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  • 1.
    Arefin, Badrul
    et al.
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Kunc, Martin
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute. Institute of Experimental Biology, Czech Republic.
    Krautz, Robert
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    Theopold, Ulrich
    Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
    The Immune Phenotype of Three Drosophila Leukemia Models2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 7, p. 2139-2149Article in journal (Refereed)
    Abstract [en]

    Many leukemia patients suffer from dysregulation of their immune system, making them more susceptible to infections and leading to general weakening (cachexia). Both adaptive and innate immunity are affected. The fruit fly Drosophila melanogaster has an innate immune system, including cells of the myeloid lineage (hemocytes). To study Drosophila immunity and physiology during leukemia, we established three models by driving expression of a dominant-active version of the Ras oncogene (Ras(V12)) alone or combined with knockdowns of tumor suppressors in Drosophila hemocytes. Our results show that phagocytosis, hemocyte migration to wound sites, wound sealing, and survival upon bacterial infection of leukemic lines are similar to wild type. We find that in all leukemic models the two major immune pathways (Toll and Imd) are dysregulated. Toll-dependent signaling is activated to comparable extents as after wounding wild-type larvae, leading to a proinflammatory status. In contrast, Imd signaling is suppressed. Finally, we notice that adult tissue formation is blocked and degradation of cell masses during metamorphosis of leukemic lines, which is akin to the state of cancer-dependent cachexia. To further analyze the immune competence of leukemic lines, we used a natural infection model that involves insect-pathogenic nematodes. We identified two leukemic lines that were sensitive to nematode infections. Further characterization demonstrates that despite the absence of behavioral abnormalities at the larval stage, leukemic larvae show reduced locomotion in the presence of nematodes. Taken together, this work establishes new Drosophila models to study the physiological, immunological, and behavioral consequences of various forms of leukemia.

  • 2.
    Bachmann, Jörg A.
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Tedder, Andrew
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Laenen, Benjamin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Steige, Kim A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Slotte, Tanja
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
    Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 4, p. 1327-1333Article in journal (Refereed)
    Abstract [en]

    Rapid advances in short-read DNA sequencing technologies have revolutionized population genomic studies, but there are genomic regions where this technology reaches its limits. Limitations mostly arise due to the difficulties in assembly or alignment to genomic regions of high sequence divergence and high repeat content, which are typical characteristics for loci under strong long-term balancing selection. Studying genetic diversity at such loci therefore remains challenging. Here, we investigate the feasibility and error rates associated with targeted long-read sequencing of a locus under balancing selection. For this purpose, we generated bacterial artificial chromosomes (BACs) containing the Brassicaceae S-locus, a region under strong negative frequency-dependent selection which has previously proven difficult to assemble in its entirety using short reads. We sequence S-locus BACs with single-molecule long-read sequencing technology and conduct de novo assembly of these S-locus haplotypes. By comparing repeated assemblies resulting from independent long-read sequencing runs on the same BAC clone we do not detect any structural errors, suggesting that reliable assemblies are generated, but we estimate an indel error rate of 5.7x10(-5). A similar error rate was estimated based on comparison of Illumina short-read sequences and BAC assemblies. Our results show that, until de novo assembly of multiple individuals using long-read sequencing becomes feasible, targeted long-read sequencing of loci under balancing selection is a viable option with low error rates for single nucleotide polymorphisms or structural variation. We further find that short-read sequencing is a valuable complement, allowing correction of the relatively high rate of indel errors that result from this approach.

  • 3.
    Bahrampour, Shahrzad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Thor, Stefan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology and Molecular Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Ctr9, a Key Component of the Paf1 Complex, Affects Proliferation and Terminal Differentiation in the Developing Drosophila Nervous System2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 10, p. 3229-3239Article in journal (Refereed)
    Abstract [en]

    The Paf1 protein complex (Paf1C) is increasingly recognized as a highly conserved and broadly utilized regulator of a variety of transcriptional processes. These include the promotion of H3K4 and H3K36 trimethylation, H2BK123 ubiquitination, RNA Pol II transcriptional termination, and also RNA-mediated gene silencing. Paf1C contains five canonical protein components, including Paf1 and Ctr9, which are critical for overall complex integrity, as well as Rtf1, Leo1, and Cdc73/Parafibromin(Hrpt2)/Hyrax. In spite of a growing appreciation for the importance of Paf1C from yeast and mammalian studies, there has only been limited work in Drosophila. Here, we provide the first detailed phenotypic study of Ctr9 function in Drosophila. We found that Ctr9 mutants die at late embryogenesis or early larval life, but can be partly rescued by nervous system reexpression of Ctr9. We observed a number of phenotypes in Ctr9 mutants, including increased neuroblast numbers, increased nervous system proliferation, as well as downregulation of many neuropeptide genes. Analysis of cell cycle and regulatory gene expression revealed upregulation of the E2f1 cell cycle factor, as well as changes in Antennapedia and Grainy head expression. We also found reduction of H3K4me3 modification in the embryonic nervous system. Genome-wide transcriptome analysis points to additional downstream genes that may underlie these Ctr9 phenotypes, revealing gene expression changes in Notch pathway target genes, cell cycle genes, and neuropeptide genes. In addition, we find significant effects on the gene expression of metabolic genes. These findings reveal that Ctr9 is an essential gene that is necessary at multiple stages of nervous system development, and provides a starting point for future studies of the Paf1C in Drosophila.

  • 4.
    Berlin, Sofia
    et al.
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Fogelqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rönnberg-Wästljung, Ann Christin
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf2011In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, no 5, p. 387-400Article in journal (Refereed)
    Abstract [en]

    We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.

