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1.	Cortés, Andrés J., et al. (författare) Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.) 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13, s. 58- Tidskriftsartikel (refereegranskat)abstract Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. Results: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. Conclusions: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.
2.	Rönnegård, Lars, et al. (författare) Modelling dominance in a flexible intercross analysis 2009 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10 Tidskriftsartikel (refereegranskat)abstract Conclusion: We have extended FIA to include QTL dominance effects. The power of FIA was superior, or similar, to standard regression methods for QTL effects with dominance. The difference in power for FIA with or without dominance is expected to be small as long as the QTL effects are not overdominant. We suggest that FIA with only additive effects should be the standard model to be used, especially since it is more computationally efficient.
3.	Cohen, JC, et al. (författare) The "Goldilocks Effect" in Cystic Fibrosis: identification of a lung phenotype in the cftr knockout and heterozygous mouse 2004 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 5 Tidskriftsartikel (refereegranskat)abstract Background: Cystic Fibrosis is a pleiotropic disease in humans with primary morbidity and mortality associated with a lung disease phenotype. However, knockout in the mouse of cftr, the gene whose mutant alleles are responsible for cystic fibrosis, has previously failed to produce a readily, quantifiable lung phenotype. Results: Using measurements of pulmonary mechanics, a definitive lung phenotype was demonstrated in the cftr-/- mouse. Lungs showed decreased compliance and increased airway resistance in young animals as compared to cftr+/+ littermates. These changes were noted in animals less than 60 days old, prior to any long term inflammatory effects that might occur, and are consistent with structural differences in the cftr-/- lungs. Surprisingly, the cftr+/- animals exhibited a lung phenotype distinct from either the homozygous normal or knockout genotypes. The heterozygous mice showed increased lung compliance and decreased airway resistance when compared to either homozygous phenotype, suggesting a heterozygous advantage that might explain the high frequency of this mutation in certain populations. Conclusions: In the mouse the gene dosage of cftr results in distinct differences in pulmonary mechanics of the adult. Distinct phenotypes were demonstrated in each genotype, cftr-/-, cftr +/-, and cftr+/+. These results are consistent with a developmental role for CFTR in the lung.
4.	Hellberg, Åsa, et al. (författare) Two previously proposed P-1/P-2-differentiating and nine novel polymorphisms at the A4GALT (P-k) locus do not correlate with the presence of the P1 blood group antigen 2005 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 6:49 Tidskriftsartikel (refereegranskat)abstract Background: The molecular genetics of the P blood group system and the absence of P1 antigen in the p phenotype are still enigmatic. One theory proposes that the same gene encodes for both the P1 and P-k glycosyltransferases, but no polymorphisms in the coding region of the P-k gene explain the P-1/P-2 phenotypes. We investigated the potential regulatory regions up- and downstream of the A4GALT (P-k) gene exons. Results: P-1 (n = 18) and P-2 (n = 9) samples from donors of mainly Swedish descent were analysed by direct sequencing of PCR-amplified 5'- and 3'-fragments surrounding the P-k coding region. Seventy-eight P-1 and P-2 samples were investigated with PCR using allele-specific primers (ASP) for two polymorphisms previously proposed as P-2-related genetic markers(- 551_-550insC, -160A>G). Haplotype analysis of single nucleotide polymorphisms was also performed with PCR-ASP. In similar to 1.5 kbp of the 3'-untranslated region one new insertion and four new substitutions compared to a GenBank sequence (AL049757) were found. In addition to the polymorphisms at positions - 550 and - 160, one insertion, two deletions and one substitution were found in similar to 1.0 kbp of the 5'-upstream region. All 20 P-2 samples investigated with PCR-ASP were homozygous for -550insC. However, so were 18 of the 58 P-1 samples investigated. Both the 20 P-2 and the 18 P-1 samples were also homozygous for -160G. Conclusion: The proposed P-2-specific polymorphisms, -551_-550insC and -160G, found in P-2 samples in a Japanese study were found here in homozygous form in both P-1 and P-2 donors. Since P-2 is the null allele in the P blood group system it is difficult to envision how these mutations would cause the P-2 phenotype. None of the novel polymorphisms reported in this study correlated with P-1/P-2 status and the P1/p mystery remains unsolved.
5.	Hosseini Maaf, Bahram, et al. (författare) ABO exon and intron analysis in individuals with the A(weak)B phenotype reveals a novel O-1v-A(2) hybrid allele that causes four missense mutations in the A transferase 2003 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 4 Tidskriftsartikel (refereegranskat)abstract Background: Since the cloning in 1990 of cDNA corresponding to mRNA transcribed at the blood-group ABO locus, polymorphisms due to ethnic and/or phenotypic variations have been reported. Some subgroups have been explained at the molecular level, but unresolved samples are frequently encountered in the reference laboratory. Results: ABO blood grouping discrepancies were investigated serologically and by ABO genotyping [duplex polymerase-chain-reaction (PCR)-restriction-fragment-length-polymorphism (RFLP) and PCR-allele-specific-primer (ASP) across intron 6] and DNA sequencing of the ABO gene and its proposed regulatory elements. Blood samples from five individuals living in Portugal, Switzerland, Sweden and the USA were analysed. These individuals were confirmed to be of Black ethnic origin and had the unusual A(weak)B phenotype but appeared to have the A(2)B genotype without previously reported mutations associated with weak A or B expression. Sequencing of this A allele (having 467C>T and 1061delC associated with the common A(2) [A201] allele) revealed three mutations regularly encountered in the O-1v [O02] allele: 106C>T (Val36Phe), 188G>A (Arg63His), 220C>T (Pro74Ser) in exons 3, 4 and 5, respectively. The additional presence of 46G>A (Ala16Thr) was noted, whilst 189C>T that normally accompanies 188G>A in O-1v was missing, as were all O-1v-related mutations in exons 6 and 7 (261delG, 297A>G, 646T>A, 681G>A, 771C>T and 829G>A). On screening other samples, 46G>A was absent, but two new O alleles were found, a Jordanian O-1 and an African O1v allele having 188G>A but lacking 189C>T. Sequencing of introns 2, 3, 4 and 5 in common alleles (A(1)[A101], A(2), B [B101], O-1, O-1v and O-2 [O03]) revealed 7, 12, 17 and 8 polymorphic positions, respectively, suggesting that alleles could be defined by intronic sequences. These polymorphic sites allowed definition of a breakpoint in intron 5 where the O-1v-related sequence was fused with A(2) to form the new hybrid. Intron 6 has previously been sequenced. Four new mutations were detected in the hybrid allele and these were subsequently also found in intron 6 of A(2) alleles in other Black African samples. Conclusions: A novel O-1v-A(2) hybrid was defined by ABO exon/intron analysis in five unrelated individuals of African descent with the A(weak)B blood group phenotype.
