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  • 1.
    da Fonseca, Rute R.
    et al.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Copenhagen, Bioinformat Ctr, DK-2200 Copenhagen, Denmark..
    Smith, Bruce D.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Anthropol, Program Human Ecol & Archaeobiol, Washington, DC 20560 USA..
    Wales, Nathan
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Cappellini, Enrico
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Skoglund, Pontus
    Harvard Univ, Sch Med, Dept Genet, Boston, MA 02115 USA..
    Fumagalli, Matteo
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Samaniego, Jose Alfredo
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Caroe, Christian
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Avila-Arcos, Mara C.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Stanford Univ, Dept Genet, Sch Med, Stanford, CA 94305 USA..
    Hufnagel, David E.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA..
    Korneliussen, Thorfinn Sand
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Vieira, Filipe Garrett
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Arriaza, Bernardo
    Univ Tarapaca, Inst Alta Invest, Arica 15101, Chile..
    Willerslev, Eske
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark..
    Nielsen, Rasmus
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Univ Calif Berkeley, Dept Integrat Biol & Stat, Berkeley, CA 94720 USA..
    Hufford, Matthew B.
    Iowa State Univ, Dept Ecol Evolut & Organismal Biol, Ames, IA 50011 USA..
    Albrechtsen, Anders
    Univ Copenhagen, Bioinformat Ctr, DK-2200 Copenhagen, Denmark..
    Ross-Ibarra, Jeffrey
    Univ Calif Davis, Dept Plant Sci, Ctr Populat Biol, Davis, CA 95616 USA.;Univ Calif Davis, Genome Ctr, Davis, CA 95616 USA..
    Gilbert, M. Thomas P.
    Univ Copenhagen, Ctr GeoGenet, DK-1350 Copenhagen, Denmark.;Curtin Univ, Trace & Environm DNA Lab, Dept Environm & Agr, Perth, WA 6102, Australia..
    The origin and evolution of maize in the Southwestern United States2015In: Nature Plants, ISSN 2055-026X, Vol. 1, no 1, article id UNSP 14003Article in journal (Refereed)
    Abstract [en]

    The origin of maize (Zea mays mays) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal(1-4) or highland(5,6) routes of diffusion of maize into the United States. Furthermore, the genetics of adaptation to the new environmental and cultural context of the Southwest is largely uncharacterized(7). To address these issues, we compared nuclear DNA from 32 archaeological maize samples spanning 6,000 years of evolution to modern landraces. We found that the initial diffusion of maize into the Southwest about 4,000 years ago is likely to have occurred along a highland route, followed by gene flow from a lowland coastal maize beginning at least 2,000 years ago. Our population genetic analysis also enabled us to differentiate selection during domestication for adaptation to the climatic and cultural environment of the Southwest, identifying adaptation loci relevant to drought tolerance and sugar content.

  • 2.
    Dinca, Vlad
    et al.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Backstrom, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dapporto, Leonardo
    Oxford Brookes Univ, Dept Biol & Med Sci, Oxford OX3 0BP, England..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Garcia-Barros, Enrique
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hebert, Paul D. N.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Hernandez-Roldan, Juan
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hornett, Emily
    Univ Cambridge, Dept Zool, Cambridge CB2 3EJ, England..
    Lukhtanov, Vladimir
    Russian Acad Sci, Inst Zool, Dept Karyosystemat, St Petersburg 199034, Russia..
    Marec, Frantisek
    Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic..
    DNA barcodes highlight unique research models in European butterflies2015In: Genome, ISSN 0831-2796, E-ISSN 1480-3321, Vol. 58, no 5, p. 212-212Article in journal (Other academic)
  • 3.
    Fegraeus, Kim Jaederkvist
    et al.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Velie, Brandon D.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Axelsson, Jeanette
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Ang, Rachel
    Univ Sydney, Fac Sci, Sydney, NSW, Australia.
    Hamilton, Natasha A.
    Univ Sydney, Fac Sci, Sydney, NSW, Australia.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden; Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX USA.
    Meadows, Jennifer R. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindgren, Gabriella
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    A potential regulatory region near the EDN3 gene may control both harness racing performance and coat color variation in horses2018In: Physiological Reports, E-ISSN 2051-817X, Vol. 6, no 10, article id e13700Article in journal (Refereed)
    Abstract [en]

    The Swedish‐Norwegian Coldblooded trotter and the heavier North‐Swedish draught horse both descend from the North‐Swedish horse, but the Coldblooded trotters have been selected for racing performance while the North‐Swedish draught horse is mainly used for agricultural and forestry work. By comparing the genomes of Coldblooded trotters, North‐Swedish draught horses and Standardbreds for a large number of single‐nucleotide polymorphisms (SNPs), the aim of the study was to identify genetic regions that may be under selection for racing performance. We hypothesized that the selection for racing performance, in combination with unauthorized crossbreeding of Coldblooded trotters and Standardbreds, has created regions in the genome where the Coldblooded trotters and Standardbreds are similar, but differ from the North‐Swedish draught horse. A fixation index (Fst) analysis was performed and sliding window Delta Fst values were calculated across the three breeds. Five windows, where the average Fst between Coldblooded trotters and Standardbreds was low and the average Fst between Coldblooded trotters and North‐Swedish draught horses was high, were selected for further investigation. Associations between the most highly ranked SNPs and harness racing performance were analyzed in 400 raced Coldblooded trotters with race records. One SNP showed a significant association with racing performance, with the CC genotype appearing to be negatively associated. The SNP identified was genotyped in 1915 horses of 18 different breeds. The frequency of the TT genotype was high in breeds typically used for racing and show jumping while the frequency of the CC genotype was high in most pony breeds and draught horses. The closest gene in this region was the Endothelin3 gene (EDN3), a gene mainly involved in melanocyte and enteric neuron development. Both functional genetic and physiological studies are needed to fully understand the possible impacts of the gene on racing performance.

  • 4.
    Felkel, S.
    et al.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria.;Vienna Grad Sch Populat Genet, Vienna, Austria..
    Vogl, C.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Rigler, D.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Jagannathan, V.
    Univ Bern, Inst Genet, Vetsuisse Fac, Bern, Switzerland..
    Leeb, T.
    Univ Bern, Inst Genet, Vetsuisse Fac, Bern, Switzerland..
    Fries, R.
    Tech Univ Munich, Lehrstuhl Tierzucht, Freising Weihenstephan, Germany..
    Neuditschko, M.
    Agroscope, Swiss Natl Stud Farm, Avenches, Switzerland..
    Rieder, S.
    Agroscope, Swiss Natl Stud Farm, Avenches, Switzerland..
    Velie, B.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Lindgren, G.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Rubin, Carl-Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Schlötterer, C.
    Univ Vet Med Vienna, Inst Populat Genet, Vienna, Austria..
    Rattei, T.
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Div Computat Syst Biol, Vienna, Austria..
    Brem, G.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Wallner, B.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Asian horses deepen the MSY phylogeny2018In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 49, no 1, p. 90-93Article in journal (Refereed)
    Abstract [en]

    Humans have shaped the population history of the horse ever since domestication about 5500years ago. Comparative analyses of the Y chromosome can illuminate the paternal origin of modern horse breeds. This may also reveal different breeding strategies that led to the formation of extant breeds. Recently, a horse Y-chromosomal phylogeny of modern horses based on 1.46Mb of the male-specific Y (MSY) was generated. We extended this dataset with 52 samples from five European, two American and seven Asian breeds. As in the previous study, almost all modern European horses fall into a crown group, connected via a few autochthonous Northern European lineages to the outgroup, the Przewalski's Horse. In total, we now distinguish 42 MSY haplotypes determined by 158 variants within domestic horses. Asian horses show much higher diversity than previously found in European breeds. The Asian breeds also introduce a deep split to the phylogeny, preliminarily dated to 5527 +/- 872years. We conclude that the deep splitting Asian Y haplotypes are remnants of a far more diverse ancient horse population, whose haplotypes were lost in other lineages.