  • 5.
    Bernhardsson, Carolina
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden; Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    Vidalis, Amaryllis
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Population Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München.
    Wang, Xi
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    Scofield, Douglas
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Uppsala Multidisciplinary Center for Advanced Computational Science; Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Uppsala, Sweden.
    Schiffthaler, Bastian
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Baison, John
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Garcia-Gil, M. Rosario
    Ingvarsson, Pär K.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden.
    An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)2019In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 5, p. 1623-1632Article in journal (Refereed)
    Abstract [en]

    Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

  • 6.
    Bernhardsson, Carolina
    et al.
    Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden;Swedish Univ Agr Sci, Umea Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umea, Sweden;Swedish Univ Agr Sci, Dept Plant Biol, Uppsala BioCtr, Uppsala, Sweden.
    Vidalis, Amaryllis
    Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden;Tech Univ Munich, Dept Populat Genet, Ctr Life & Food Sci Weihenstephan, D-85354 Freising Weihenstephan, Germany.
    Wang, Xi
    Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden;Swedish Univ Agr Sci, Dept Plant Biol, Uppsala BioCtr, Uppsala, Sweden.
    Scofield, Douglas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden.
    Schiffthaler, Bastian
    Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, Umea, Sweden.
    Baison, John
    Swedish Univ Agr Sci, Umea Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umea, Sweden.
    Street, Nathaniel R.
    Umea Univ, Umea Plant Sci Ctr, Dept Plant Physiol, Umea, Sweden.
    Garcia-Gil, M. Rosario
    Swedish Univ Agr Sci, Umea Plant Sci Ctr, Dept Forest Genet & Plant Physiol, Umea, Sweden.
    Ingvarsson, Pär K.
    Umea Univ, Dept Ecol & Environm Sci, Umea, Sweden;Swedish Univ Agr Sci, Dept Plant Biol, Uppsala BioCtr, Uppsala, Sweden.
    An Ultra-Dense Haploid Genetic Map for Evaluating the Highly Fragmented Genome Assembly of Norway Spruce (Picea abies)2019In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 5, p. 1623-1632Article in journal (Refereed)
    Abstract [en]

    Norway spruce (Picea abies (L.) Karst.) is a conifer species of substanital economic and ecological importance. In common with most conifers, the P. abies genome is very large (similar to 20 Gbp) and contains a high fraction of repetitive DNA. The current P. abies genome assembly (v1.0) covers approximately 60% of the total genome size but is highly fragmented, consisting of >10 million scaffolds. The genome annotation contains 66,632 gene models that are at least partially validated (), however, the fragmented nature of the assembly means that there is currently little information available on how these genes are physically distributed over the 12 P. abies chromosomes. By creating an ultra-dense genetic linkage map, we anchored and ordered scaffolds into linkage groups, which complements the fine-scale information available in assembly contigs. Our ultra-dense haploid consensus genetic map consists of 21,056 markers derived from 14,336 scaffolds that contain 17,079 gene models (25.6% of the validated gene models) that we have anchored to the 12 linkage groups. We used data from three independent component maps, as well as comparisons with previously published Picea maps to evaluate the accuracy and marker ordering of the linkage groups. We demonstrate that approximately 3.8% of the anchored scaffolds and 1.6% of the gene models covered by the consensus map have likely assembly errors as they contain genetic markers that map to different regions within or between linkage groups. We further evaluate the utility of the genetic map for the conifer research community by using an independent data set of unrelated individuals to assess genome-wide variation in genetic diversity using the genomic regions anchored to linkage groups. The results show that our map is sufficiently dense to enable detailed evolutionary analyses across the P. abies genome.

  • 7.
    Brandt, Monika
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Ahsan, Muhammad
    Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, S-75007 Uppsala, Sweden.
    Honaker, Christa F.
    Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Siegel, Paul B.
    Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 1, p. 119-128Article in journal (Refereed)
    Abstract [en]

    The Virginia chicken lines have been divergently selected for juvenile body weight for more than 50 generations. Today, the high- and low-weight lines show a >12-fold difference for the selected trait, 56-d body weight. These lines provide unique opportunities to study the genetic architecture of long-term, single-trait selection. Previously, several quantitative trait loci (QTL) contributing to weight differences between the lines were mapped in an F2-cross between them, and these were later replicated and fine-mapped in a nine-generation advanced intercross of them. Here, we explore the possibility to further increase the fine-mapping resolution of these QTL via a pedigree-based imputation strategy that aims to better capture the genetic diversity in the divergently selected, but outbred, founder lines. The founders of the intercross were high-density genotyped, and then pedigree-based imputation was used to assign genotypes throughout the pedigree. Imputation increased the marker density 20-fold in the selected QTL, providing 6911 markers for the subsequent analysis. Both single-marker association and multi-marker backward-elimination analyses were used to explore regions associated with 56-d body weight. The approach revealed several statistically and population structure independent associations and increased the mapping resolution. Further, most QTL were also found to contain multiple independent associations to markers that were not fixed in the founder populations, implying a complex underlying architecture due to the combined effects of multiple, linked loci perhaps located on independent haplotypes that still segregate in the selected lines.

  • 8.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ma, Xiao-Fei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Chinese Acad Sci, Key Lab Stress Physiol & Ecol Cold & Arid Reg, Lanzhou, Peoples R China..
    Zaina, Giusi
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Morgante, Michele
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, p. 1979-1989Article in journal (Refereed)
    Abstract [en]

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

  • 9.
    Crooks, Lucy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Carlborg, Örjan
    Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Marklund, Stefan
    Johansson, Anna M.
    Identification of Null Alleles and Deletions from SNP Genotypes for an Intercross Between Domestic and Wild Chickens2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, no 8, p. 1253-1260Article in journal (Refereed)
    Abstract [en]

    We analyzed genotypes from similar to 10K single-nucleotide polymorphisms (SNPs) in two families of an F-2 intercross between Red Junglefowl and White Leghorn chickens. Possible null alleles were found by patterns of incompatible and missing genotypes. We estimated that 2.6% of SNPs had null alleles compared with 2.3% with genotyping errors and that 40% of SNPs in which a parent and offspring were genotyped as different homozygotes had null alleles. Putative deletions were identified by null alleles at adjacent markers. We found two candidate deletions that were supported by fluorescence intensity data from a 60K SNP chip. One of the candidate deletions was from the Red Junglefowl, and one was present in both the Red Junglefowl and White Leghorn. Both candidate deletions spanned protein-coding regions and were close to a previously detected quantitative trait locus affecting body weight in this population. This study demonstrates that the similar to 50K SNP genotyping arrays now available for several agricultural species can be used to identify null alleles and deletions in data from large families. We suggest that our approach could be a useful complement to linkage analysis in experimental crosses.

  • 10.
    Crooks, Lucy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines2011In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, p. 57-64Article in journal (Refereed)
  • 11.
    Fallahshahroudi, Amir
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    de Kock, Neil
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Johnsson, Martin
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Bektic, Lejla
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Ubhayasekera, S J Kumari A
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Bergquist, Jonas
    Department of Chemistry, BMC, Analytical Chemistry and Neurochemistry, University of.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication.2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 2Article in journal (Refereed)
    Abstract [en]

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic-pituitary-adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in chickens. Improved understanding of the genes associated with HPA-axis reactivity can provide insights into the pathways and mechanisms causing stress-related pathologies.