6.	Andersen, Oivind, et al. (författare) Polymorphism, selection and tandem duplication of transferrin genes in Atlantic cod (Gadus morhua) - Conserved synteny between fish monolobal and tetrapod bilobal transferrin loci. 2011 Ingår i: BMC genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 12:1 Tidskriftsartikel (refereegranskat)abstract ABSTRACT: BACKGROUND: The two homologous iron-binding lobes of transferrins are thought to have evolved by gene duplication of an ancestral monolobal form, but any conserved synteny between bilobal and monolobal transferrin loci remains unexplored. The important role played by transferrin in the resistance to invading pathogens makes this polymorphic gene a highly valuable candidate for studying adaptive divergence among local populations. RESULTS: The Atlantic cod genome was shown to harbour two tandem duplicated serum transferrin genes (Tf1, Tf2), a melanotransferrin gene (MTf), and a monolobal transferrin gene (Omp) expressed in the otoliths. Fish, chicken and mammals showed highly conserved syntenic regions in which monolobal and bilobal transferrins reside, but contrasting with tetrapods, the fish transferrin genes are positioned on three different linkage groups. Sequence alignment of cod Tf1 cDNAs from Northeast (NE) and Northwest (NW) Atlantic populations revealed 22 single nucleotide polymorphisms (SNP) causing the replacement of 16 amino acids, including eight surface residues revealed by the modelled 3D-structures, which might influence the binding of pathogens for removal of iron. SNP analysis of a total of 375 individuals from 14 trans-Atlantic populations showed that the Tf1-NE variant was almost fixed in the Baltic cod and predominated in the other NE Atlantic populations, whereas the NW Atlantic populations were more heterozygous and showed high frequencies of the Tf-NW SNP alleles. CONCLUSIONS: The highly conserved synteny between fish and tetrapod transferrin loci infers that the fusion of tandem duplicated Omp-like genes gave rise to the modern transferrins. The multiple nonsynonymous substitutions in cod Tf1 with putative structural effects, together with highly divergent allele frequencies among different cod populations, strongly suggest evidence for positive selection and local adaptation in trans-Atlantic cod populations.
7.	Bains, Ripudaman K., et al. (författare) Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa 2013 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 14, s. 34- Tidskriftsartikel (refereegranskat)abstract Background: Cytochrome P450 3A5 (CYP3A5) is an enzyme involved in the metabolism of many therapeutic drugs. CYP3A5 expression levels vary between individuals and populations, and this contributes to adverse clinical outcomes. Variable expression is largely attributed to four alleles, CYP3A51 (expresser allele); CYP3A53 (rs776746), CYP3A56 (rs10264272) and CYP3A57 (rs41303343) (low/non-expresser alleles). Little is known about CYP3A5 variability in Africa, a region with considerable genetic diversity. Here we used a multi-disciplinary approach to characterize CYP3A5 variation in geographically and ethnically diverse populations from in and around Africa, and infer the evolutionary processes that have shaped patterns of diversity in this gene. We genotyped 2538 individuals from 36 diverse populations in and around Africa for common low/non-expresser CYP3A5 alleles, and re-sequenced the CYP3A5 gene in five Ethiopian ethnic groups. We estimated the ages of low/non-expresser CYP3A5 alleles using a linked microsatellite and assuming a step-wise mutation model of evolution. Finally, we examined a hypothesis that CYP3A5 is important in salt retention adaptation by performing correlations with ecological data relating to aridity for the present day, 10,000 and 50,000 years ago. Results: We estimate that similar to 43% of individuals within our African dataset express CYP3A5, which is lower than previous independent estimates for the region. We found significant intra-African variability in CYP3A5 expression phenotypes. Within Africa the highest frequencies of high-activity alleles were observed in equatorial and Niger-Congo speaking populations. Ethiopian allele frequencies were intermediate between those of other sub-Saharan African and non-African groups. Re-sequencing of CYP3A5 identified few additional variants likely to affect CYP3A5 expression. We estimate the ages of CYP3A53 as similar to 76,400 years and CYP3A56 as similar to 218,400 years. Finally we report that global CYP3A5 expression levels correlated significantly with aridity measures for 10,000 [Spearmann's Rho= -0.465, p=0.004] and 50,000 years ago [Spearmann's Rho= -0.379, p=0.02]. Conclusions: Significant intra-African diversity at the CYP3A5 gene is likely to contribute to multiple pharmacogenetic profiles across the continent. Significant correlations between CYP3A5 expression phenotypes and aridity data are consistent with a hypothesis that the enzyme is important in salt-retention adaptation.
8.	Berlin, Sofia, et al. (författare) A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus) 2008 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 9, s. 89- Tidskriftsartikel (refereegranskat)abstract Background: There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (similar to 10(-3)) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results: We sequenced 18 autosomal protein coding loci from approximately 15-18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (pi(t)) was between 1.30 x 10(-4) and 7.66 x 10(-3) (average pi(t) = 2.72 x 10(-3) +/- 2.06 x 10(-3)) and silent nucleotide diversity varied between 4.20 x 10(-4) and 2.76 x 10(-2) (average pi(S) = 9.22 x 10(-3) +/- 7.43 x 10(-4)). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 x 10(-3) (average pi(a) = 5.08 x 10(-4) +/- 7.43 x 10(3)), which suggest that purifying selection is strong in these genes. F-ST values based on synonymous SNP's varied between -5.60 x 10(-4) and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of F-ST = 0.03 (95% CI: 0.006 -0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r(2) = 0.084 +/- 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (rho) was comparably high (0.028 +/- 0.018), indicating high recombination rates in these genes. Conclusion: We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.
9.	Besnier, Francois, et al. (författare) A genetic algorithm based method for stringent haplotyping of family data 2009 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10 Tidskriftsartikel (refereegranskat)abstract Background: The linkage phase, or haplotype, is an extra level of information that in addition to genotype and pedigree can be useful for reconstructing the inheritance pattern of the alleles in a pedigree, and computing for example Identity By Descent probabilities. If a haplotype is provided, the precision of estimated IBD probabilities increases, as long as the haplotype is estimated without errors. It is therefore important to only use haplotypes that are strongly supported by the available data for IBD estimation, to avoid introducing new errors due to erroneous linkage phases.Results: We propose a genetic algorithm based method for haplotype estimation in family data that includes a stringency parameter. This allows the user to decide the error tolerance level when inferring parental origin of the alleles. This is a novel feature compared to existing methods for haplotype estimation. We show that using a high stringency produces haplotype data with few errors, whereas a low stringency provides haplotype estimates in most situations, but with an increased number of errors.Conclusion: By including a stringency criterion in our haplotyping method, the user is able to maintain the error rate at a suitable level for the particular study; one can select anything from haplotyped data with very small proportion of errors and a higher proportion of non-inferred haplotypes, to data with phase estimates for every marker, when haplotype errors are tolerable. Giving this choice makes the method more flexible and useful in a wide range of applications as it is able to fulfil different requirements regarding the tolerance for haplotype errors, or uncertain marker-phases.