  • 5.
    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.

  • 6.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Warnefors, Maria
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    Kaessmann, Henrik
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    The evolution of duplicate gene expression in mammalian organs2017In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 9, p. 1461-1474Article in journal (Refereed)
    Abstract [en]

    Gene duplications generate genomic raw material that allows the emergence of novel functions, likely facilitating adaptive evolutionary innovations. However, global assessments of the functional and evolutionary relevance of duplicate genes in mammals were until recently limited by the lack of appropriate comparative data. Here, we report a large-scale study of the expression evolution of DNA-based functional gene duplicates in three major mammalian lineages (placental mammals, marsupials, egg-laying monotremes) and birds, on the basis of RNA sequencing (RNA-seq) data from nine species and eight organs. We observe dynamic changes in tissue expression preference of paralogs with different duplication ages, suggesting differential contribution of paralogs to specific organ functions during vertebrate evolution. Specifically, we show that paralogs that emerged in the common ancestor of bony vertebrates are enriched for genes with brain-specific expression and provide evidence for differential forces underlying the preferential emergence of young testis-and liver-specific expressed genes. Further analyses uncovered that the overall spatial expression profiles of gene families tend to be conserved, with several exceptions of pronounced tissue specificity shifts among lineage-specific gene family expansions. Finally, we trace new lineage-specific genes that may have contributed to the specific biology of mammalian organs, including the little-studied placenta. Overall, our study provides novel and taxonomically broad evidence for the differential contribution of duplicate genes to tissue-specific transcriptomes and for their importance for the phenotypic evolution of vertebrates.

  • 7. Hall, Hardy C.
    et al.
    Fakhrzadeh, Azadeh
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Luengo Hendriks, Cris L.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Fischer, Urs
    Precision automation of cell type classification and sub-cellular fluorescence quantification from laser scanning confocal images2016In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 7, article id 119Article in journal (Refereed)
    Abstract [en]

    While novel whole-plant phenotyping technologies have been successfully implemented into functional genomics and breeding programs, the potential of automated phenotyping with cellular resolution is largely unexploited. Laser scanning confocal microscopy has the potential to close this gap by providing spatially highly resolved images containing anatomic as well as chemical information on a subcellular basis. However, in the absence of automated methods, the assessment of the spatial patterns and abundance of fluorescent markers with subcellular resolution is still largely qualitative and time-consuming. Recent advances in image acquisition and analysis, coupled with improvements in microprocessor performance, have brought such automated methods within reach, so that information from thousands of cells per image for hundreds of images may be derived in an experimentally convenient time-frame. Here, we present a MATLAB-based analytical pipeline to (1) segment radial plant organs into individual cells, (2) classify cells into cell type categories based upon Random Forest classification, (3) divide each cell into sub-regions, and (4) quantify fluorescence intensity to a subcellular degree of precision for a separate fluorescence channel. In this research advance, we demonstrate the precision of this analytical process for the relatively complex tissues of Arabidopsis hypocotyls at various stages of development. High speed and robustness make our approach suitable for phenotyping of large collections of stem-like material and other tissue types.

  • 8.
    Imsland, Freyja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Monogenic Traits Associated with Structural Variants in Chicken and Horse: Allelic and Phenotypic Diversity of Visually Appealing Traits2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Domestic animals have rich phenotypic diversity that can be explored to advance our understanding of the relationship between molecular genetics and phenotypic variation. Since the advent of second generation sequencing, it has become easier to identify structural variants and associate them with phenotypic outcomes. This thesis details studies on three such variants associated with monogenic traits.

    The first studies on Rose-comb in the chicken were published over a century ago, seminally describing Mendelian inheritance and epistatic interaction in animals. Homozygosity for the otherwise dominant Rose-comb allele was later associated with reduced rooster fertility. We show that a 7.38 Mb inversion is causal for Rose-comb, and that two alleles exist for Rose-comb, R1 and R2. A novel genomic context for the gene MNR2 is causative for the comb phenotype, and the bisection of the gene CCDC108 is associated with fertility issues. The recombined R2 allele has intact CCDC108, and normal fertility.

    The dominant phenotype Greying with Age in horses was previously associated with an intronic duplication in STX17. By utilising second generation sequencing we have examined the genomic region surrounding the duplication in detail, and excluded all other discovered variants as causative for Grey.

    Dun is the ancestral coat colour of equids, where the individual is mostly pale in colour, but carries intensely pigmented primitive markings, most notably a dorsal stripe. Dun is a dominant trait, and yet most domestic horses are non-dun in colour and intensely pigmented. We show that Dun colour is established by radially asymmetric expression of the transcription factor TBX3 in hair follicles. This results in a microscopic spotting phenotype on the level of the individual hair, giving the impression of pigment dilution. Non-dun colour is caused by two different alleles, non-dun1 and non-dun2, both of which disrupt the TBX3-mediated regulation of pigmentation. Non-dun1 is associated with a SNP variant 5 kb downstream of TBX3, and non-dun2 with a 1.6 kb deletion that overlaps the non-dun1 SNP. Homozygotes for non-dun2 show a more intensely pigmented appearance than horses with one or two non-dun1 alleles. We have also shown by genotyping of ancient DNA that non-dun1 predates domestication.

    List of papers
    1. The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility
    Open this publication in new window or tab >>The Rose-comb Mutation in Chickens Constitutes a Structural Rearrangement Causing Both Altered Comb Morphology and Defective Sperm Motility
    Show others...
    2012 (English)In: PLOS Genetics, ISSN 1553-7404, Vol. 8, no 6, p. e1002775-Article in journal (Refereed) Published
    Abstract [en]

    Rose-comb, a classical monogenic trait of chickens, is characterized by a drastically altered comb morphology compared to the single-combed wild-type. Here we show that Rose-comb is caused by a 7.4 Mb inversion on chromosome 7 and that a second Rose-comb allele arose by unequal crossing over between a Rose-comb and wild-type chromosome. The comb phenotype is caused by the relocalization of the MNR2 homeodomain protein gene leading to transient ectopic expression of MNR2 during comb development. We also provide a molecular explanation for the first example of epistatic interaction reported by Bateson and Punnett 104 years ago, namely that walnut-comb is caused by the combined effects of the Rose-comb and Pea-comb alleles. Transient ectopic expression of MNR2 and SOX5 (causing the Pea-comb phenotype) occurs in the same population of mesenchymal cells and with at least partially overlapping expression in individual cells in the comb primordium. Rose-comb has pleiotropic effects, as homozygosity in males has been associated with poor sperm motility. We postulate that this is caused by the disruption of the CCDC108 gene located at one of the inversion breakpoints. CCDC108 is a poorly characterized protein, but it contains a MSP (major sperm protein) domain and is expressed in testis. The study illustrates several characteristic features of the genetic diversity present in domestic animals, including the evolution of alleles by two or more consecutive mutations and the fact that structural changes have contributed to fast phenotypic evolution.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-178136 (URN)10.1371/journal.pgen.1002775 (DOI)000305961000037 ()
    Available from: 2012-07-30 Created: 2012-07-30 Last updated: 2015-10-01Bibliographically approved
    2. Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses
    Open this publication in new window or tab >>Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses
    Show others...
    2012 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 365-Article in journal (Refereed) Published
    Abstract [en]

    Background: Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation.