  • 12.
    Fallahsharoudi, Amir
    et al.
    Linkoping Univ, Dept Phys Chem & Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    de Kock, Neil
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Johnsson, Martin
    Linkoping Univ, Dept Phys Chem & Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Bektic, Lejla
    Linkoping Univ, Dept Phys Chem & Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Ubhayasekera, S. J. Kumari A.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Bergquist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC, Analytical Chemistry.
    Wright, Dominic
    Linkoping Univ, Dept Phys Chem & Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Jensen, Per
    Linkoping Univ, Dept Phys Chem & Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 2, p. 497-504Article in journal (Refereed)
    Abstract [en]

    The stress response has been largely modified in all domesticated animals, offering a strong tool for genetic mapping. In chickens, ancestral Red Junglefowl react stronger both in terms of physiology and behavior to a brief restraint stress than domesticated White Leghorn, demonstrating modified functions of the hypothalamic-pituitary-adrenal (HPA) axis. We mapped quantitative trait loci (QTL) underlying variations in stress-induced hormone levels using 232 birds from the 12th generation of an advanced intercross between White Leghorn and Red Junglefowl, genotyped for 739 genetic markers. Plasma levels of corticosterone, dehydroepiandrosterone (DHEA), and pregnenolone (PREG) were measured using LC-MS/MS in all genotyped birds. Transcription levels of the candidate genes were measured in the adrenal glands or hypothalamus of 88 out of the 232 birds used for hormone assessment. Genes were targeted for expression analysis when they were located in a hormone QTL region and were differentially expressed in the pure breed birds. One genome-wide significant QTL on chromosome 5 and two suggestive QTL together explained 20% of the variance in corticosterone response. Two significant QTL for aldosterone on chromosome 2 and 5 (explaining 19% of the variance), and one QTL for DHEA on chromosome 4 (explaining 5% of the variance), were detected. Orthologous DNA regions to the significant corticosterone QTL have been previously associated with the physiological stress response in other species but, to our knowledge, the underlying gene(s) have not been identified. SERPINA10 had an expression QTL (eQTL) colocalized with the corticosterone QTL on chromosome 5 and PDE1C had an eQTL colocalized with the aldosterone QTL on chromosome 2. Furthermore, in both cases, the expression levels of the genes were correlated with the plasma levels of the hormones. Hence, both these genes are strong putative candidates for the domestication-induced modifications of the stress response in chickens. Improved understanding of the genes associated with HPA-axis reactivity can provide insights into the pathways and mechanisms causing stress-related pathologies.

  • 13.
    Fountain, Toby
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Helsinki, Dept Biosci, Helsinki, Finland.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England..
    Ravinet, Mark
    Natl Inst Genet, Ecol Genet Div, Mishima, Shizuoka, Japan..
    Naylor, Richard
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Reinhardt, Klaus
    Tech Univ Dresden, Appl Zool, Dept Biol, D-01069 Dresden, Germany..
    Butlin, Roger K.
    Univ Gothenburg, Dept Marine Sci, Gothenburg, Sweden.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 12, p. 4059-4066Article in journal (Refereed)
    Abstract [en]

    The rapid evolution of insecticide resistance remains one of the biggest challenges in the control of medically and economically important pests. Insects have evolved a diverse range of mechanisms to reduce the efficacy of the commonly used classes of insecticides, and finding the genetic basis of resistance is a major aid to management. In a previously unstudied population, we performed an F-2 resistance mapping cross for the common bed bug, Cimex lectularius, for which insecticide resistance is increasingly widespread. Using 334 SNP markers obtained through RAD-sequencing, we constructed the first linkage map for the species, consisting of 14 putative linkage groups (LG), with a length of 407 cM and an average marker spacing of 1.3 cM. The linkage map was used to reassemble the recently published reference genome, facilitating refinement and validation of the current genome assembly. We detected a major QTL on LG12 associated with insecticide resistance, occurring in close proximity (1.2 Mb) to a carboxylesterase encoding candidate gene for pyrethroid resistance. This provides another example of this candidate gene playing a major role in determining survival in a bed bug population following pesticide resistance evolution. The recent availability of the bed bug genome, complete with a full list of potential candidate genes related to insecticide resistance, in addition to the linkage map generated here, provides an excellent resource for future research on the development and spread of insecticide resistance in this resurging pest species.

  • 14.
    Griffin, Robert M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Turku, Dept Biol, Turku 20014, Finland..
    Schielzeth, Holger
    Univ Bielefeld, Dept Evolutionary Biol, D-33615 Bielefeld, Germany.;Friedrich Schiller Univ Jena, Inst Ecol, Dept Populat Ecol, D-07743 Jena, Germany..
    Friberg, Urban
    Linkoping Univ, AVIAN Behav Genom & Physiol Grp, IFM Biol, S-58183 Linkoping, Sweden..
    Autosomal and X-Linked Additive Genetic Variation for Lifespan and Aging: Comparisons Within and Between the Sexes in Drosophila melanogaster2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 12, p. 3903-3911Article in journal (Refereed)
    Abstract [en]

    Theory makes several predictions concerning differences in genetic variation between the X chromosome and the autosomes due to male X hemizygosity. The X chromosome should: (i) typically show relatively less standing genetic variation than the autosomes, (ii) exhibit more variation in males compared to females because of dosage compensation, and (iii) potentially be enriched with sex-specific genetic variation. Here, we address each of these predictions for lifespan and aging in Drosophila melanogaster. To achieve unbiased estimates of X and autosomal additive genetic variance, we use 80 chromosome substitution lines; 40 for the X chromosome and 40 combining the two major autosomes, which we assay for sex-specific and cross-sex genetic (co)variation. We find significant X and autosomal additive genetic variance for both traits in both sexes (with reservation for X-linked variation of aging in females), but no conclusive evidence for depletion of X-linked variation (measured through females). Males display more X-linked variation for lifespan than females, but it is unclear if this is due to dosage compensation since also autosomal variation is larger in males. Finally, our results suggest that the X chromosome is enriched for sex-specific genetic variation in lifespan but results were less conclusive for aging overall. Collectively, these results suggest that the X chromosome has reduced capacity to respond to sexually concordant selection on lifespan from standing genetic variation, while its ability to respond to sexually antagonistic selection may be augmented.

