Sharifi, Ahmad Reza

[["dc.bibliographiccitation.artnumber","687"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Reimer, C."],["dc.contributor.author","Rubin, C.-J."],["dc.contributor.author","Sharifi, A. R"],["dc.contributor.author","Ha, N.-T."],["dc.contributor.author","Weigend, S."],["dc.contributor.author","Waldmann, K.-H."],["dc.contributor.author","Distl, O."],["dc.contributor.author","Pant, S. D"],["dc.contributor.author","Fredholm, M."],["dc.contributor.author","Schlather, M."],["dc.contributor.author","Simianer, H."],["dc.date.accessioned","2019-07-09T11:45:53Z"],["dc.date.available","2019-07-09T11:45:53Z"],["dc.date.issued","2018"],["dc.description.abstract","Abstract Background Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in “SweepFinder”, to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely FST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F2 individuals from a cross of Goettingen Minipigs and large pigs. Results Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F2 cross-breds. Conclusion The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono- or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2018"],["dc.identifier.doi","10.1186/s12864-018-5009-y"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15334"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59327"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/15406 but duplicate"],["dc.publisher","BioMed Central"],["dc.rights","CC BY 4.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.subject.ddc","630"],["dc.title","Analysis of porcine body size variation using re-sequencing data of miniature and large pigs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","22"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","19"],["dc.contributor.author","Malomane, Dorcus Kholofelo"],["dc.contributor.author","Reimer, Christian"],["dc.contributor.author","Weigend, Steffen"],["dc.contributor.author","Weigend, Annett"],["dc.contributor.author","Sharifi, Ahmad Reza"],["dc.contributor.author","Simianer, Henner"],["dc.date.accessioned","2019-07-09T11:45:10Z"],["dc.date.available","2019-07-09T11:45:10Z"],["dc.date.issued","2018"],["dc.description.abstract","BACKGROUND: Single nucleotide polymorphism (SNP) panels have been widely used to study genomic variations within and between populations. Methods of SNP discovery have been a matter of debate for their potential of introducing ascertainment bias, and genetic diversity results obtained from the SNP genotype data can be misleading. We used a total of 42 chicken populations where both individual genotyped array data and pool whole genome resequencing (WGS) data were available. We compared allele frequency distributions and genetic diversity measures (expected heterozygosity (He), fixation index (FST) values, genetic distances and principal components analysis (PCA)) between the two data types. With the array data, we applied different filtering options (SNPs polymorphic in samples of two Gallus gallus wild populations, linkage disequilibrium (LD) based pruning and minor allele frequency (MAF) filtering, and combinations thereof) to assess their potential to mitigate the ascertainment bias. RESULTS: Rare SNPs were underrepresented in the array data. Array data consistently overestimated Hecompared to WGS data, however, with a similar ranking of the breeds, as demonstrated by Spearman's rank correlations ranging between 0.956 and 0.985. LD based pruning resulted in a reduced overestimation of Hecompared to the other filters and slightly improved the relationship with the WGS results. The raw array data and those with polymorphic SNPs in the wild samples underestimated pairwise FSTvalues between breeds which had low FST(<0.15) in the WGS, and overestimated this parameter for high WGS FST(>0.15). LD based pruned data underestimated FSTin a consistent manner. The genetic distance matrix from LD pruned data was more closely related to that of WGS than the other array versions. PCA was rather robust in all array versions, since the population structure on the PCA plot was generally well captured in comparison to the WGS data. CONCLUSIONS: Among the tested filtering strategies, LD based pruning was found to account for the effects of ascertainment bias in the relatively best way, producing results which are most comparable to those obtained from WGS data and therefore is recommended for practical use."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2018"],["dc.identifier.doi","10.1186/s12864-017-4416-9"],["dc.identifier.pmid","29304727"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15124"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59173"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/15049 but duplicate"],["dc.relation.issn","1471-2164"],["dc.rights","CC BY 4.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.subject.ddc","630"],["dc.title","Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies."],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]