    Results: We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the similar to 350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present.

    Conclusions: These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.

    Keywords
    STX17, Melanoma, Hair greying, Copy number variation, Melanocytes
    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-183233 (URN)10.1186/1471-2164-13-365 (DOI)000308940000001 ()
    Available from: 2012-10-25 Created: 2012-10-23 Last updated: 2017-12-07Bibliographically approved
    3. Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses
    Open this publication in new window or tab >>Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation underlying Dun camouflage colour in horses
    Show others...
    2016 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 2, p. 152-158Article in journal (Refereed) Published
    Abstract [en]

    Dun is a wild-type coat color in horses characterized by pigment dilution with a striking pattern of dark areas termed primitive markings. Here we show that pigment dilution in Dun horses is due to radially asymmetric deposition of pigment in the growing hair caused by localized expression of the T-box 3 (TBX3) transcription factor in hair follicles, which in turn determines the distribution of hair follicle melanocytes. Most domestic horses are non-dun, a more intensely pigmented phenotype caused by regulatory mutations impairing TBX3 expression in the hair follicle, resulting in a more circumferential distribution of melanocytes and pigment granules in individual hairs. We identified two different alleles (non-dun1 and non-dun2) causing non-dun color. non-dun2 is a recently derived allele, whereas the Dun and non-dun1 alleles are found in ancient horse DNA, demonstrating that this polymorphism predates horse domestication. These findings uncover a new developmental role for T-box genes and new aspects of hair follicle biology and pigmentation.

    National Category
    Genetics Cell Biology
    Identifiers
    urn:nbn:se:uu:diva-254473 (URN)10.1038/ng.3475 (DOI)000369043900012 ()26691985 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationNIH (National Institute of Health)Swedish Research Council, 80576801Swedish Research Council, 70374401Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
    Available from: 2015-08-10 Created: 2015-06-08 Last updated: 2017-12-04Bibliographically approved
  • 9.
    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.

  • 10.
    Karlgren, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic Control of Annual Growth Rhythm in the Conifer Norway Spruce (Picea Abies L. Karst)2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Norway spruce (Picea abies L. Karst) is a conifer belonging to the group gymnosperms and is an ecologically and economically important species in several parts of Europe. It is crucial for trees like Norway spruce to adapt timing of events such as bud set and growth cessation to the local environment in order to maximize the growth period while avoiding frost damage.

    This thesis aims at widening the knowledge about genetic control of annual growth rhythm in Norway spruce and particularly the control of bud set. Using spruce transformants ectopically expressing PaFT/TFL1-LIKE 2 (PaFTL2) the prior hypothesis that PaFTL2 induces bud set is confirmed. This is further supported by spatial and temporal expression patterns in seedlings and adult trees. It is further shown that gymnosperms possess at least two FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like genes with TFL1-like function, suggesting the ancestor of FT and TFL1 to be more TFL1-like. PaFTL1 appears to have complementary expression patterns to that of PaFTL2 both spatially and temporally indicating they may act together to control growth in Norway spruce.

    Since bud set is controlled by photoperiod and circadian clock genes are implicated in this process, putative clock homologs were studied to gain insight into the circadian clock in gymnosperms. Several clock homologs were identified and their expression showed a diurnal pattern but the expression was rapidly damped in constant conditions. Transgenic Arabidopsis expressing putative core clock genes from spruce indicate that at least three genes, PaCCA1, PaGI and PaZTL, appear to have a conserved function between angiosperms and gymnosperms. Taken together these results suggest that gymnosperms have a similar core clock structure as angiosperms even though fundamental differences might exist since the cycling of the clock genes were rapidly damped in free-running conditions.

    The studies presented in this thesis support substantial conservation of pathway components controlling photoperiodic responses in angiosperms and gymnosperms and identify PaFTL2 as a component of growth rhythm control. However, important changes in these processes are also evident. The results provide a solid basis for future research on molecular mechanisms controlling an adaptive trait in an important non-model organism.

    List of papers
    1. Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution
    Open this publication in new window or tab >>Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution
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    2011 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 156, no 4, p. 1967-1977Article in journal (Refereed) Published
    Abstract [en]

    The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-157251 (URN)10.1104/pp.111.176206 (DOI)000293568800025 ()
    Available from: 2011-08-25 Created: 2011-08-22 Last updated: 2017-12-08Bibliographically approved
    2. FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce
    Open this publication in new window or tab >>FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce
    2013 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 163, no 2, p. 792-803Article in journal (Refereed) Published
    Abstract [en]

    The timing of bud set, as one determinant of the annual growth rhythm, is critical for local adaptation of the conifer Norway spruce (Picea abies). Previous gene expression and population genetic studies have suggested a role for P. abies FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (PaFTL2) in the control of growth cessation and bud set in Norway spruce as well as in local adaptation resulting in clinal variation for timing of bud set. Using transgenic plants with PaFTL2 driven by an inducible promoter, we found that PaFTL2 indeed induces bud set and most probably also growth cessation. PaFTL2 shows high expression around the procambium and vascular tissue and in the crown region in buds of both seedlings and older trees. Furthermore, PaFTL2 expression is induced in vegetative shoots and all bud types in late summer, when growth cessation occurs. This supports the notion that PaFTL2 is involved in growth cessation. A close paralog to PaFTL2, PaFTL1, is strongly expressed in meristems during the summer, possibly to repress meristem activity and the formation of needle primordia during this period. The temporal and spatial expression of PaFTL1 and PaFTL2 largely complement each other, which suggests that they act in concert to control perennial growth in Norway spruce.