  • 15.
    Holt, Carson
    et al.
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Campbell, Michael
    Dept Human Genet, Vienna, Austria;Cold Spring Harbor Lab, Div Plant Biol, POB 100, Cold Spring Harbor, NY 11724 USA.
    Keays, David A.
    Res Inst Mol Pathol, Vienna, Austria.
    Edelman, Nathaniel
    Res Inst Mol Pathol, Vienna, Austria;Harvard Univ, Dept Organism & Evolutionary Biol, Cambridge, MA 02138 USA.
    Kapusta, Aurelie
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Maclary, Emily
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA.
    Domyan, Eric T.
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA;Utah Valley Univ, Dept Biol, Orem, UT USA.
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Warren, Wesley C.
    Washington Univ, Genome Inst, St Louis, MO USA.
    Yandell, Mark
    Dept Human Genet, Vienna, Austria;USTAR Ctr Genet Discovery, Vienna, Austria.
    Gilbert, M. Thomas P.
    Univ Copenhagen, Nat Hist Museum Denmark, Copenhagen, Denmark;Norwegian Univ Sci & Technol, Univ Museum, Trondheim, Norway.
    Shapiro, Michael D.
    Univ Utah, Dept Biol, 257 S 1400 E, Salt Lake City, UT 84108 USA.
    Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia)2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 5, p. 1391-1398Article in journal (Refereed)
    Abstract [en]

    The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and has recently emerged as a model for understanding the molecular basis of anatomical diversity, the magnetic sense, and other key aspects of avian biology. Here we report an update to the C. livia genome reference assembly and gene annotation dataset. Greatly increased scaffold lengths in the updated reference assembly, along with an updated annotation set, provide improved tools for evolutionary and functional genetic studies of the pigeon, and for comparative avian genomics in general.

  • 16.
    Hotopp, Julie C. Dunning
    et al.
    Univ Maryland, Sch Med, Greenebaum Canc Ctr, Inst Genome Sci,Dept Microbiol & Immunol, Baltimore, MD 21201 USA..
    Klasson, Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 1, p. 373-374Article in journal (Refereed)
    Abstract [en]

    In "Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element," Leung et al. (2017) improved contigs attributed to the Muller F element from the original CAF1 assembly, and used them to conclude that most of the sequence expansion of the fourth chromosome of D. ananassae is due to a higher transposon load than previously thought, but is not due to Wolbachia DNA integrations. While we do not disagree with the first conclusion, the authors base their second conclusion on the lack of homology detected between their improved CAF1 genome assembly attributed to D. ananassae and reference Wolbachia genomes. While the consensus CAF1 genome assembly lacks any sequence similarity to the reference genome of the Wolbachia endosymbiont of Drosophila melanogaster (wMel), numerous studies from multiple laboratories provide experimental support for a large lateral/horizontal gene transfer (LGT) of a Wolbachia genome into this D. ananassae line. As such, we strongly suspect that the original whole genome assembly was either constructed after the removal of all Wolbachia reads, or that Wolbachia sequences were directly removed from the contigs in the CAF1 assembly. Hence, Leung et al. (2017) could not have identified the Wolbachia LGT using the CAF1 assembly. This manuscript by Leung et al. (2017) highlights that an assembly of the Wolbachia sequence reads and their mate pairs was erroneously attributed solely to the Wolbachia endosymbiont, albeit before we understood the extent of LGT in D. ananassae. As such, we recommend that the sequences deposited at the National Center for Biotechnology Information (NCBI) under PRJNA13365 should not be attributed to Wolbachia endosymbiont of D. ananassae, but should have their taxonomy reclassified by NCBI as "Unclassified sequences." As our knowledge about genome biology improves, we need to reconsider and reanalyze earlier genomes removing the prejudice introduced from now defunct paradigms.

  • 17.
    Humble, Emily
    et al.
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    Dasmahapatra, Kanchon K.
    Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England..
    Martínez Barrio, Álvaro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Gregorio, Ines
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany..
    Forcada, Jaume
    British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    Polikeit, Ann-Christin
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany..
    Goldsworthy, Simon D.
    South Australian Res & Dev Inst, 2 Hamra Ave, West Beach, SA 5024, Australia..
    Goebel, Michael E.
    NOAA, Antarctic Ecosyst Res Div, SWFSC, NMFS, La Jolla, CA 92037 USA..
    Kalinowski, Jorn
    Univ Bielefeld, CeBiTec, Ctr Biotechnol, Univ Str 27, D-33615 Bielefeld, Germany..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Ludwig Maximilians Univ Munchen, Fac Biol, Div Evolutionary Biol, Planegg Martinstried, Germany..
    Hoffman, Joseph, I
    Univ Bielefeld, Dept Anim Behav, Postfach 100131, D-33501 Bielefeld, Germany.;British Antarctic Survey, Madingley Rd, Cambridge CB3 OET, England..
    RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 8, p. 2709-2722Article in journal (Refereed)
    Abstract [en]

    Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level by around 400 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organization.

  • 18.
    Johnsson, Martin
    et al.
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Jonsson, Kenneth B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jensen, Per
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Wright, Dominic
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 2, p. 311-319Article in journal (Refereed)
    Abstract [en]

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait-gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  • 19.
    Johnsson, Martin
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Jonsson, Kenneth B
    Department of Surgical Sciences, Orthopaedics, Akademiska Sjukhuset, Uppsala University, Uppasla, Sweden.
    Andersson, Leif
    Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Quantitative trait locus and genetical genomics analysis identifies putatively causal genes for fecundity and brooding in the chicken2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 2, p. 311-319Article in journal (Refereed)
    Abstract [en]

    Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.