10.	Brunberg, Emma, et al. (författare) A missense mutation in PMEL17 is associated with the Silver coat color in the horse 2006 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 7, s. 46- Tidskriftsartikel (refereegranskat)abstract Background: The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results: Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34 offspring and their 29 non-Silver dams. We typed 41 genetic markers well spread over the horse genome, including one single microsatellite marker (TKY284) close to the candidate gene PMEL17 on horse chromosome 6 (ECA6q23). Significant linkage was found between the Silver phenotype and TKY284 (theta = 0, z = 9.0). DNA sequencing of PMEL17 in Silver and non-Silver horses revealed a missense mutation in exon 11 changing the second amino acid in the cytoplasmic region from arginine to cysteine (Arg618Cys). This mutation showed complete association with the Silver phenotype across multiple horse breeds, and was not found among non-Silver horses with one clear exception; a chestnut colored individual that had several Silver offspring when mated to different non-Silver stallions also carried the exon 11 mutation. In total, 64 Silver horses from six breeds and 85 non-Silver horses from 14 breeds were tested for the exon 11 mutation. One additional mutation located in intron 9, only 759 bases from the missense mutation, also showed complete association with the Silver phenotype. However, as one could expect to find several non-causative mutations completely associated with the Silver mutation, we argue that the missense mutation is more likely to be causative. Conclusion: The present study shows that PMEL17 causes the Silver coat color in the horse and enable genetic testing for this trait.
11.	Bygren, Lars Olov, 1936-, et al. (författare) Change in paternal grandmothers' early food supply influenced cardiovascular mortality of the female grandchildren 2014 Ingår i: BMC Genetics. - : BioMed Central. - 1471-2156. ; 15, s. 12- Tidskriftsartikel (refereegranskat)abstract Background: This study investigated whether large fluctuations in food availability during grandparents' early development influenced grandchildren's cardiovascular mortality. We reported earlier that changes in availability of food - from good to poor or from poor to good - during intrauterine development was followed by a double risk of sudden death as an adult, and that mortality rate can be associated with ancestors' childhood availability of food. We have now studied transgenerational responses (TGR) to sharp differences of harvest between two consecutive years' for ancestors of 317 people in Overkalix, Sweden. Results: The confidence intervals were very wide but we found a striking TGR. There was no response in cardiovascular mortality in the grandchild from sharp changes of early exposure, experienced by three of the four grandparents (maternal grandparents and paternal grandfathers). If, however, the paternal grandmother up to puberty lived through a sharp change in food supply from one year to next, her sons' daughters had an excess risk for cardiovascular mortality (HR 2.69, 95% confidence interval 1.05-6.92). Selection or learning and imitation are unlikely explanations. X-linked epigenetic inheritance via spermatozoa seemed to be plausible, with the transmission, limited to being through the father, possibly explained by the sex differences in meiosis. Conclusion: The shock of change in food availability seems to give specific transgenerational responses.
12.	Ching, Yung-Hao, et al. (författare) High resolution mapping and positional cloning of ENU-induced mutations in the Rw region of mouse chromosome 5 2010 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 11, s. 106- Tidskriftsartikel (refereegranskat)abstract Background: Forward genetic screens in mice provide an unbiased means to identify genes and other functional genetic elements in the genome. Previously, a large scale ENU mutagenesis screen was conducted to query the functional content of a similar to 50 Mb region of the mouse genome on proximal Chr 5. The majority of phenotypic mutants recovered were embryonic lethals. Results: We report the high resolution genetic mapping, complementation analyses, and positional cloning of mutations in the target region. The collection of identified alleles include several with known or presumed functions for which no mutant models have been reported (Tbc1d14, Nol14, Tyms, Cad, Fbxl5, Haus3), and mutations in genes we or others previously reported (Tapt1, Rest, Ugdh, Paxip1, Hmx1, Otoe, Nsun7). We also confirmed the causative nature of a homeotic mutation with a targeted allele, mapped a lethal mutation to a large gene desert, and localized a spermiogenesis mutation to a region in which no annotated genes have coding mutations. The mutation in Tbc1d14 provides the first implication of a critical developmental role for RAB-GAP-mediated protein transport in early embryogenesis. Conclusion: This collection of alleles contributes to the goal of assigning biological functions to all known genes, as well as identifying novel functional elements that would be missed by reverse genetic approaches.
13.	Dedukh, Dmitry, et al. (författare) Cytological maps of lampbrush chromosomes of European water frogs (Pelophylax esculentus complex) from the Eastern Ukraine 2013 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 14, s. 26- Tidskriftsartikel (refereegranskat)abstract Background: Hybridogenesis (hemiclonal inheritance) is a kind of clonal reproduction in which hybrids between parental species are reproduced by crossing with one of the parental species. European water frogs (Pelophylax esculentus complex) represent an appropriate model for studying interspecies hybridization, processes of hemiclonal inheritance and polyploidization. P. esculentus complex consists of two parental species, P. ridibundus (the lake frog) and P. lessonae (the pool frog), and their hybridogenetic hybrid - P. esculentus (the edible frog). Parental and hybrid frogs can reproduce syntopically and form hemiclonal population systems. For studying mechanisms underlying the maintenance of water frog population systems it is required to characterize the karyotypes transmitted in gametes of parental and different hybrid animals of both sexes. Results: In order to obtain an instrument for characterization of oocyte karyotypes in hybrid female frogs, we constructed cytological maps of lampbrush chromosomes from oocytes of both parental species originating in Eastern Ukraine. We further identified certain molecular components of chromosomal marker structures and mapped coilin-rich spheres and granules, chromosome associated nucleoli and special loops accumulating splicing factors. We recorded the dissimilarities between P. ridibundus and P. lessonae lampbrush chromosomes in the length of orthologous chromosomes, number and location of marker structures and interstitial (TTAGGG)(n)-repeat sites as well as activity of nucleolus organizer. Satellite repeat RrS1 was mapped in centromere regions of lampbrush chromosomes of the both species. Additionally, we discovered transcripts of RrS1 repeat in oocytes of P. ridibundus and P. lessonae. Moreover, G-rich transcripts of telomere repeat were revealed in association with terminal regions of P. ridibundus and P. lessonae lampbrush chromosomes. Conclusions: The constructed cytological maps of lampbrush chromosomes of P. ridibundus and P. lessonae provide basis to define the type of genome transmitted within individual oocytes of P. esculentus females with different ploidy and from various population systems.
14.	Galeano, C.H., et al. (författare) Gene-based single nucleotide polymorphism markers for genetic and association mapping in common bean 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 12 Tidskriftsartikel (refereegranskat)abstract Background: In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results: In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 x G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 x JALO EEP558 and DOR364 x BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions: In short, this study illustrates the power of intron-based markers for linkage and association mapping in common bean. The utility of these markers is discussed in relation with the usefulness of microsatellites, the molecular markers by excellence in this crop.
