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  • 1.
    Androsiuk, P.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. University of Warmia & Mazury, Poland.
    Shimono, A.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Westin, J.
    Lindgren, D.
    Fries, A.
    Wang, X. -R
    Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden2013Inngår i: Silvae Genetica, ISSN 0037-5349, Vol. 62, nr 3, 127-136 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Efficient use of any breeding resources requires a good understanding of the genetic value of the founder breeding materials for predicting the gain and diversity in future generations. This study evaluates the distribution of genetic variation and level of relatedness among and within nine breeding populations of Norway spruce for Northern Sweden using nuclear microsatellite markers. A sample set of 456 individuals selected from 140 stands were genotyped with, 15 SSR loci. Over all loci each individual was identified with unique multilocus genotype. High genetic diversity (average H-e=0.820) and low population differentiation (F-ST = 0.0087) characterized this material. Although low in F-ST, the two northernmost populations were clustered as a distinct group diverged from the central populations. The population differentiation pattern corresponds well with the post glacial migration history of Norway spruce and the current gene flow and human activity in the region. The average inbreeding coefficient was 0.084 after removal loci with high frequency of null alleles. The estimated relatedness of the trees gathered in the breeding populations was very low (average kinship coefficient 0.0077) and not structured. The high genetic variation and low and not structured relatedness between individuals found in the breeding populations confirm that the Norway spruce breeding stock for northern Sweden represent valuable genetic resources for both long-term breeding and conservation programs.

  • 2.
    Atikuzzaman, Mohammad
    et al.
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Rubér, Marie
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Wright, Dominic
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköpings universitet, Institutionen för klinisk och experimentell medicin, Avdelningen för kliniska vetenskaper. Linköpings universitet, Medicinska fakulteten.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017Inngår i: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, 27-40 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The high egg-laying capacity of the modern domestic chicken (i.e. White Leghorn, WL) has arisen from the low egg-laying ancestor Red Junglefowl (RJF) via continuous trait selection and breeding. To investigate whether this long-term selection impacted the seminal fluid (SF)-proteome, 2DE electrophoresis-based proteomic analyses and immunoassays were conducted to map SF-proteins/cytokines in RJF, WL and a 9th generation Advanced Intercross Line (AIL) of RJF/WL-L13, including individual SF (n = 4, from each RJF, WL and AIL groups) and pools of the SF from 15 males of each group, analyzed by 2DE to determine their degree of intra-group (AIL, WL, and RJF) variability using Principal Component Analysis (PCA); respectively an inter-breed comparative analysis of intergroup fold change of specific SF protein spots intensity between breeds. The PCA clearly highlighted a clear intra-group similarity among individual roosters as well as a clear inter-group variability (e.g. between RJF, WL and AIL) validating the use of pools to minimize confounding individual variation. Protein expression varied considerably for processes related to sperm motility, nutrition, transport and survival in the female, including signaling towards immunomodulation. The major conserved SF-proteins were serum albumin and ovotransferrin. Aspartate aminotransferase, annexin A5, arginosuccinate synthase, glutathione S-transferase 2 and l-lactate dehydrogenase-A were RJF-specific. Glyceraldehyde-3-phosphate dehydrogenase appeared specific to the WL-SF while angiotensin-converting enzyme, γ-enolase, coagulation factor IX, fibrinogen α-chain, hemoglobin subunit α-D, lysozyme C, phosphoglycerate kinase, Src-substrate protein p85, tubulins and thioredoxin were AIL-specific. The RJF-SF contained fewer immune system process proteins and lower amounts of the anti-inflammatory/immunomodulatory TGF-β2 compared to WL and AIL, which had low levels- or lacked pro-inflammatory CXCL10 compared to RJF. The seminal fluid proteome differs between ancestor and modern chicken, with a clear enrichment of proteins and peptides related to immune-modulation for sperm survival in the female and fertility.

  • 3.
    Biswas, M. K.
    et al.
    Huazhong Agricultural University, China.
    Ahmed, M. B.
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    Mondal, M. A. A.
    University of Rajshahi, Bangladesh.
    Razvy, M. A.
    Huazhong Agricultural University, China.
    Hoque, A.
    University of Rajshahi, Bangladesh.
    Islam, R.
    University of Rajshahi, Bangladesh.
    Hossaina, M.
    University of Rajshahi, Bangladesh.
    Mandal, Abul
    Högskolan i Skövde, Institutionen för vård och natur. Högskolan i Skövde, Forskningscentrum för Systembiologi.
    In exploitation of genetic diversity in potato breeding2010Inngår i: Agronomski Glasnik (Agronomy Journal), ISSN 1848-8900, Vol. 72, nr 4-5, 261-276 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    With a view to select divergent parents genetic diversity was estimated among twenty genotypes. Thirty F1 progenies developed by line-tester mating were studied from seedling generation to first clonal generation for five important agronomic traits. Cluster analysis reveals that the parents could be grouped into seven different clusters. Cluster means showed wide range of variation for several traits among singles as well as multi genotypic clusters. Considering diversity pattern, parents should select from cluster I, III, IV, and V for the improvement of potato. Analysis of variance revealed that all most all the sources of variation were highly significant for all the studied traits in both generations. Parents Challisha, Lalpakri, Patnai, Chamak, Sadagoti, TPS-67 and TPS-364 were found to be good general combiners for tuber yield and yield contribution traits due to their gca effects. The sca effects showed that out of 30 hybrids 12 were found to have specific combining ability for tuber yield and those hybrids also exhibited considerable heterosis for tuber yield and yield contributing traits.