    Keywords
    bud set, Picea abies, transformants, FT/TFL1-like genes, growth cessation
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192123 (URN)10.1104/pp.113.224139 (DOI)000325554100031 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
    3. No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)
    Open this publication in new window or tab >>No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)
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    2014 (English)In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 55, no 3, p. 535-550Article in journal (Refereed) Published
    Keywords
    Picea abies, circadian clock, diurnal cycling, phylogeny, gene expression, delayed fluorescence
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192178 (URN)10.1093/pcp/pct199 (DOI)000333096200007 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
    4. Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)
    Open this publication in new window or tab >>Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)
    2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 3, p. e60110-Article in journal (Refereed) Published
    Abstract [en]

    From studies of the circadian clock in the plant model species Arabidopsis (Arabidopsis thaliana), a number of important properties and components have emerged. These include the genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB EXPRESSION 1 (TOC1 also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)) that via gene expression feedback loops participate in the circadian clock. Here, we present results from ectopic expression of four Norway spruce (Picea abies) putative homologs (PaCCA1, PaGI, PaZTL and PaPRR1) in Arabidopsis, their flowering time, circadian period length, red light response phenotypes and their effect on endogenous clock genes were assessed. For PaCCA1-ox and PaZTL-ox the results were consistent with Arabidopsis lines overexpressing the corresponding Arabidopsis genes. For PaGI consistent results were obtained when expressed in the gi2 mutant, while PaGI and PaPRR1 expressed in wild type did not display the expected phenotypes. These results suggest that protein function of PaCCA1, PaGI and PaZTL are at least partlyconserved compared to Arabidopsis homologs, however further studies are needed to reveal the protein function of PaPRR1. Our data suggest that components of thethree-loop network typical of the circadian clock in angiosperms were present beforethe split of gymnosperms and angiosperms.

    Keywords
    circadian clock, Picea abies (Norway spruce), transformants, gymnosperm, ZEITLUPE (ZTL), GIGANTEA (GI), TIMING OF CAB1 (TOC1 or PRR1), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192151 (URN)10.1371/journal.pone.0060110 (DOI)000317262200084 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
  • 11.
    Lamichhaney, Sangeet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    The genetic basis for adaptation in natural populations2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many previous studies in evolutionary genetics have been based on few model organisms that can be reared at ease in the laboratory. In contrast, genetic studies of non-model, natural populations are desirable as they provide a wider range of adaptive phenotypes throughout evolutionary timescales and allow a more realistic understanding of how natural selection drives adaptive evolution. This thesis represents an example of how modern genomic tools can be effectively used to study adaptation in natural populations.

    Atlantic herring is one of the world’s most numerous fish having multiple populations with phenotypic differences adapted to strikingly different environments. Our study demonstrated insignificant level of genetic drift in herring that resulted in minute genetic differences in the majority of the genome among these populations. In contrast, a small percentage of the loci showed striking genetic differentiation that were potentially under natural selection. We identified loci associated with adaptation to the Baltic Sea and with seasonal reproduction (spring- and autumn-spawning) and demonstrated that ecological adaptation in Atlantic herring is highly polygenic but controlled by a finite number of loci.

    The study of Darwin’s finches constitutes a breakthrough in characterizing their evolution. We identified two loci, ALX1 and HMGA2, which most likely are the two most prominent loci that contributed to beak diversification and thereby to expanded food utilization. These loci have played a key role in adaptive evolution of Darwin’s finches. Our study also demonstrated that interspecies gene flow played a significant role in the radiation of Darwin’s finches and some species have a mixed ancestry.

    This thesis also explored the genetic basis for the remarkable phenotypic differences between three male morphs in the ruff. Identification of two different versions of a 4.5 MB inversion in Satellites and Faeders that occurred about 4 million years ago revealed clues about the genetic foundation of male mating strategies in ruff. We highlighted two genes in the inverted region; HSD17B2 that affects metabolism of testosterone and MC1R that has a key role in regulating pigmentation, as the major loci associated with this adaptation.

    List of papers
    1. Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
    Open this publication in new window or tab >>Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring
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    2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 47, p. 19345-19350Article in journal (Refereed) Published
    Abstract [en]

    The Atlantic herring (Clupea harengus), one of the most abundant marine fishes in the world, has historically been a critical food source in Northern Europe. It is one of the few marine species that can reproduce throughout the brackish salinity gradient of the Baltic Sea. Previous studies based on few genetic markers have revealed a conspicuous lack of genetic differentiation between geographic regions, consistent with huge population sizes and minute genetic drift. Here, we present a cost-effective genome-wide study in a species that lacks a genome sequence. We first assembled amuscle transcriptome and then aligned genomic reads to the transcripts, creating an "exome assembly," capturing both exons and flanking sequences. We then resequenced pools of fish from a wide geographic range, including the Northeast Atlantic, as well as different regions in the Baltic Sea, aligned the reads to the exome assembly, and identified 440,817 SNPs. The great majority of SNPs showed no appreciable differences in allele frequency among populations; however, several thousand SNPs showed striking differences, some approaching fixation for different alleles. The contrast between low genetic differentiation at most loci and striking differences at others implies that the latter category primarily reflects natural selection. A simulation study confirmed that the distribution of the fixation index F-ST deviated significantly from expectation for selectively neutral loci. This study provides insights concerning the population structure of an important marine fish and establishes the Atlantic herring as a model for population genetic studies of adaptation and natural selection.

    Keywords
    Baltic herring, genetics, population biology
    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-191049 (URN)10.1073/pnas.1216128109 (DOI)000311997200067 ()
    Available from: 2013-01-09 Created: 2013-01-09 Last updated: 2017-12-06Bibliographically approved
    2. The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
    Open this publication in new window or tab >>The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
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    2016 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed) Published
    Abstract [en]

    Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

    National Category
    Genetics and Breeding Evolutionary Biology Genetics Fish and Aquacultural Science
    Identifiers
    urn:nbn:se:uu:diva-279967 (URN)10.7554/eLife.12081 (DOI)000387459700001 ()27138043 (PubMedID)
    Funder
    EU, European Research CouncilSwedish Research Council FormasKnut and Alice Wallenberg Foundation
    Note

    Alvaro Martinez Barrio, Sangeet Lamichhaney, Guangyi Fan and Nima Rafati contributed equally to this work.

    Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-11-29Bibliographically approved
    3. Evolution of Darwin's finches and their beaks revealed by genome sequencing
    Open this publication in new window or tab >>Evolution of Darwin's finches and their beaks revealed by genome sequencing
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    2015 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 518, no 7539Article in journal (Refereed) Published
    Abstract [en]

    Darwin's finches, inhabiting the Galapagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives' Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial. development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis) a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and thereby, to an expanded utilization of food resources.

    National Category
    Medical Genetics Microbiology in the medical area
    Identifiers
    urn:nbn:se:uu:diva-247384 (URN)10.1038/nature14181 (DOI)000349547400036 ()25686609 (PubMedID)
    Available from: 2015-03-20 Created: 2015-03-18 Last updated: 2018-01-11Bibliographically approved
    4. A beak size locus in Darwin’s finches facilitated character displacement during a drought
    Open this publication in new window or tab >>A beak size locus in Darwin’s finches facilitated character displacement during a drought
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    2016 (English)In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed) Published
    Abstract [en]

    Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

    National Category
    Genetics and Breeding
    Identifiers
    urn:nbn:se:uu:diva-279968 (URN)10.1126/science.aad8786 (DOI)000374479700050 ()27102486 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 80576801Swedish Research Council, 70374401
    Available from: 2016-03-06 Created: 2016-03-06 Last updated: 2017-11-30Bibliographically approved
    5. Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
    Open this publication in new window or tab >>Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax)
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    2016 (English)In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 1, p. 84-+Article in journal (Refereed) Published
    Abstract [en]