15.	Guo, Jiazhong, et al. (författare) A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed. 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13 Tidskriftsartikel (refereegranskat)abstract BACKGROUND: The genome-wide association study (GWAS) is a useful approach to identify genes affecting economically important traits in dairy cattle. Here, we report the results from a GWAS based on high-density SNP genotype data and estimated breeding values for nine production, fertility, body conformation, udder health and workability traits in the Brown Swiss cattle population that is part of the international genomic evaluation program.RESULT: GWASs were performed using 50 k SNP chip data and deregressed estimated breeding values (DEBVs) for nine traits from between 2061 and 5043 bulls that were part of the international genomic evaluation program coordinated by Interbull Center. The nine traits were milk yield (MY), fat yield (FY), protein yield (PY), lactating cow's ability to recycle after calving (CRC), angularity (ANG), body depth (BDE), stature (STA), milk somatic cell score (SCS) and milk speed (MSP). Analyses were performed using a linear mixed model correcting for population confounding. A total of 74 SNPs were detected to be genome-wide significantly associated with one or several of the nine analyzed traits. The strongest signal was identified on chromosome 25 for milk production traits, stature and body depth. Other signals were on chromosome 11 for angularity, chromosome 24 for somatic cell score, and chromosome 6 for milking speed. Some signals overlapped with earlier reported QTL for similar traits in other cattle populations and were located close to interesting candidate genes worthy of further investigations.CONCLUSIONS: Our study shows that international genetic evaluation data is a useful resource for identifying genetic factors influencing complex traits in livestock. Several genome wide significant association signals could be identified in the Brown Swiss population, including a major signal on BTA25. Our findings report several associations and plausible candidate genes that deserve further exploration in other populations and molecular dissection to explore the potential economic impact and the genetic mechanisms underlying these production traits in cattle.
16.	Hallander, Jon, et al. (författare) Optimization of selection contribution and mate allocations in monoecious tree breeding populations 2009 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10 Tidskriftsartikel (refereegranskat)abstract Conclusion: The main reason why MCM schemes yielded higher genetic gains was the improvement in managing the long term genetic contribution of founders in the population; this was achieved by connecting unrelated families. In addition, the accumulation of inbreeding was reduced by MCM schemes since the variance in long term genetic contributions of founders was smaller than in the other schemes. Consequently, by combining an MCM scheme with an algorithm that optimizes contributions of the selected individuals, a higher long term response is obtained while reducing the risk within the breeding program.
17.	Hannelius, U, et al. (författare) Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs 2008 Ingår i: BMC genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 9, s. 54- Tidskriftsartikel (refereegranskat)
18.	Hidalgo, André (författare) On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis 2014 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 15 Tidskriftsartikel (refereegranskat)abstract Background: Androstenone is one of the major compounds responsible for boar taint, a pronounced urine-like odor produced when cooking boar meat. Several studies have identified quantitative trait loci (QTL) for androstenone level on Sus scrofa chromosome (SSC) 6. For one of the candidate genes in the region SULT2A1, a difference in expression levels in the testis has been shown at the protein and RNA level.Results: Haplotypes were predicted for the QTL region and their effects were estimated showing that haplotype 1 was consistently related with a lower level, and haplotype 2 with a higher level of androstenone. A recombinant haplotype allowed us to narrow down the QTL region from 3.75 Mbp to 1.94 Mbp. An RNA-seq analysis of the liver and testis revealed six genes that were differentially expressed between homozygotes of haplotypes 1 and 2. Genomic sequences of these differentially expressed genes were checked for variations within potential regulatory regions. We identified one variant located within a CpG island that could affect expression of SULT2A1 gene. An allele-specific expression analysis in the testis did not show differential expression between the alleles of SULT2A1 located on the different haplotypes in heterozygous animals. However a synonymous mutation C166T (SSC6: 49,117,861 bp in Sscrofa 10.2; C/T) was identified within the exon 2 of SULT2A1 for which the haplotype 2 only had the C allele which was higher expressed than the T allele, indicating haplotype-independent allelic-imbalanced expression between the two alleles. A phylogenetic analysis for the 1.94 Mbp region revealed that haplotype 1, associated with low androstenone level, originated from Asia.Conclusions: Differential expression could be observed for six genes by RNA-seq analysis. No difference in the ratio of C:T expression of SULT2A1 for the haplotypes was found by the allele-specific expression analysis, however, a difference in expression between the C over T allele was found for a variation within SULT2A1, showing that the difference in androstenone levels between the haplotypes is not caused by the SNP in exon 2.
19.	Höglund, Johanna Karolina (författare) Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle 2014 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 15 Tidskriftsartikel (refereegranskat)abstract Background: The results obtained from genome-wide association studies (GWAS) often show pronounced disagreements. Validation of association studies is therefore desired before marker information is incorporated in selection decisions. A reliable way to confirm a discovered association between genetic markers and phenotypes is to validate the results in different populations. Therefore, the objective of this study was to validate single nucleotide polymorphism (SNP) marker associations to female fertility traits identified in the Nordic Holstein (NH) cattle population in the Nordic Red (NR) and Jersey (JER) cattle breeds. In the present study, we used data from 3,475 NH sires which were genotyped with the BovineSNP50 Beadchip to discover associations between SNP markers and eight female fertility-related traits. The significant SNP markers were then tested in NR and JER cattle.Results: A total of 4,474 significant associations between SNP markers and eight female fertility traits were detected in NH cattle. These significant associations were then validated in the NR (4,998 sires) and JER (1,225 sires) dairy cattle populations. We were able to validate 836 of the SNPs discovered in NH cattle in the NR population, as well as 686 SNPs in the JER population. 152 SNPs could be confirmed in both the NR and JER populations.Conclusions: The present study presents strong evidence for association of SNPs with fertility traits across three cattle breeds. We provide strong evidence that SNPs for many fertility traits are concentrated at certain areas on the genome (BTA1, BTA4, BTA7, BTA9, BTA11 and BTA13), and these areas would be highly suitable for further study in order to identify candidate genes for female fertility traits in dairy cattle.
20.	Markljung, Ellen, et al. (författare) Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace II : meat quality traits 2008 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 9, s. 22- Tidskriftsartikel (refereegranskat)abstract BACKGROUND: Meat quality traits are important in pig breeding programs, but they are difficult to include in a traditional selection program. Marker assisted selection (MAS) of meat quality traits is therefore of interest in breeding programs and a Quantitative Trait Locus (QTL) analysis is the key to identifying markers that can be used in MAS. In this study, Landrace and Hampshire intercross and backcross families were used to investigate meat quality traits. Hampshire pigs are commonly used as the sire line in commercial pig breeding. This is the first time a pedigree including Hampshire pigs has been used for a QTL analysis of meat quality traits. RESULTS: In total, we analyzed 39 meat quality traits and identified eight genome-wide significant QTL peaks in four regions: one on chromosome 3, two on chromosome 6 and one on chromosome 16. At least two of the QTLs do not appear to have been detected in previous studies. On chromosome 6 we identified QTLs for water content in M. longissimus dorsi (LD), drip loss in LD and post mortem pH decline in LD. On chromosomes 3 and 16 we identified previously undetected QTLs for protein content in LD and for freezing and cooking loss respectively. CONCLUSION: We identified at least two new meat quality trait QTLs at the genome-wide significance level. We detected two QTLs on chromosome 6 that possibly coincide with QTLs detected in other studies. We were also able to exclude the C1843T mutation in the ryanodine receptor (RYR1) as a causative mutation for one of the chromosome 6 QTLs in this cross.