  • 20.
    Kopps, Anna M.
    et al.
    Groningen, The Netherlands.
    Kang, Jungkoo
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Groningen, The Netherlands.
    Sherwin, William B.
    Sydney, New South Wales 2052, Australia; Murdoch, WA 6150, Australia.
    Palsböll, Per J.
    Groningen, The Netherlands.
    How Well Do Molecular and Pedigree Relatedness Correspond, in Populations with Diverse Mating Systems, and Various Types and Quantities of Molecular and Demographic Data?2015In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 5, no 9, p. 1815-1826Article in journal (Refereed)
    Abstract [en]

    Kinship analyses are important pillars of ecological and conservation genetic studies with potentially far-reaching implications. There is a need for power analyses that address a range of possible relationships. Nevertheless, such analyses are rarely applied, and studies that use genetic-data-based-kinship inference often ignore the influence of intrinsic population characteristics. We investigated 11 questions regarding the correct classification rate of dyads to relatedness categories (relatedness category assignments; RCA) using an individual-based model with realistic life history parameters. We investigated the effects of the number of genetic markers; marker type (microsatellite, single nucleotide polymorphism SNP, or both); minor allele frequency; typing error; mating system; and the number of overlapping generations under different demographic conditions. We found that (i) an increasing number of genetic markers increased the correct classification rate of the RCA so that up to >80% first cousins can be correctly assigned; (ii) the minimum number of genetic markers required for assignments with 80 and 95% correct classifications differed between relatedness categories, mating systems, and the number of overlapping generations; (iii) the correct classification rate was improved by adding additional relatedness categories and age and mitochondrial DNA data; and (iv) a combination of microsatellite and single-nucleotide polymorphism data increased the correct classification rate if <800 SNP loci were available. This study shows how intrinsic population characteristics, such as mating system and the number of overlapping generations, life history traits, and genetic marker characteristics, can influence the correct classification rate of an RCA study. Therefore, species-specific power analyses are essential for empirical studies.

  • 21.
    Kronholm, Ilkka
    et al.
    Univ Jyvaskyla, Dept Biol & Environm Sci, Ctr Excellence Biol Interact, POB 35, FI-40014 Jyvaskyla, Finland..
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ketola, Tarmo
    Univ Jyvaskyla, Dept Biol & Environm Sci, Ctr Excellence Biol Interact, POB 35, FI-40014 Jyvaskyla, Finland..
    Epigenetic Control of Phenotypic Plasticity in the Filamentous Fungus Neurospora crassa2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 12, p. 4009-4022Article in journal (Refereed)
    Abstract [en]

    Phenotypic plasticity is the ability of a genotype to produce different phenotypes under different environmental or developmental conditions. Phenotypic plasticity is a ubiquitous feature of living organisms, and is typically based on variable patterns of gene expression. However, the mechanisms by which gene expression is influenced and regulated during plastic responses are poorly understood in most organisms. While modifications to DNA and histone proteins have been implicated as likely candidates for generating and regulating phenotypic plasticity, specific details of each modification and its mode of operation have remained largely unknown. In this study, we investigated how epigenetic mechanisms affect phenotypic plasticity in the filamentous fungus Neurospora crassa. By measuring reaction norms of strains that are deficient in one of several key physiological processes, we show that epigenetic mechanisms play a role in homeostasis and phenotypic plasticity of the fungus across a range of controlled environments. In general, effects on plasticity are specific to an environment and mechanism, indicating that epigenetic regulation is context dependent and is not governed by general plasticity genes. Specifically, we found that, in Neurospora, histone methylation at H3K36 affected plastic response to high temperatures, H3K4 methylation affected plastic response to pH, but H3K27 methylation had no effect. Similarly, DNA methylation had only a small effect in response to sucrose. Histone deacetylation mainly decreased reaction norm elevation, as did genes involved in histone demethylation and acetylation. In contrast, the RNA interference pathway was involved in plastic responses to multiple environments.

  • 22.
    Larsson, Hanna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kallman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Distribution of Long-Range Linkage Disequilibrium and Tajima's D Values in Scandinavian Populations of Norway Spruce (Picea abies)2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, no 5, p. 795-806Article in journal (Refereed)
    Abstract [en]

    The site frequency spectrum of mutations (SFS) and linkage disequilibrium (LD) are the two major sources of information in population genetics studies. In this study we focus on the levels of LD and the SFS and on the effect of sample size on summary statistics in 10 Scandinavian populations of Norway spruce. We found that previous estimates of a low level of LD were highly influenced by both sampling strategy and the fact that data from multiple loci were analyzed jointly. Estimates of LD were in fact heterogeneous across loci and increased within individual populations compared with the estimate from the total data. The variation in levels of LD among populations most likely reflects different demographic histories, although we were unable to detect population structure by using standard approaches. As in previous studies, we also found that the SFS-based test Tajima's D was highly sensitive to sample size, revealing that care should be taken to draw strong conclusions from this test when sample size is small. In conclusion, the results from this study are in line with recent studies in other conifers that have revealed a more complex and variable pattern of LD than earlier studies suggested and with studies in trees and humans that suggest that Tajima's D is sensitive to sample size. This has large consequences for the design of future association and population genetic studies in Norway spruce.

  • 23.
    Li, Xidan
    et al.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Liu, Xiaodong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Nadaf, Javad
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France.;Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Le Bihan-Duval, Elisabeth
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France..
    Berri, Cecile
    INRA, Rech Avicoles UR83, F-37380 Nouzilly, France..
    Dunn, Ian
    Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Talbot, Richard
    Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    De Koning, Dirk-Jan
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden.;Univ Edinburgh, Roslin Inst, Roslin EH25 9RG, Midlothian, Scotland.;Univ Edinburgh, R D SVS, Roslin EH25 9RG, Midlothian, Scotland..
    Using Targeted Resequencing for Identification of Candidate Genes and SNPs for a QTL Affecting the pH Value of Chicken Meat2015In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 5, no 10, p. 2085-2089Article in journal (Refereed)
    Abstract [en]

    Using targeted genetical genomics, a quantitative trait locus (QTL) affecting the initial postmortem pH value of chicken breast muscle (Pectoralis major) on chromosome 1 (GGA1) recently was fine-mapped. Thirteen genes were present in the QTL region of approximately 1 Mb. In this study, 10 birds that were inferred to be homozygous for either the high (QQ) or low (qq) QTL allele were selected for resequencing. After enrichment for 1 Mb around the QTL region, >500 x coverage for the QTL region in each of the 10 birds was obtained. In total 5056 single-nucleotide polymorphisms (SNPs) were identified for which the genotypes were consistent with one of the QTL genotypes. We used custom tools to identify putative causal mutations in the mapped QTL region from these SNPs. Four nonsynonymous SNPs differentiating the two QTL genotype groups were identified within four local genes (PRDX4, EIF2S3, PCYT1B, and E1BTD2). Although these are likely candidate SNPs to explain the QTL effect, 54 additional consensus SNPs were detected within gene-related regions (untranslated regions, splicing sites CpG island, and promoter regions) for the QQ birds and 71 for the qq birds. These could also play a role explaining the observed QTL effect. The results provide an important step for prioritizing among a large amount of candidate mutations and significantly contribute to the understanding of the genetic mechanisms affecting the initial postmortem pH value of chicken muscle.