    The ruff is a Palearctic wader with a spectacular lekking behavior where highly ornamented males compete for females(1-4). This bird has one of the most remarkable mating systems in the animal kingdom, comprising three different male morphs (independents, satellites and faeders) that differ in behavior, plumage color and body size. Remarkably, the satellite and faeder morphs are controlled by dominant alleles(5,6). Here we have used whole-genome sequencing and resolved the enigma of how such complex phenotypic differences can have a simple genetic basis. The Satellite and Faeder alleles are both associated with a 4.5-Mb inversion that occurred about 3.8 million years ago. We propose an evolutionary scenario where the Satellite chromosome arose by a rare recombination event about 500,000 years ago. The ruff mating system is the result of an evolutionary process in which multiple genetic changes contributing to phenotypic differences between morphs have accumulated within the inverted region.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-274919 (URN)10.1038/ng.3430 (DOI)000367255300018 ()26569123 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council, 1989-2546Swedish Research Council, 1992-2685Swedish Research Council, 2013-5418Swedish Research Council, 2001-6005Swedish Research Council, 80576801Swedish Research Council, 70374401
    Available from: 2016-01-27 Created: 2016-01-26 Last updated: 2017-11-30Bibliographically approved
  • 12.
    Lamichhaney, Sangeet
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Han, Fan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Berglund, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wang, Chao
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sällman Almen, Markus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    T. Webster, Matthew
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Grant, B. Rosemary
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA..
    R. Grant, Peter
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    A beak size locus in Darwin’s finches facilitated character displacement during a drought2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed)
    Abstract [en]

    Ecological character displacement is a process of morphological divergence that reducescompetition for limited resources. We used genomic analysis to investigate the geneticbasis of a documented character displacement event in Darwin’s finches on Daphne Majorin the Galápagos Islands: The medium ground finch diverged from its competitor, the largeground finch, during a severe drought. We discovered a genomic region containing theHMGA2gene that varies systematically among Darwin’s finch species with different beaksizes. Two haplotypes that diverged early in the radiation were involved in the characterdisplacement event: Genotypes associated with large beak size were at a strong selectivedisadvantage in medium ground finches (selection coefficients= 0.59). Thus, a majorlocus has apparently facilitated a rapid ecological diversification in the adaptive radiationof Darwin’s finches.

  • 13.
    Martínez Barrio, Álvaro
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lamichhaney, Sangeet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fan, Guangyi
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; BGI-Shenzhen, Shenzen, China; 5 College of Physics, Qingdao University, Qingdao, China .
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zhang, He
    BGI-Shenzhen, Shenzen, China; College of Physics, Qingdao University, Qingdao, China.
    Dainat, Jacques
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ekman, Diana
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Höppner, Marc P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martin, Marcel
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liu, Xin
    BGI-Shenzhen, Shenzen, China.
    Chen, Wenbin
    BGI-Shenzhen, Shenzhen, China.
    Liang, Xinming
    BGI-Shenzhen, Shenzhen, China.
    Shi, Chengcheng
    BGI-Shenzhen, Shenzhen, China.
    Fu, Yuanyuan
    BGI-Shenzhen, Shenzhen, China.
    Ma, Kailong
    BGI-Shenzhen, Shenzhen, China.
    Zhan, Xiao
    BGI-Shenzhen, Shenzhen, China.
    Feng, Chungang
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gustafson, Ulla
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sällman Almén, Markus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Blass, Martina
    Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden.
    Casini, Michele
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research.
    Folkvord, Arild
    Department of Biology, University of Bergen, Bergen, Norway; Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway; Institute of Marine Research, Bergen, Norway .
    Laikre, Linda
    Department of Zoology, Stockholm University.
    Ryman, Nils
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Lee, Simon Ming-Yuen Lee
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao.
    Xu, Xun
    BGI-Shenzhen, Shenzhen, China.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States.
    The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed)
    Abstract [en]

    Ecological adaptation is of major relevance to speciation and sustainable population management, but the underlying genetic factors are typically hard to study in natural populations due to genetic differentiation caused by natural selection being confounded with genetic drift in subdivided populations. Here, we use whole genome population sequencing of Atlantic and Baltic herring to reveal the underlying genetic architecture at an unprecedented detailed resolution for both adaptation to a new niche environment and timing of reproduction. We identify almost 500 independent loci associated with a recent niche expansion from marine (Atlantic Ocean) to brackish waters (Baltic Sea), and more than 100 independent loci showing genetic differentiation between spring- and autumn-spawning populations irrespective of geographic origin. Our results show that both coding and non-coding changes contribute to adaptation. Haplotype blocks, often spanning multiple genes and maintained by selection, are associated with genetic differentiation.

  • 14.
    Moritz, Kim K.
    et al.
    Swedish Univ Agr Sci, Dept Ecol, POB 7044, SE-75007 Uppsala, Sweden..
    Bjorkman, Christer
    Swedish Univ Agr Sci, Dept Ecol, POB 7044, SE-75007 Uppsala, Sweden..
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stenberg, Johan A.
    Swedish Univ Agr Sci, Dept Plant Protect Biol, Alnarp, Sweden..
    Plant sex effects on insect herbivores and biological control in a Short Rotation Coppice willow2017In: Biological control (Print), ISSN 1049-9644, E-ISSN 1090-2112, Vol. 115, p. 30-36Article in journal (Refereed)
    Abstract [en]

    In the wild, plant sex can affect plant-herbivore interactions and higher trophic levels, including natural enemies of the herbivores. However, the possibility of manipulating plant sex to improve biological control and reduce herbivory in domesticated dioecious crops remains unexplored. The dioecious bioenergy crop, Salix viminalis, is often planted in monoclonal, and thus monosexual, fields. We investigated whether using plant clones of either sex, or mixing plants of both sexes, reduced the performance and abundance of the herbivorous pest insect Phratora vulgatissima and its main natural enemy, Anthocoris nemorum, and whether predation was affected. The herbivore laid more eggs, and the predator survived longer, on female plants in the lab. However, these effects did not translate into differences in predation rates in laboratory experiments or differential insect abundances on plants of either sex or plantation sex composition in the field. Plant genotype did have a significant effect on insect abundances, but this was due to plant traits other than sex. The results indicate that manipulating plant sex will not lead to improved biological control or reduced insect herbivory in S. viminalis energy forestry, but suggest that a focus on plant genotypic differences offers promise for improving management practices.

  • 15. Nahalka, J
    et al.
    Nahalkova, Jarmila
    Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta, Bratislava, Slovak-Republic.
    Gemeiner, P
    Blanarik, P
    Elicitation of plumbagin by chitin and its release into the medium in Drosophyllum lusitanicum Link. suspension cultures1998In: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 20, no 9, p. 841-845Article in journal (Refereed)
    Abstract [en]

    Polysaccharides (chitin/pectin) that are involved in the interactions between plants and microorganisms were applied to the cultured cells of Drosophyllum lusitanicum. In the case of chitin addition, elicitation and crystallization of plumbagin in the medium were observed. N-Acetylchitooligosaccharides smaller than heptamers [(GlcNAc)(n) (n<7)] elicited the biosynthesis of plumbagin but did not increase the hypersensitive response (HR). On the other hand, carboxymethylchitin (DP similar to 200) led to the accumulation of plumbagin in cells and to HR death as well as to the lysis of the cells and release of plumbagin into the medium. The response of cultured cells to the N-Acetylchitosaccharides varied depending on the chemo/physiological conditions of the cells. Addition of pectin (1 g/l) resulted in enhanced HR and decreased biosynthesis of plumbagin.