21.	Meyer-Lucht, Yvonne, et al. (författare) Selection, diversity and evolutionary patterns of the MHC class II DAB in free-ranging Neotropical marsupials 2008 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 9, s. 39- Tidskriftsartikel (refereegranskat)abstract Background: Research on the genetic architecture and diversity of the MHC has focused mainly on eutherian mammals, birds and fish. So far, studies on model marsupials used in laboratory investigations indicated very little or even no variation in MHC class II genes. However, natural levels of diversity and selection are unknown in marsupials as studies on wild populations are virtually absent. We used two endemic South American mouse opossums, Gracilinanus microtarsus and Marmosops incanus, to investigate characteristic features of MHC selection. This study is the first investigation of MHC selection in free-ranging Neotropical marsupials. In addition, the evolutionary history of MHC lineages within the group of marsupials was examined.Results: G. microtarsus showed extensive levels of MHC diversity within and among individuals as 47 MHC-DAB alleles and high levels of sequence divergence were detected at a minimum of four loci. Positively selected codon sites were identified, of which most were congruent with human antigen binding sites. The diversity in M. incanus was rather low with only eight observed alleles at presumably two loci. However, these alleles also revealed high sequence divergence. Again, positive selection was identified on specific codon sites, all congruent with human ABS and with positively selected sites observed in G. microtarsus. In a phylogenetic comparison alleles of M. incanus interspersed widely within alleles of G. microtarsus with four alleles being present in both species.Conclusion: Our investigations revealed extensive MHC class II polymorphism in a natural marsupial population, contrary to previous assumptions. Furthermore, our study confirms for the first time in marsupials the presence of three characteristic features common at MHC loci of eutherian mammals, birds and fish: large allelic sequence divergence, positive selection on specific sites and trans-specific polymorphism.
22.	Nassir, Rami, et al. (författare) An ancestry informative marker set for determining continental origin : validation and extension using human genome diversity panels 2009 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10, s. 39- Tidskriftsartikel (refereegranskat)abstract Background: Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia. Results: In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups. Conclusion: These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.
23.	Natanaelsson, Christian, et al. (författare) Dog Y chromosomal DNA sequence : identification, sequencing and SNP discovery 2006 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 7 Tidskriftsartikel (refereegranskat)abstract Background: Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results: The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion: We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and giving a first description of the dog Y-chromosome phylogeny.
24.	Nettelblad, Carl (författare) Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13, s. 85:1-13 Tidskriftsartikel (refereegranskat)
25.	Oliveira, Hugo R., et al. (författare) Wheat in the Mediterranean revisited - tetraploid wheat landraces assessed with elite bread wheat Single Nucleotide Polymorphism markers 2014 Ingår i: BMC Genetics. - : BioMed Central. - 1471-2156. ; 15:54 Tidskriftsartikel (refereegranskat)abstract Background: Single Nucleotide Polymorphism (SNP) panels recently developed for the assessment of genetic diversity in wheat are primarily based on elite varieties, mostly those of bread wheat. The usefulness of such SNP panels for studying wheat evolution and domestication has not yet been fully explored and ascertainment bias issues can potentially affect their applicability when studying landraces and tetraploid ancestors of bread wheat. We here evaluate whether population structure and evolutionary history can be assessed in tetraploid landrace wheats using SNP markers previously developed for the analysis of elite cultivars of hexaploid wheat. Results: We genotyped more than 100 tetraploid wheat landraces and wild emmer wheat accessions, some of which had previously been screened with SSR markers, for an existing SNP panel and obtained publically available genotypes for the same SNPs for hexaploid wheat varieties and landraces. Results showed that quantification of genetic diversity can be affected by ascertainment bias but that the effects of ascertainment bias can at least partly be alleviated by merging SNPs to haplotypes. Analyses of population structure and genetic differentiation show strong subdivision between the tetraploid wheat subspecies, except for durum and rivet that are not separable. A more detailed population structure of durum landraces could be obtained than with SSR markers. The results also suggest an emmer, rather than durum, ancestry of bread wheat and with gene flow from wild emmer. Conclusions: SNP markers developed for elite cultivars show great potential for inferring population structure and can address evolutionary questions in landrace wheat. Issues of marker genome specificity and mapping need, however, to be addressed. Ascertainment bias does not seem to interfere with the ability of a SNP marker system developed for elite bread wheat accessions to detect population structure in other types of wheat.
26.	Olsen, Morten Tange, 1978-, et al. (författare) Empirical evaluation of humpback whale telomere length estimates; quality control and factors causing variability in the singleplex and multiplex qpcr methods 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13, s. 77- Tidskriftsartikel (refereegranskat)abstract Background: Telomeres, the protective cap of chromosomes, have emerged as powerful markers of biological age and life history in model and non-model species. The qPCR method for telomere length estimation is one of the most common methods for telomere length estimation, but has received recent critique for being too error-prone and yielding unreliable results. This critique coincides with an increasing awareness of the potentials and limitations of the qPCR technique in general and the proposal of a general set of guidelines (MIQE) for standardization of experimental, analytical, and reporting steps of qPCR. In order to evaluate the utility of the qPCR method for telomere length estimation in non-model species, we carried out four different qPCR assays directed at humpback whale telomeres, and subsequently performed a rigorous quality control to evaluate the performance of each assay. Results: Performance differed substantially among assays and only one assay was found useful for telomere length estimation in humpback whales. The most notable factors causing these inter-assay differences were primer design and choice of using singleplex or multiplex assays. Inferred amplification efficiencies differed by up to 40% depending on assay and quantification method, however this variation only affected telomere length estimates in the worst performing assays. Conclusion: Our results suggest that seemingly well performing qPCR assays may contain biases that will only be detected by extensive quality control. Moreover, we show that the qPCR method for telomere length estimation can be highly precise and accurate, and thus suitable for telomere measurement in non-model species, if effort is devoted to optimization at all experimental and analytical steps. We conclude by highlighting a set of quality controls which may serve for further standardization of the qPCR method for telomere length estimation, and discuss some of the factors that may cause variation in qPCR experiments.
27.	Putnik, M, et al. (författare) Effects of two common polymorphisms in the 3' untranslated regions of estrogen receptor beta on mRNA stability and translatability 2009 Ingår i: BMC genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 10, s. 55- Tidskriftsartikel (refereegranskat)
28.	Rönnegård, Lars, et al. (författare) Recent developments in statistical methods for detecting genetic loci affecting phenotypic variability 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13 Tidskriftsartikel (refereegranskat)abstract A number of recent works have introduced statistical methods for detecting genetic loci that affect phenotypic variability, which we refer to as variability-controlling quantitative trait loci (vQTL). These are genetic variants whose allelic state predicts how much phenotype values will vary about their expected means. Such loci are of great potential interest in both human and non-human genetic studies, one reason being that a detected vQTL could represent a previously undetected interaction with other genes or environmental factors. The simultaneous publication of these new methods in different journals has in many cases precluded opportunity for comparison. We survey some of these methods, the respective trade-offs they imply, and the connections between them. The methods fall into three main groups: classical non-parametric, fully parametric, and semi-parametric two-stage approximations. Choosing between alternatives involves balancing the need for robustness, flexibility, and speed. For each method, we identify important assumptions and limitations, including those of practical importance, such as their scope for including covariates and random effects. We show in simulations that both parametric methods and their semi-parametric approximations can give elevated false positive rates when they ignore mean-variance relationships intrinsic to the data generation process. We conclude that choice of method depends on the trait distribution, the need to include non-genetic covariates, and the population size and structure, coupled with a critical evaluation of how these fit with the assumptions of the statistical model.