  • 24.
    Lillie, Mette
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Honaker, Christa F.
    Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA USA.
    Siegel, Paul B.
    Virginia Polytech Inst & State Univ, Dept Anim & Poultry Sci, Blacksburg, VA USA.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model2019In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 9, no 4, p. 1165-1173Article in journal (Refereed)
    Abstract [en]

    Experimental populations of model organisms provide valuable opportunities to unravel the genomic impact of selection in a controlled system. The Virginia body weight chicken lines represent a unique resource to investigate signatures of selection in a system where long-term, single-trait, bidirectional selection has been carried out for more than 60 generations. At 55 generations of divergent selection, earlier analyses of pooled genome resequencing data from these lines revealed that 14.2% of the genome showed extreme differentiation between the selected lines, contained within 395 genomic regions. Here, we report more detailed analyses of these data exploring the regions displaying within- and between-line genomic signatures of the bidirectional selection applied in these lines. Despite the strict selection regime for opposite extremes in body weight, this did not result in opposite genomic signatures between the lines. The lines often displayed a duality of the sweep signatures, where an extended region of homozygosity in one line, in contrast to mosaic pattern of heterozygosity in the other line. These haplotype mosaics consisted of short, distinct haploblocks of variable between-line divergence, likely the results of a complex demographic history involving bottlenecks, introgressions and moderate inbreeding. We demonstrate this using the example of complex haplotype mosaicism in the growth1 QTL. These mosaics represent the standing genetic variation available at the onset of selection in the founder population. Selection on standing genetic variation can thus result in different signatures depending on the intensity and direction of selection.

  • 25.
    Lundberg, Lina E
    et al.
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Kim, Maria
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Johansson, Anna-Mia
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Faucillion, Marie-Line
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Josupeit, Rafael
    German Cancer Research Center (DKFZ).
    Larsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Targeting of painting of fourth to roX1 and roX2 proximal sites suggests evolutionary links between dosage compensation and the regulation of the 4th chromosome in Drosophila melanogaster2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, no 8, p. 1325-1334Article in journal (Refereed)
    Abstract [en]

    In Drosophila melanogaster, two chromosome-specific targeting and regulatory systems have been described. The male-specific lethal (MSL) complex supports dosage compensation by stimulating gene expression from the male X-chromosome and the protein Painting of fourth (POF) specifically targets and stimulates expression from the heterochromatic 4(th) chromosome. The targeting sites of both systems are well characterized, but the principles underlying the targeting mechanisms have remained elusive. Here we present an original observation, namely that POF specifically targets two loci on the X-chromosome, PoX1 and PoX2 (POF-on-X). PoX1 and PoX2 are located close to the roX1 and roX2 genes, which encode ncRNAs important for the correct targeting and spreading of the MSL-complex. We also found that the targeting of POF to PoX1 and PoX2 is largely dependent on roX expression and identified a high-affinity target region which ectopically recruits POF. The results presented support a model linking the MSL-complex to POF and dosage compensation to regulation of heterochromatin.

  • 26.
    Makrantoni, Vasso
    et al.
    Centre for Gene Regulation and Expression, University of Dundee, UK.
    Ciesiolka, Adam
    Institute for Cell and Molecular Biosciences, Newcastle University, UK.
    Lawless, Conor
    Institute for Cell and Molecular Biosciences, Newcastle University, UK.
    Fernius, Josefin
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK.
    Marston, Adele
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, UK.
    Lydall, David
    Newcastle University, England.
    Stark, Michael J. R.
    Centre for Gene Regulation and Expression, University of Dundee, UK.
    A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 9, p. 3203-3215Article in journal (Refereed)
    Abstract [en]

    The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/Ipl1 in association with its activator (INCENP/Sli15) and two additional proteins (Survivin/Bir1 and Borealin/Nbl1). Here, we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1-17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1-17, while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay pathway caused strong phenotypic suppression. Thus, cells lacking a functional Ctf19 complex become highly dependent on Bir1 function and vice versa. The negative genetic interaction profiles of bir1-17 and the cohesin mutant mcd1-1 showed considerable overlap, underlining the strong functional connection between sister chromatid cohesion and chromosome biorientation. Loss of some Ctf19 components, such as Iml3 or Chl4, impacted differentially on bir1-17 compared with mutations affecting other CPC components: despite the synthetic lethality shown by either iml3 Delta or chl4 Delta in combination with bir1-17, neither gene knockout showed any genetic interaction with either ipl1-321 or sli15-3. Our data therefore imply a specific functional connection between the Ctf19 complex and Bir1 that is not shared with Ipl1.

  • 27.
    Mouresan, Elena Flavia
    et al.
    Swedish University of Agricultural Sciences.
    Selle, Maria
    Norwegian University of Science and Technology.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Genomic Prediction Including SNP-Specific Variance Predictors2019In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, article id g3.400381.2019Article in journal (Refereed)
    Abstract [en]

    The increasing amount of available biological information on the markers can be used to inform the models applied for genomic selection to improve predictions. The objective of this study was to propose a general model for genomic selection using a link function approach within the hierarchical generalized linear model framework (hglm) that can include external information on the markers. These models can be fitted using the well-established hglm package in R. We also present an R package (CodataGS) to fit these models, which is significantly faster than the hglm package. Simulated data was used to validate the proposed model. We tested categorical, continuous and combination models where the external information on the markers was related to 1) the location of the QTLs on the genome with varying degree of uncertainty, 2) the relationship of the markers with the QTLs calculated as the LD between them, and 3) a combination of both. The proposed models showed improved accuracies from 3.8% up to 23.2% compared to the SNP-BLUP method in a simulated population derived from a base population with 100 individuals. Moreover, the proposed categorical model was tested on a dairy cattle dataset for two traits (Milk Yield and Fat Percentage). These results also showed improved accuracy compared to SNP-BLUP, especially for the Fat% trait. The performance of the proposed models depended on the genetic architecture of the trait, as traits that deviate from the infinitesimal model benefited more from the external information. Also, the gain in accuracy depended on the degree of uncertainty of the external information provided to the model. The usefulness of these type of models is expected to increase with time as more accurate information on the markers becomes available.