  • 16. Nahalkova, J
    et al.
    Chrtiansky, J
    Hrib, J
    Vookova, B
    Gemeiner, P
    Hajduch, M
    Lectin-like and antifungal activity of protein body proteins from Pinus nigra seeds1996In: Chemické listy (Print), ISSN 0009-2770, E-ISSN 1213-7103, Vol. 90, no 9, p. 698-699Article in journal (Refereed)
  • 17. Olivain, C
    et al.
    Humbert, C
    Nahalkova, Jarmila
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Molecular Evolution.
    Fatehi, J
    L'Haridon, F
    Alabouvette, C
    Colonization of tomato root by pathogenic and nonpathogenic Fusarium oxysporum strains inoculated together and separately into the soil2006In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 72, no 2, p. 1523-1531Article in journal (Refereed)
    Abstract [en]

    In soil, fungal colonization of plant roots has been traditionally studied by indirect methods such as microbial isolation that do not enable direct observation of infection sites or of interactions between fungal pathogens and their antagonists. Confocal laser scanning microscopy was used to visualize the colonization of tomato roots in heat-treated soil and to observe the interactions between a nonpathogenic strain, Fo47, and a pathogenic strain, Fo18, inoculated onto tomato roots in soil. When inoculated separately, both fungi colonized the entire root surface, with the exception of the apical zone. When both strains were introduced together, they both colonized the root surface and were observed at the same locations. When Fo47 was introduced at a higher concentration than Fo18, it colonized much of the root surface, but hyphae of Fo18 could still be observed at the same location on the root. There was no exclusion of the pathogenic strain by the presence of the nonpathogenic strain. These results are not consistent with the hypothesis that specific infection sites exist on the root for Fusarium oxysporum and instead support the hypothesis that competition occurs for nutrients rather than for infection sites.

  • 18.
    Palmqvist, N. G. Martin
    et al.
    Swedish University Agricultural Sciences, Department of Chemistry and Biotechnology.
    Seisenbaeva, Gulaim A.
    Swedish University Agricultural Sciences, Department of Chemistry and Biotechnology.
    Svedlindh, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Kessler, Vadim G.
    Swedish University Agricultural Sciences, Department of Chemistry and Biotechnology.
    Maghemite Nanoparticles Acts as Nanozymes, Improving Growth and Abiotic Stress Tolerance in Brassica napus2017In: Nanoscale Research Letters, ISSN 1931-7573, E-ISSN 1556-276X, Vol. 12, article id 631Article in journal (Refereed)
    Abstract [en]

    Yttrium doping-stabilized γ-Fe2O3 nanoparticles were studied for its potential to serve as a plant fertilizer and, through enzymatic activity, support drought stress management. Levels of both hydrogen peroxide and lipid peroxidation, after drought, were reduced when γ-Fe2O3 nanoparticles were delivered by irrigation in a nutrient solution to Brassica napus plants grown in soil. Hydrogen peroxide was reduced from 151 to 83 μM g−1 compared to control, and the malondialdehyde formation was reduced from 36 to 26 mM g−1. Growth rate of leaves was enhanced from 33 to 50% growth compared to fully fertilized plants and SPAD-measurements of chlorophyll increased from 47 to 52 suggesting improved agronomic properties by use of γ-Fe2O3 nanoparticles as fertilizer as compared to chelated iron.

  • 19.
    Park, Sungkyu
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Yoo, Ki-Oug
    Kangwon National University, Department of Biological Sciencesi.
    Marcussen, Thomas
    University of Oslo, Centre for Ecological and Evolutionary Synthesis, Department of Biosciences.
    Backlund, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Jacobsson, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Rosengren, K. Johan
    The University of Queensland, School of Biomedical Sciences.
    Doo, Inseok
    Dong-A Pharm Co Ltd, Biotech Research Center, Biotech Research Team.
    Göransson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola)2017In: Frontiers in Plant Science, ISSN 1664-462X, E-ISSN 1664-462X, Vol. 8, article id 2058Article in journal (Refereed)
    Abstract [en]

    Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species). Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.

  • 20.
    Seroussi, Eyal
    et al.
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Cinnamon, Yuval
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Yosefi, Sara
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Genin, Olga
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Smith, Julia Gage
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bornelöv, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    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, SE-75007 Uppsala, Sweden.;Texas A&M Univ, Dept Vet Integrat Biosci, Coll Vet Med & Biomed Sci, College Stn, TX 77843 USA..
    Friedman-Einat, Miriam
    Agr Res Org, Volcani Ctr, IL-50250 Bet Dagan, Israel..
    Identification of the Long-Sought Leptin in Chicken and Duck: Expression Pattern of the Highly GC-Rich Avian leptin Fits an Autocrine/Paracrine Rather Than Endocrine Function2016In: Endocrinology, ISSN 0013-7227, E-ISSN 1945-7170, Vol. 157, no 2, p. 737-751Article in journal (Refereed)
    Abstract [en]

    More than 20 years after characterization of the key regulator of mammalian energy balance, leptin, we identified the leptin (LEP) genes of chicken (Gallus gallus) and duck (Anas platyrhynchos). The extreme guanine-cytosine content (similar to 70%), the location in a genomic region with low-complexity repetitive and palindromic sequence elements, the relatively low sequence conservation, and low level of expression have hampered the identification of these genes until now. In vitro-expressed chicken and duck leptins specifically activated signaling through the chicken leptin receptor in cell culture. In situ hybridization demonstrated expression of LEP mRNA in granular and Purkinje cells of the cerebellum, anterior pituitary, and in embryonic limb buds, somites, and branchial arches, suggesting roles in adult brain control of energy balance and during embryonic development. The expression patterns of LEP and the leptin receptor (LEPR) were explored in chicken, duck, and quail (Coturnix japonica) using RNA-sequencing experiments available in the Short Read Archive and by quantitative RT-PCR. In adipose tissue, LEP and LEPR were scarcely transcribed, and the expression level was not correlated to adiposity. Our identification of the leptin genes in chicken and duck genomes resolves a long lasting controversy regarding the existence of leptin genes in these species. This identification was confirmed by sequence and structural similarity, conserved exon-intron boundaries, detection in numerous genomic, and transcriptomic datasets and characterization by PCR, quantitative RT-PCR, in situ hybridization, and bioassays. Our results point to an autocrine/paracrine mode of action for bird leptin instead of being a circulating hormone as in mammals.