29.	Rönnegård, Lars, et al. (författare) Separation of base allele and sampling term effects gives new insights in variance component QTL analysis 2007 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 8, s. 1- Tidskriftsartikel (refereegranskat)abstract BackgroundVariance component (VC) models are commonly used for Quantitative Trait Loci (QTL) mapping in outbred populations. Here, the QTL effect is given as a random effect and a critical part of the model is the relationship between the phenotypic values and the random effect. In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix).ResultsWe present an alternative notation of the variance component model, where the elements of the random effect are independent base generation allele effects and sampling term effects. The relationship between the phenotypic vales and the random effect is given by an incidence matrix, which results in a novel, but statistically equivalent, version of the traditional VC model. A general algorithm to estimate this incidence matrix is presented. Since the model is given in terms of base generation allele effects and sampling term effects, these effects can be estimated separately using best linear unbiased prediction (BLUP). From simulated data, we showed that biallelic QTL effects could be accurately clustered using the BLUP obtained from our model notation when markers are fully informative, and that the accuracy increased with the size of the QTL effect. We also developed a measure indicating whether a base generation marker homozygote is a QTL heterozygote or not, by comparing the variances of the sampling term BLUP and the base generation allele BLUP. A ratio greater than one gives strong support for a QTL heterozygote.ConclusionWe developed a simple presentation of the VC QTL model for identification of base generation allele effects in QTL linkage analysis. The base generation allele effects and sampling term effects were separated in our model notation. This clarifies the assumptions of the model and should also enhance the development of genome scan methods.
30.	Schwartz, Yuri B, et al. (författare) Molecular characterization of the singed wings locus of Drosophila melanogaster 2004 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 5, s. 15- Tidskriftsartikel (refereegranskat)abstract It is not entirely clear from the present molecular analysis how the SWI protein may function in the ecdysone induced cascade. Currently all predictions agree in that SWI is very unlikely to be a nuclear protein. Thus it probably exercises its control of "late" ecdysone genes indirectly. Apparently the genetic regulation of ecdysone signaling is much more complex then was previously anticipated.
31.	Sjöstrand, Agnès E., et al. (författare) Private haplotypes can reveal local adaptation 2014 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 15, s. 61- Tidskriftsartikel (refereegranskat)abstract Background: Genome-wide scans for regions that demonstrate deviating patterns of genetic variation have become common approaches for finding genes targeted by selection. Several genomic patterns have been utilized for this purpose, including deviations in haplotype homozygosity, frequency spectra and genetic differentiation between populations. Results: We describe a novel approach based on the Maximum Frequency of Private Haplotypes - MFPH - to search for signals of recent population-specific selection. The MFPH statistic is straightforward to compute for phased SNP-and sequence-data. Using both simulated and empirical data, we show that MFPH can be a powerful statistic to detect recent population-specific selection, that it performs at the same level as other commonly used summary statistics (e.g. F-ST, iHS and XP-EHH), and that MFPH in some cases capture signals of selection that are missed by other statistics. For instance, in the Maasai, MFPH reveals a strong signal of selection in a region where other investigated statistics fail to pick up a clear signal that contains the genes DOCK3, MAPKAPK3 and CISH. This region has been suggested to affect height in many populations based on phenotype-genotype association studies. It has specifically been suggested to be targeted by selection in Pygmy groups, which are on the opposite end of the human height spectrum compared to the Maasai. Conclusions: From the analysis of both simulated and publicly available empirical data, we show that MFPH represents a summary statistic that can provide further insight concerning population-specific adaptation.
32.	Strand, Tanja, et al. (författare) Evolutionary history of black grouse major histocompatibility complex class IIB genes revealed through single locus sequence-based genotyping 2013 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 14, s. 29- Tidskriftsartikel (refereegranskat)abstract Background: Gene duplications are frequently observed in the Major Histocompatibility Complex (MHC) of many species, and as a consequence loci belonging to the same MHC class are often too similar to tell apart. In birds, single locus genotyping of MHC genes has proven difficult due to concerted evolution homogenizing sequences at different loci. But studies on evolutionary history, mode of selection and heterozygosity correlations on the MHC cannot be performed before it is possible to analyse duplicated genes separately. In this study we investigate the architecture and evolution of the MHC class IIB genes in black grouse. We developed a sequence-based genotyping method for separate amplification of the two black grouse MHC class IIB genes BLB1 and BLB2. Based on this approach we are able to study differences in structure and selection between the two genes in black grouse and relate these results to the chicken MHC structure and organization. Results: Sequences were obtained from 12 individuals and separated into alleles using the software PHASE. We compared nucleotide diversity measures and employed selection tests for BLB1 and BLB2 to explore their modes of selection. Both BLB1 and BLB2 are transcribed and display classic characteristics of balancing selection as predicted for expressed MHC class IIB genes. We found evidence for both intra- and interlocus recombination or gene conversion, as well as indication for positive but differential selection at both loci. Moreover, the two loci appear to be linked. Phylogenetic analyses revealed orthology of the black grouse MHC class IIB genes to the respective BLB loci in chicken. Conclusions: The results indicate that the duplication of the BLB gene occurred before the species divergence into black grouse, chicken and pheasant. Further, we conclude that BLB1 and BLB2 in black grouse are subjected to homogenizing concerted evolution due to interlocus genetic exchange after species divergence. The loci are in linkage disequilibrium, which is in line with the theory of tightly coevolving genes within the MHC under the minimal essential MHC hypothesis. Our results support the conclusion that MHC form and function in birds derived from studies on the domesticated chicken are not artefacts of the domestication process.
33.	Väli, Ulo, et al. (författare) Insertion-deletion polymorphisms (indels) as genetic markers in natural populations 2008 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 9, s. 8- Tidskriftsartikel (refereegranskat)abstract BACKGROUND: We introduce the use of short insertion-deletion polymorphisms (indels) for genetic analysis of natural populations. RESULTS: Sequence reads from light shot-gun sequencing efforts of different dog breeds were aligned to the dog genome reference sequence and gaps corresponding to indels were identified. One hundred candidate markers (4-bp indels) were selected and genotyped in unrelated dogs (n=7) and wolves (n=18). Eighty-one and 76 out of 94 could be validated as polymorphic loci in the respective sample. Mean indel heterozygosity in a diverse set of wolves was 19%, and 74% of the loci had a minor allele frequency of >10%. Indels found to be polymorphic in wolves were subsequently genotyped in a highly bottlenecked Scandinavian wolf population. Fifty-one loci turned out to be polymorphic, showing their utility even in a population with low genetic diversity. In this population, individual heterozygosity measured at indel and microsatellite loci, respectively were highly correlated. CONCLUSIONS: With an increasing amount of sequence information gathered from non-model organisms, we suggest that indels will come to form an important source of genetic markers, easy and cheap to genotype, for studies of natural populations.