  • 28.
    Mugal, Carina F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Arndt, Peter F.
    Holm, Lena
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes2015In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 5, no 3, p. 441-447Article in journal (Refereed)
    Abstract [en]

    The genomes of many vertebrates show a characteristic variation in GC content. To explain its origin and evolution, mainly three mechanisms have been proposed: selection for GC content, mutation bias, and GC-biased gene conversion. At present, the mechanism of GC-biased gene conversion, i.e., short-scale, unidirectional exchanges between homologous chromosomes in the neighborhood of recombination-initiating double-strand breaks in favor for GC nucleotides, is the most widely accepted hypothesis. We here suggest that DNA methylation also plays an important role in the evolution of GC content in vertebrate genomes. To test this hypothesis, we investigated one mammalian (human) and one avian (chicken) genome. We used bisulfite sequencing to generate a whole-genome methylation map of chicken sperm and made use of a publicly available whole-genome methylation map of human sperm. Inclusion of these methylation maps into a model of GC content evolution provided significant support for the impact of DNA methylation on the local equilibrium GC content. Moreover, two different estimates of equilibrium GC content, one that neglects and one that incorporates the impact of DNA methylation and the concomitant CpG hypermutability, give estimates that differ by approximately 15% in both genomes, arguing for a strong impact of DNA methylation on the evolution of GC content. Thus, our results put forward that previous estimates of equilibrium GC content, which neglect the hypermutability of CpG dinucleotides, need to be reevaluated.

  • 29. Nelson, Ronald M.
    et al.
    Nettelblad, Carl
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Pettersson, Mats E.
    Shen, Xia
    Crooks, Lucy
    Besnier, François
    Álvarez-Castro, José
    Rönnegård, Lars
    Ek, Weronica
    Sheng, Zheya
    Kierczak, Marcin
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Carlborg, Örjan
    Swedish University of Agricultural Sciences, Division of Computational Genetics.
    MAPfastR: Quantitative trait loci mapping in outbred line crosses2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, p. 2147-2149Article in journal (Refereed)
  • 30.
    Nelson, Ronald Michael
    et al.
    Swedish University of Agricultural Sciences.
    Nettelblad, Carl
    Uppsala University.
    Pettersson, Mats E
    Swedish University of Agricultural Sciences.
    Shen, Xia
    Swedish University of Agricultural Sciences; Uppsala University;.
    Crooks, Lucy
    Swedish University of Agricultural Sciences.
    Besnier, Francois
    Swedish University of Agricultural Sciences.
    Alvarez-Castro, José
    Swedish University of Agricultural Sciences.
    Rönnegård, Lars
    Dalarna University, School of Technology and Business Studies, Statistics.
    Ek, Weronica
    Swedish University of Agricultural Sciences.
    Carlborg, Örjan
    Swedish University of Agricultural Sciences.
    MAPfastR: quantitative trait loci mapping in outbred line crosses2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 12, no 3, p. 2147-2149Article in journal (Refereed)
    Abstract [en]

    MAPfastR is a software package developed to analyze QTL data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate QTL analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.

  • 31. Pettersson, Mats E
    et al.
    Johansson, Anna M
    Siegel, Paul B
    Carlborg, Örjan
    SLU.
    Dynamics of adaptive alleles in divergently selected body weight lines of chickens.2013In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, no 12Article in journal (Refereed)
    Abstract [en]

    By studying genomic changes over time in populations subjected to strong artificial directional selection, we can gain insights to the dynamics of beneficial alleles originating from the founder population or emerging as novel mutations undergoing ongoing selection. The Virginia lines are a chicken resource population generated by long-term bi-directional, single-trait selection for juvenile body weight. We studied genome-wide allele frequency changes from generation 40 to 53 using genome-wide genotypes from directional and relaxed selection lines. Overall, there were small changes in allele frequencies at individual loci over the studied time period; but, on average, the changes were greater in lines with larger phenotypic changes. This is consistent with previous findings that much of the response to selection over the first 40 years of selection was attributable to utilization of standing genetic variation at many loci in the genome, indicating a mostly polygenic architecture for body weight. Over the course of the selection experiment, the largest phenotypic response to selection was observed in the high-weight selected line, and in this line we detected a single locus where the allele frequency changed rapidly during a late stage of the experiment. This locus likely contains a novel, beneficial mutation that appeared between generations 40 and 45 and was driven to fixation in 5 to 10 generations. This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations.

  • 32.
    Rafati, Nima
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Lisa S.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Mikko, Sofia
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Feng, Chungang
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Raudsepp, Terje
    Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA..
    Pettersson, Jessica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Janecka, Jan
    Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA..
    Wattle, Ove
    Swedish Univ Agr Sci, Dept Clin Sci, S-75007 Uppsala, Sweden..
    Ameur, Adam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    Thyreen, Gunilla
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Eberth, John
    Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA..
    Huddleston, John
    Univ Washington, Sch Med, Dept Genome Sci, Seattle, WA 98105 USA.;Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA..
    Malig, Maika
    Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA..
    Bailey, Ernest
    Univ Kentucky, Gluck Equine Res Ctr, Dept Vet Sci, Lexington, KY 40546 USA..
    Eichler, Evan E.
    Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA..
    Dalin, Goran
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, S-75007 Uppsala, Sweden..
    Chowdary, Bhanu
    Qatar Univ, New Res Complex, Doha 2713, Qatar..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77845 USA..
    Lindgren, Gabriella
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden..
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, p. 2213-2223Article in journal (Refereed)
    Abstract [en]

    Skeletal atavism in Shetland ponies is a heritable disorder characterized by abnormal growth of the ulna and fibula that extend the carpal and tarsal joints, respectively. This causes abnormal skeletal structure and impaired movements, and affected foals are usually killed. In order to identify the causal mutation we subjected six confirmed Swedish cases and a DNA pool consisting of 21 control individuals to whole genome resequencing. We screened for polymorphisms where the cases and the control pool were fixed for opposite alleles and observed this signature for only 25 SNPs, most of which were scattered on genome assembly unassigned scaffolds. Read depth analysis at these loci revealed homozygosity or compound heterozygosity for two partially overlapping large deletions in the pseudoautosomal region (PAR) of chromosome X/Y in cases but not in the control pool. One of these deletions removes the entire coding region of the SHOX gene and both deletions remove parts of the CRLF2 gene located downstream of SHOX. The horse reference assembly of the PAR is highly fragmented, and in order to characterize this region we sequenced bacterial artificial chromosome (BAC) clones by single-molecule real-time (SMRT) sequencing technology. This considerably improved the assembly and enabled size estimations of the two deletions to 1602180 kb and 60280 kb, respectively. Complete association between the presence of these deletions and disease status was verified in eight other affected horses. The result of the present study is consistent with previous studies in humans showing crucial importance of SHOX for normal skeletal development.