  • 21.
    Sharwood, Robert
    et al.
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Ghannoum, Oula
    Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia.; Univ Western Sydney, Hawkesbury Inst Environm, Richmond, NSW 2753, Australia..
    Kapralov, Maxim
    Liverpool John Moores Univ, Sch Nat Sci & Psychol, Liverpool L3 3AF, Merseyside, England..
    Gunn, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia..
    Whitney, Spencer
    Australian Natl Univ, Res Sch Biol, Canberra, ACT 2601, Australia.; Australian Natl Univ, ARC Ctr Excellence Translat Photosynthesis, Canberra, ACT 2601, Australia..
    Temperature responses of Rubisco from Paniceae grasses provide opportunities for improving C3 photosynthesis2016In: Nature Plants, ISSN 2055-0278, Vol. 2, no 12, article id 16186Article in journal (Refereed)
    Abstract [en]

    Enhancing the catalytic properties of the CO2-fixing enzyme Rubisco is a target for improving agricultural crop productivity. Here, we reveal extensive diversity in the kinetic response between 10 and 37 °C by Rubisco from C3 and C4 species within the grass tribe Paniceae. The CO2 fixation rate (kccat) for Rubisco from the C4 grasses with nicotinamide adenine dinucleotide (NAD) phosphate malic enzyme (NADP-ME) and phosphoenolpyruvate carboxykinase (PCK) photosynthetic pathways was twofold greater than the kccat of Rubisco from NAD-ME species across all temperatures. The declining response of CO2/O2 specificity with increasing temperature was less pronounced for PCK and NADP-ME Rubisco, which would be advantageous in warmer climates relative to the NAD-ME grasses. Modelled variation in the temperature kinetics of Paniceae C3 Rubisco and PCK Rubisco differentially stimulated C3 photosynthesis relative to tobacco above and below 25 °C under current and elevated CO2. Amino acid substitutions in the large subunit that could account for the catalytic variation among Paniceae Rubisco are identified; however, incompatibilities with Paniceae Rubisco biogenesis in tobacco hindered their mutagenic testing by chloroplast transformation. Circumventing these bioengineering limitations is critical to tailoring the properties of crop Rubisco to suit future climates.

  • 22.
    Silva, C. N. S.
    et al.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;James Cook Univ, Coll Marine & Environm Sci, Ctr Sustainable Trop Fisheries & Aquaculture, Townsville, Qld, Australia.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hagen, I. J.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronnegard, L.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Dalarna Univ, Sch Technol & Business Studies, Falun, Sweden.
    Billing, A. M.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kvalnes, T.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kemppainen, P.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronning, B.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ringsby, T. H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Saether, B-E
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jensen, H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Husby, A.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Insights into the genetic architecture of morphological traits in two passerine bird species2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, no 3, p. 197-205Article in journal (Refereed)
    Abstract [en]

    Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict evolutionary dynamics. The number of causal loci, magnitude of the effects and location in the genome are, however, still largely unknown. Here, we use genome-wide single-nucleotide polymorphism (SNP) data from two large-scale data sets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared with collared flycatchers, as expected given marker density (6348 SNPs in house sparrows versus 38 689 SNPs in collared flycatchers). Indeed, after downsampling to similar SNP density and sample size, this estimate was no longer markedly different between species. Chromosome-partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small-effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (V-P), and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of V-P). Although we cannot exclude the possibility of undetected large-effect loci, our results indicate a polygenic basis for morphological traits.

  • 23. Sorahinobar, Mona
    et al.
    Niknam, Vahid
    Ebrahimzadeh, Hassan
    Soltanloo, Hassan
    Moradi, Babak
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lack of association between Fusarium graminearum resistance in spike and crude extract tolerance in seedling of wheat2016In: European journal of plant pathology, ISSN 0929-1873, E-ISSN 1573-8469, Vol. 144, no 3, p. 525-538Article in journal (Refereed)
    Abstract [en]

    Fusarium graminearum is a hemibiotrophic plant fungal pathogen that causes head and seedling blight in wheat and other cereals; however little is known about the mechanisms involved in its pathogenicity. To examine the role of pathogen metabolites in pathogenecity, we studied the effects of F. graminearum crude extract on physiological and morphological responses of Falat and Sumai3, as respectively susceptible and resistant wheat cultivars to Fusarium head blight (FHB). Our results showed that seed germination, seedling growth and coleoptile cell development were highly affected by the pathogen crude extract in both cultivars, with Sumai3 growth being more affected than Falat. These results show little correspondence between wheat seedling tolerance to F. graminearumcrude extract and resistance to FHB. Crude extract treatment resulted in significant increase of hydrogen peroxide (H2O2) and malondialdehyde (MDA) content in both cultivars which indicated an oxidative stress. Differential antioxidative responses to crude extract was observed; as activity of polyphenol oxidase (PPO), superoxide dismutase (SOD) and ascorbate peroxidases (APX) increased in Falat and decreased in Sumai3. In addition, a greater phenylalanine ammonia-lyase (PAL) activity was observed in treated seedlings of both cultivars. Quantitative Real- time PCR analysis showed that PAL gene expression in Falat was induced about 4 folds higher than Sumai3 under treatment. Taken together, our data suggest that a better employment of enzymatic and none enzymatic antioxidative systems in Falat could explain its higher degree of tolerance compared with Sumai3.

  • 24.
    Sundström, Elisabeth
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Imsland, Freyja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mikko, Sofia
    Wade, Claire
    Sigurdsson, Snaevar
    Pielberg, Gerli R
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Golovko, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Curik, Ino
    Seltenhammer, Monika H.
    Soelkner, Johann
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 365-Article in journal (Refereed)
    Abstract [en]

    Background: Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation.

    Results: We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the similar to 350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present.

    Conclusions: These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.

  • 25.
    Sutherland, D. A. T.
    et al.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Honaker, C. F.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Dorshorst, B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Siegel, P. B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Asymmetries, heterosis, and phenotypic profiles of red junglefowl, White Plymouth Rocks, and F-1 and F-2 reciprocal crosses2018In: Journal of Applied Genetics, ISSN 1234-1983, E-ISSN 2190-3883, Vol. 59, no 2, p. 193-201Article in journal (Refereed)
    Abstract [en]

    During the domestication of farm animals, humans have manipulated genetic variation for growth and reproduction through artificial selection. Here, data are presented for growth, reproductive, and behavior traits for the red junglefowl, a line of White Plymouth Rock chickens, and their F-1 and F-2 reciprocal crosses. Intra- and intergenerational comparisons for growth related traits reflected considerable additive genetic variation. In contrast, those traits associated with reproduction exhibited heterosis. The role of sexual selection was seen in the evolution of prominent secondary sexual ornaments that lend to female choice and male-male competition. The large differences between parental lines in fearfulness to humans were only mitigated slightly in the intercross generations. Whereas, overall F-1 generation heterosis was not transferred to the F-2, there was developmental stability in the F-2, as measured by relative asymmetry of bilateral traits. Through multigenerational analyses between the red junglefowl and the domestic White Plymouth Rocks, we observed plasticity and considerable residual genetic variation. These factors likely facilitated the adaptability of the chicken to a broad range of husbandry practices throughout the world.