34.	Li, Sen, et al. (författare) Estimating demographic parameters from large-scale population genomic data using Approximate Bayesian Computation 2012 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 13, s. 22- Tidskriftsartikel (refereegranskat)abstract BACKGROUND: The Approximate Bayesian Computation (ABC) approach has been used to infer demographic parameters for numerous species, including humans. However, most applications of ABC still use limited amounts of data, from a small number of loci, compared to the large amount of genome-wide population-genetic data which have become available in the last few years.RESULTS: We evaluated the performance of the ABC approach for three 'population divergence' models - similar to the 'isolation with migration' model - when the data consists of several hundred thousand SNPs typed for multiple individuals by simulating data from known demographic models. The ABC approach was used to infer demographic parameters of interest and we compared the inferred values to the true parameter values that was used to generate hypothetical "observed" data. For all three case models, the ABC approach inferred most demographic parameters quite well with narrow credible intervals, for example, population divergence times and past population sizes, but some parameters were more difficult to infer, such as population sizes at present and migration rates. We compared the ability of different summary statistics to infer demographic parameters, including haplotype and LD based statistics, and found that the accuracy of the parameter estimates can be improved by combining summary statistics that capture different parts of information in the data. Furthermore, our results suggest that poor choices of prior distributions can in some circumstances be detected using ABC. Finally, increasing the amount of data beyond some hundred loci will substantially improve the accuracy of many parameter estimates using ABC.CONCLUSIONS: We conclude that the ABC approach can accommodate realistic genome-wide population genetic data, which may be difficult to analyze with full likelihood approaches, and that the ABC can provide accurate and precise inference of demographic parameters from these data, suggesting that the ABC approach will be a useful tool for analyzing large genome-wide datasets.
35.	Humphreys, K, et al. (författare) Fine-scale mapping in case-control samples using locus scoring and haplotype-sharing methods 2005 Ingår i: BMC genetics. - 1471-2156. ; 66 Suppl 1, s. S74- Tidskriftsartikel (refereegranskat)
36.	Jonasdottir, G, et al. (författare) Analysis of binary traits: testing association in the presence of linkage 2005 Ingår i: BMC genetics. - 1471-2156. ; 66 Suppl 1, s. S92- Tidskriftsartikel (refereegranskat)
37.	Andonov, Sreten (författare) Modeling honey yield, defensive and swarming behaviors of Italian honey bees (Apis mellifera ligustica) using linear-threshold approaches 2019 Ingår i: BMC genomic data. - : Springer Science and Business Media LLC. - 2730-6844 .- 1471-2156. ; 20 Tidskriftsartikel (refereegranskat)abstract Background: Genetic improvement of honey bees is more difficult compared to other livestock, due to the very different reproductive behavior. Estimation of breeding values requires specific adjustment and the use of sires in the pedigree is only possible when mating of queens and drones is strictly controlled. In the breeding program of the National Registry for Italian Queen Breeders and Bee Producers the paternal contribution is mostly unknown. As stronger modeling may compensate for the lack of pedigree information, we tested two models that differed in the way the direct and maternal effects were considered. The two models were tested using 4003 records for honey yield, defensive and swarming behaviors of Italian honey bee queens produced between 2002 and 2014. The first model accounted for the direct genetic effect of worker bees and the genetic maternal effect of the queen, whereas model 2 considered the direct genetic effect of the queen without maternal effect. The analyses were performed by linear (honey production) and threshold (defensive and swarming behavior) single-trait models; estimated genetic correlations among traits were obtained by a three-trait linear-threshold model. Results: For all traits, the highest predictability (correlation between breeding values estimated with and without performance records) was obtained with model 2, where direct genetic effect of queens was considered. With this model, heritability estimates were 0.26 for honey yield, 0.36 for defensive behavior, and 0.34 for swarming behavior. Multi-trait estimation resulted in similar or higher heritability estimates for all traits. A low, positive genetic correlation (0.19) was found between honey yield and defensive behavior, whereas the genetic correlation between honey yield and swarming behavior was moderate (0.41). A strong, positive genetic correlation was found between defensive and swarming behaviors (0.62). Predictability for multi-trait evaluations was higher for honey yield (0.46) and defensive behavior (0.30) but almost identical for swarming behavior (0.45) compared to corresponding single-trait predictability. Conclusions: Multi-trait evaluation using a model that accounts for the direct genetic effect of queen was the best approach for breeding value estimation of Italian honey bees. The results suggest a new direction for selection of linear and categorical traits in breeding programs where drone origin is unknown.
38.	Berg, Frida, et al. (författare) Refined localization of the FAT1 quantitative trait locus on pig chromosome 4 by marker-assisted backcrossing. 2006 Ingår i: BMC Genetics. - 1471-2156. ; 7, s. 17- Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
39.	Botwe, AK, et al. (författare) Dynamics in multiplicity of Plasmodium falciparum infection among children with asymptomatic malaria in central Ghana 2017 Ingår i: BMC genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 18:1, s. 67- Tidskriftsartikel (refereegranskat)
40.	Bryngelsson, Tomas, et al. (författare) Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers 2017 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 18 Tidskriftsartikel (refereegranskat)abstract Background: Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia.Results: We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools.Conclusion: The 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation.
41.	Cortazar-Chinarro, Maria, et al. (författare) Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans 2020 Ingår i: BMC Genetics. - : BMC. - 1471-2156. ; 21:1 Tidskriftsartikel (refereegranskat)abstract Background While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain ( 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns. Results We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values. Conclusion Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
42.	Da Silva, Vinicius, et al. (författare) Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity 2018 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 19 Tidskriftsartikel (refereegranskat)abstract Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide.Results: Genotypes were obtained using the Axiom (R) Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH.Conclusions: CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture.
43.	Dida, Mulatu Geleta (författare) Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system 2018 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 19 Tidskriftsartikel (refereegranskat)abstract Background: Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia.Results: Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop.Conclusions: These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.
44.	Hagenblad, Jenny, et al. (författare) Low genetic diversity despite multipleintroductions of the invasive plant species Impatiens glandulifera in Europe 2015 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 16:103 Tidskriftsartikel (refereegranskat)abstract Background: Invasive species can be a major threat to native biodiversity and the number of invasive plant speciesis increasing across the globe. Population genetic studies of invasive species can provide key insights into theirinvasion history and ensuing evolution, but also for their control. Here we genetically characterise populations ofImpatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. Wecompared populations from the species’ native range in Kashmir, India, to those in its invaded range, along alatitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasivespecies were collated.Results: Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an areaoutside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations ofI. glandulifera is unusually low compared to native populations, in particular when compared to other invasivespecies. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. Wefind evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in thenative range. I. glandulifera populations with significant inbreeding were only found in the species’ native rangeand invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe wedetect cases of migration between distantly located populations. Human activities therefore seem to, at leastpartially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe.Conclusions: Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges,widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypicplasticity may therefore be an important component of the successful spread of Impatiens glandulifera across Europe.