  • 33.
    Talla, Venkat
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Kalsoom, Faheema
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Shipilina, Daria
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow 119991, Russia..
    Marova, Irina
    Lomonosov Moscow State Univ, Dept Vertebrate Zool, Moscow 119991, Russia..
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)2017In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 7, no 12, p. 3983-3998Article in journal (Refereed)
    Abstract [en]

    Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps toward understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations, since they allow us to study how genomes evolve as species exchange genetic material and to associate particular genetic regions with phenotypic traits of interest. Here, we use whole-genome resequencing of both allopatric and hybridizing populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P. tristis)-two recently diverged species which differ in morphology, plumage, song, habitat, and migration-to quantify the regional variation in genome-wide genetic diversity and differentiation, and to identify candidate regions for trait variation. We find that the levels of diversity, differentiation, and divergence are highly heterogeneous, with significantly reduced global differentiation, and more pronounced differentiation peaks in sympatry than in allopatry. This pattern is consistent with regional differences in effective population size and recurrent background selection or selective sweeps reducing the genetic diversity in specific regions prior to lineage divergence, but the data also suggest that post-divergence selection has resulted in increased differentiation and fixed differences in specific regions. We find that hybridization and backcrossing is common in sympatry, and that phenotype is a poor predictor of the genomic composition of sympatric birds. The combination of a differentiation scan approach with identification of fixed differences pinpoint a handful of candidate regions that might be important for trait variation between the two species.

  • 34. van Mourik, Paula M
    et al.
    de Jong, Jannie
    Sharma, Sushma
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
    Kavšek, Alan
    Chabes, Andrei
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Chang, Michael
    Upregulation of dNTP Levels After Telomerase Inactivation Influences Telomerase-Independent Telomere Maintenance Pathway Choice in Saccharomyces cerevisiae2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 8, p. 2551-2558Article in journal (Refereed)
    Abstract [en]

    In 10–15% of cancers, telomere length is maintained by a telomerase-independent, recombination-mediated pathway called alternative lengthening of telomeres (ALT). ALT mechanisms were first seen, and have been best studied, in telomerase-null Saccharomyces cerevisiae cells called “survivors”. There are two main types of survivors. Type I survivors amplify Y′ subtelomeric elements while type II survivors, similar to the majority of human ALT cells, amplify the terminal telomeric repeats. Both types of survivors require Rad52, a key homologous recombination protein, and Pol32, a non-essential subunit of DNA polymerase δ. A number of additional proteins have been reported to be important for either type I or type II survivor formation, but it is still unclear how these two pathways maintain telomeres. In this study, we performed a genome-wide screen to identify novel genes that are important for the formation of type II ALT-like survivors. We identified 23 genes that disrupt type II survivor formation when deleted. 17 of these genes had not been previously reported to do so. Several of these genes (DUN1CCR4, and MOT2) are known to be involved in the regulation of dNTP levels. We find that dNTP levels are elevated early after telomerase inactivation and that this increase favors the formation of type II survivors.

  • 35.
    Zan, Yanjun
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Forsberg, Simon K. G.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology. Princeton Univ, Ecol & Evolutionary Biol Dept, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08540 USA.
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    On the Relationship Between High-Order Linkage Disequilibrium and Epistasis2018In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 8, no 8, p. 2817-2824Article in journal (Refereed)
    Abstract [en]

    A plausible explanation for statistical epistasis revealed in genome wide association analyses is the presence of high order linkage disequilibrium (LD) between the genotyped markers tested for interactions and unobserved functional polymorphisms. Based on findings in experimental data, it has been suggested that high order LD might be a common explanation for statistical epistasis inferred between local polymorphisms in the same genomic region. Here, we empirically evaluate how prevalent high order LD is between local, as well as distal, polymorphisms in the genome. This could provide insights into whether we should account for this when interpreting results from genome wide scans for statistical epistasis. An extensive and strong genome wide high order LD was revealed between pairs of markers on the high density 250k SNP-chip and individual markers revealed by whole genome sequencing in the Arabidopsis thaliana 1001-genomes collection. The high order LD was found to be more prevalent in smaller populations, but present also in samples including several hundred individuals. An empirical example illustrates that high order LD might be an even greater challenge in cases when the genetic architecture is more complex than the common assumption of bi-allelic loci. The example shows how significant statistical epistasis is detected for a pair of markers in high order LD with a complex multi allelic locus. Overall, our study illustrates the importance of considering also other explanations than functional genetic interactions when genome wide statistical epistasis is detected, in particular when the results are obtained in small populations of inbred individuals.

  • 36.
    Zan, Yanjun
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden.
    Shen, Xia
    Univ Edinburgh, Usher Inst Populat Hlth Sci & Informat, Edinburgh EH16 4UX, Midlothian, Scotland; Univ Edinburgh, MRC Inst Genet & Mol Med, MRC Human Genet Unit, Edinburgh EH16 4UX, Midlothian, Scotland; Karolinska Inst, Dept Med Epidemiol & Biostat, SE-17177 Stockholm, Sweden.
    Forsberg, Simon
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden.
    Carlborg, Orjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Div Computat Genet, Dept Clin Sci, SE-75651 Uppsala, Sweden.
    Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 8, p. 2319-2328Article in journal (Refereed)
    Abstract [en]

    An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalysed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaf of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions but no transcripts at all in others and this pattern was correlated with the genome-wide genotype. In total, 2,669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. 646 cis-eQTLs regulated genes that lacked detectable transcripts in some accessions, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA-transcripts for these genes. This study thus provides new insights on the overall genetic regulation of global gene-expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population.

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