole-genome scan for both methods are presented. Several regions showing the highest P-values in the EHH test are related to breeding goals relevant in the GMP, such as growth (SOCS2, TXN, DDR2 and GRB10 genes) and white colour (PRLR gene). Additionally, the calculated proportion of the founder breeds diverged significantly in many regions from the pedigree-based expectations and the genome average. The results provide a genome-wide map of selection signatures in the GMP, which leads to a better understanding of selection that took place over the last decades in GMP breed development."],["dc.identifier.doi","10.1111/age.12150"],["dc.identifier.isi","000333997700009"],["dc.identifier.pmid","24684393"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/33398"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Wiley-blackwell"],["dc.relation.issn","1365-2052"],["dc.relation.issn","0268-9146"],["dc.title","Footprints of recent selection and variability in breed composition in the Gottingen Minipig genome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]