45.	Hammenhag, Cecilia, et al. (författare) Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop 2018 Ingår i: BMC Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 19 Tidskriftsartikel (refereegranskat)abstract Background: The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits.Results: Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine nonsynonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum.Conclusions: There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.
46.	Helsen, Kenny, et al. (författare) No genetic erosion after five generations for Impatiens glandulifera populationsacross the invaded range in Europe 2019 Ingår i: BMC Genetics. - : BioMed Central. - 1471-2156. ; 20 Tidskriftsartikel (refereegranskat)abstract Background: The observation that many alien species become invasive despite low genetic diversity has long been considered the ‘genetic paradox’ in invasion biology. This paradox is often resolved through the temporal buildup genetic diversity through multiple introduction events. These temporal dynamics in genetic diversity are especially important for annual invasive plants that lack a persistent seed bank, for which population persistence is strongly dependent on consecutive seed ‘re-establishment’ in each growing season. Theory predicts that the number of seeds during re-establishment, and the levels of among-population gene flow can strongly affect recolonization dynamics, resulting in either an erosion or build-up of population genetic diversity through time. This study focuses on temporal changes in the population genetic structure of the annual invasive plant Impatiens glandulifera across Europe. We resampled 13 populations in 6 regions along a 1600 km long latitudinal gradient from northern France to central Norway after 5 years, and assessed population genetic diversity with 9 microsatellite markers.Results: Our study suggests sufficiently high numbers of genetically diverse founders during population re- establishment, which prevent the erosion of local genetic diversity. We furthermore observe that I. glanduliferaexperiences significant among-population gene flow, gradually resulting in higher genetic diversity and lower overall genetic differentiation through time. Nonetheless, moderate founder effects concerning population genetic composition (allele frequencies) were evident, especially for smaller populations.Despite the initially low genetic diversity, this species seems to be successful at persisting across its invaded range, and will likely continue to build up higher genetic diversity at the local scale.
47.	Jansson, E., et al. (författare) Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations 2020 Ingår i: Bmc Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 21:1 Tidskriftsartikel (refereegranskat)abstract Background: Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results: After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of similar to 600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. GlobalF(ST)among these populations was 0.015-0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and similar to 1% within Scandinavia. SNPs showing large divergence (F-ST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species' Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (meanF(ST_173_loci) = 0.065, F-ST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (>= 94%) to their populations of origin. Conclusions: Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
48.	Kariminejad, A., et al. (författare) Truncating CHRNG mutations associated with interfamilial variability of the severity of the Escobar variant of multiple pterygium syndrome 2016 Ingår i: Bmc Genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 17 Tidskriftsartikel (refereegranskat)abstract Background: In humans, muscle-specific nicotinergic acetylcholine receptor (AChR) is a transmembrane protein with five different subunits, coded by CHRNA1, CHRNB, CHRND and CHRNG/CHRNE. The gamma subunit of AChR encoded by CHRNG is expressed during early foetal development, whereas in the adult, the. subunit is replaced by a epsilon subunit. Mutations in the CHRNG encoding the embryonal acetylcholine receptor may cause the non-lethal Escobar variant (EVMPS) and lethal form (LMPS) of multiple pterygium syndrome. The MPS is a condition characterised by prenatal growth failure with pterygium and akinesia leading to muscle weakness and severe congenital contractures, as well as scoliosis. Results: Our whole exome sequencing studies have identified one novel and two previously reported homozygous mutations in CHRNG in three families affected by non-lethal EVMPS. The mutations consist of deletion of two nucleotides, cause a frameshift predicted to result in premature termination of the foetally expressed gamma subunit of the AChR. Conclusions: Our data suggest that severity of the phenotype varies significantly both within and between families with MPS and that there is no apparent correlation between mutation position and clinical phenotype. Although individuals with CHRNG mutations can survive, there is an increased frequency of abortions and stillbirth in their families. Furthermore, genetic background and environmental modifiers might be of significance for decisiveness of the lethal spectrum, rather than the state of the mutation per se. Detailed clinical examination of our patients further indicates the changing phenotype from infancy to childhood.
49.	Karppanen, T, et al. (författare) An RGS2 3'UTR polymorphism is associated with preeclampsia in overweight women 2016 Ingår i: BMC genetics. - : Springer Science and Business Media LLC. - 1471-2156. ; 17:1, s. 121- Tidskriftsartikel (refereegranskat)
50.	Lona-Durazo, Frida, et al. (författare) Meta-analysis of GWA studies provides new insights on the genetic architecture of skin pigmentation in recently admixed populations 2019 Ingår i: BMC Genetics. - : BMC. - 1471-2156. ; 20 Tidskriftsartikel (refereegranskat)abstract Background: Association studies in recently admixed populations are extremely useful to identify the genetic architecture of pigmentation, due to their high genotypic and phenotypic variation. However, to date only four Genome-Wide Association Studies (GWAS) have been carried out in these populations.Results: We present a GWAS of skin pigmentation in an admixed sample from Cuba (N=762). Additionally, we conducted a meta-analysis including the Cuban sample, and admixed samples from Cape Verde, Puerto Rico and African-Americans from San Francisco. This meta-analysis is one of the largest efforts so far to characterize the genetic basis of skin pigmentation in admixed populations (N=2,104). We identified five genome-wide significant regions in the meta-analysis, and explored if the markers observed in these regions are associated with the expression of relevant pigmentary genes in human melanocyte cultures. In three of the regions identified in the meta-analysis (SLC24A5, SLC45A2, and GRM5/TYR), the association seems to be driven by non-synonymous variants (rs1426654, rs16891982, and rs1042602, respectively). The rs16891982 polymorphism is strongly associated with the expression of the SLC45A2 gene. In the GRM5/TYR region, in addition to the rs1042602 non-synonymous SNP located on the TYR gene, variants located in the nearby GRM5 gene have an independent effect on pigmentation, possibly through regulation of gene expression of the TYR gene. We also replicated an association recently described near the MFSD12 gene on chromosome 19 (lead variant rs112332856). Additionally, our analyses support the presence of multiple signals in the OCA2/HERC2/APBA2 region on chromosome 15. A clear causal candidate is the HERC2 intronic variant rs12913832, which has a profound influence on OCA2 expression. This variant has pleiotropic effects on eye, hair, and skin pigmentation. However, conditional and haplotype-based analyses indicate the presence of other variants with independent effects on melanin levels in OCA2 and APBA2. Finally, a follow-up of genome-wide signals identified in a recent GWAS for tanning response indicates that there is a substantial overlap in the genetic factors influencing skin pigmentation and tanning response.Conclusions: Our meta-analysis of skin pigmentation GWAS in recently admixed populations provides new insights about the genetic architecture of this complex trait.

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