  • 26.
    Sutherland, Dez-Ann Antoinette Therese
    et al.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Honaker, Christa Ferst
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Dorshorst, Ben
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Brisbin, I. Lehr, Jr.
    Univ Georgia, Savannah River Ecol Lab, Odum Sch Ecol, Aiken, SC USA.
    Siegel, Paul B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Growth patterns for three generations of an intercross between red junglefowl and chickens selected for low body weight2018In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 135, no 4, p. 300-310Article in journal (Refereed)
    Abstract [en]

    Growth is a complex and dynamic process that may be measured at a specific point or over a period of time. Compared was the growth of male and female chickens over a three-generation period. Involved were red junglefowl (RJF; Gallus gallus), a line of White Plymouth Rock chickens (LWS; Gallus gallus domesticus) selected for low body weight, and their reciprocal F-1 and F-2 crosses. In both sexes, Gompertz's description of growth showed that RJF had significantly lower asymptotes, earlier inflection points, and faster growth rates than LWS. Heterosis for these measures was positive for asymptote and negative for growth rate and inflection point. The RJF commenced egg production at a significantly younger age and lower body weight than LWS. Although F-1 and F-2 reciprocal crosses were similar for body weight and for age at first egg, the F-1 reciprocal crosses began lay at significantly younger ages than the F-2 crosses and parental lines. When viewed on a physiological basis where age and body weight were simultaneously standardized, both parental lines and reciprocal F-1 and F-2 crosses had differing rapid and lag growth phases. Overall, sexual dimorphism increased in all populations from hatch to sexual maturity. The LWS males had a longer growth period consistent with their female counterparts who became sexually mature at older ages. Comprehensively, these results indicate additive and nonadditive genetic variation for distinct growth patterns and changes in resource allocation strategies over time.

  • 27.
    Tóth, Peter
    Slovak University of Agriculture, Nitra, Slovak Republic.
    27 Biological Control2012In: Sustainable Agriculture / [ed] Christine Jakobsson, Uppsala: Baltic University Press , 2012, 1500, p. 206-213Chapter in book (Other (popular science, discussion, etc.))
  • 28.
    Weston, David J.
    et al.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA; Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA.
    Turetsky, Merritt R.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Johnson, Matthew G.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX USA.
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lindo, Zoe
    Univ Western Ontario, Dept Biol, London, ON, Canada.
    Belyea, Lisa R.
    Queen Mary Univ London, Sch Geog, London, England.
    Rice, Steven K.
    Union Coll, Dept Biol Sci, Schenectady, NY USA.
    Hanson, David T.
    Univ New Mexico, Dept Biol, Albuquerque, NM USA.
    Engelhardt, Katharina A. M.
    Univ Maryland, Appalachian Lab, Ctr Environm Sci, Frostburg, MD USA.
    Schmutz, Jeremy
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA; Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
    Dorrepaal, Ellen
    Ume Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, Abisko, Sweden.
    Euskirchen, Eugenie S.
    Univ Alaska, Inst Arctic Biol, Fairbanks, AK USA.
    Stenoien, Hans K.
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Trondheim, Norway.
    Szovenyi, Peter
    Univ Zurich, Dept Systemat & Evolutionary Bot, Zurich, Switzerland.
    Jackson, Michelle
    Duke Univ, Dept Biol, Durham, NC USA.
    Piatkowski, Bryan T.
    Duke Univ, Dept Biol, Durham, NC USA.
    Muchero, Wellington
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Norby, Richard J.
    Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA ;Oak Ridge Natl Lab, Environm Sci Div, Oak Ridge, TN USA.
    Kostka, Joel E.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Glass, Jennifer B.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Limpens, Juul
    Wageningen Univ, Dept Environm Sci, Plant Ecol & Nat Conservat Grp, Wageningen, Netherlands.
    Tuittila, Eeva-Stiina
    Univ Eastern Finland, Sch Forest Sci, Peatland & Soil Ecol Grp, Joensuu, Finland.
    Ullrich, Kristian K.
    Max Planck Inst Evolutionary Biol, Plon, Germany.
    Carrell, Alyssa
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Benscoter, Brian W.
    Florida Atlantic Univ, Dept Biol Sci, Davie, FL USA.
    Chen, Jin-Gui
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Oke, Tobi A.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Nilsson, Mats B.
    Swedish Univ Agr Sci, Dept Forest Ecol & Management, Umeå, Sweden.
    Ranjan, Priya
    Univ Tennessee, Dept Plant Sci, Knoxville, TN USA.
    Jacobson, Daniel
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Lilleskov, Erik A.
    US Forest Serv, Res Stn, Houghton, MI USA.
    Clymo, R. S.
    Queen Mary Univ London, Sch Biol & Chem Sci, London, England.
    Shaw, A. Jonathan
    Duke Univ, Dept Biol, Durham, NC USA.
    The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 1, p. 16-25Article in journal (Other academic)
    Abstract [en]

    Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.

  • 29.
    Yusnizar, Y.
    et al.
    Bogor Agr Univ IPB, Grad Sch, Bogor 16680, Indonesia.;Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden.;Indonesian Inst Sci LIPI, Biotechnol Res Ctr, Cibinong 16912, Indonesia..
    Wilbe, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Herlino, A. O.
    Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Sumantri, C.
    Bogor Agr Univ IPB, Fac Anim Sci, Dept Anim Prod & Technol, Bogor 16680, Indonesia..
    Noor, R. Rachman
    Bogor Agr Univ IPB, Fac Anim Sci, Dept Anim Prod & Technol, Bogor 16680, Indonesia..
    Boediono, A.
    Bogor Agr Univ IPB, Fac Vet Med, Dept Anat Physiol & Pharmacol, Bogor 16680, Indonesia..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Andersson, G.
    Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Microphthalmia-associated transcription factor mutations are associated with white-spotted coat color in swamp buffalo2015In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 46, no 6, p. 676-682Article in journal (Refereed)
    Abstract [en]

    A candidate gene analysis of the microphthalmia-associated transcription factor (MITF) gene was used in an attempt to identify the genetic basis for a white-spotted coat color phenotype in the Asian swamp buffalo (Bubalus bubalis carabanensis). Ninety-three buffaloes32 solid, 38 spotted and 23 white individualswere Sanger-sequenced for all MITF exons as well as highly conserved intronic and flanking regions. MITFcDNA representing skin and iris tissue from six spotted, nine solid and one white buffaloes was also Sanger-sequenced to confirm detected mutations. Two independent loss-of-function mutations, a premature stop codon (c.328C>T, p.Arg110*) and a donor splice-site mutation (c.840+2T>A, p.Glu281_Leu282Ins8), both of which cause white-spotted coat color in swamp buffaloes, were identified. The nonsense mutation leads to a premature stop codon in exon 3, and likely removal of the resulting mRNA via nonsense-mediated decay pathway, whereas the donor splice-site mutation leads to aberrant splicing of exon 8 that encodes part of a highly conserved region of MITF. The resulting insertion of eight amino acid residues is expected to perturb the leucine zipper part in the basic helix-loop-helix leucine zipper (bHLH-Zip) domain and will most likely influence dimerization and DNA binding capacity. Electrophoretic mobility shift assay was performed using mutant and wild-type MITF proteins and showed that the mutant MITF protein resulting from the splice-site mutation decreased invitro DNA binding capacity compared to wild-type MITF. White-spotted buffalo bulls are sacrificed in funeral ceremonies in Tana Toraja, Indonesia, because they are considered holy, and our results show that genetic variation causes a tie to the cultural use of these buffaloes.

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