  • 4.
    Danielsson-Tham, Marie-Louise
    et al.
    Örebro universitet, Restaurang- och hotellhögskolan.
    Tham, WilhelmÖrebro universitet, Restaurang- och hotellhögskolan.
    Nordic PFGE meeting January 27–28, 2000, Uppsala, Sweden2000Konferanseproceedings (Fagfellevurdert)
  • 5.
    Fagerlind, Magnus
    et al.
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    Stålhammar, Hans
    VikingGenetics, Skara.
    Olsson, Björn
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    Klinga-Levan, Karin
    Högskolan i Skövde, Forskningscentrum för Systembiologi. Högskolan i Skövde, Institutionen för biovetenskap.
    Expression of miRNAs in Bull Spermatozoa Correlates with Fertility Rates2015Inngår i: Reproduction in domestic animals, ISSN 0936-6768, E-ISSN 1439-0531, Vol. 50, nr 4, 587-594 s.Artikkel i tidsskrift (Fagfellevurdert)
  • 6.
    Fallahshahroudi, Amir
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Domestication Effects on the Stress Response in Chickens: Genetics, Physiology, and Behaviour2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Animal domestication, the process where animals become adapted to living in proximity to humans, is associated with the alteration of multiple traits, including decreased fearfulness and stress response. With an estimated population of 50 billion, the domesticated chicken is the most populous avian species in the world. Hundreds of chicken breeds have been developed for meat and egg production, hobby or research purposes. Multidirectional selection and the relaxation of natural selection in captivity have created immense phenotypic diversity amongst domesticates in a relatively short evolutionary time. The extensive phenotypic diversity, existence of the wild ancestor, and feasibility of intercrossing various breeds makes the chicken a suitable model animal for deciphering genetic determinants of complex traits such as stress response. We used chicken domestication as a model to gain insights about the mechanisms that regulate stress response in an avian species. We studied behavioural and physiological stress response in the ancestral Red Junglefowl and one of its domesticated progenies, White Leghorn. An advanced intercross between the aforementioned breeds was later used to map genetic loci underlying modification of stress response. The general pattern of the stress response in chickens was comparable with that reported in mammals, however we identified distinctive differences in the stress modulatory pathways in chickens. We showed that changes in the expression levels of several stress modulatory genes in the brain, the pituitary and the adrenal glands underlie the observed modified stress response in domesticated chickens. Using quantitative trait loci (QTL) mapping, several QTL underlying stress induced corticosterone, aldosterone and baseline dehydroepiandrosterone (DHEA) levels were detected. As a next step, we combined QTL mapping with gene expression (eQTL) mapping and narrowed two QTL down to the putative causal genes, SERPINA10 and PDE1C. Both of these genes were differentially expressed in the adrenal glands of White Leghorn and the Red Junglefowl, had overlapping eQTL with hormonal QTL, and their expression levels in the adrenal glands were correlated with plasma levels of corticosterone and al-dosterone. These two genes thus serve as strong candidates for further functional investigation concerning modification of the stress response during domestication. This dissertation increase the knowledge about genetics and physiology of the stress response in an avian species and its modification during domestication. Our findings expand the basic knowledge about the stress response in chicken, which can potentially be used to improve welfare through appropriate genetic selection.

  • 7.
    Fountain, Toby
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi. 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 lectularius2016Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, nr 12, 4059-4066 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 8.
    Foyer, Pernilla
    et al.
    Försvarshögskolan, Militärvetenskapliga institutionen (MVI), Militärtekniska avdelningen (MTA). Linköpings universitet, Biologi.
    Svedberg, Anna-Maria
    Linköpings universitet, Biologi.
    Nilsson, Emma
    Linköpings universitet, Biologi.
    Wilsson, Erik
    Swedish Armed Forces Dog Training Unit, Märsta, Sweden.
    Olsen Faresjö, Åshild
    Linköpings universitet, Avdelningen för samhällsmedicin.
    Jensen, Per
    Linköpings universitet, Biologi.
    Behavior and cortisol responses of dogs evaluated in a standardized temperament test for military working dogs2016Inngår i: Journal of Veterinary Behavior: Clinical Applications and Research, ISSN 1558-7878, E-ISSN 1878-7517, Vol. 11, 7-12 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Military and police working dogs are often exposed to stressful or threatening events, and an improper response, e.g., fear, may implicate both reduced working efficiency and welfare. Therefore, identifying individuals that display a favorable response to potentially threatening situations is of great interest. In the present study, we investigated behavior responses of 85 prospective military working dogs in 4 subtests in a standardized temperament test used to select working dogs for the Swedish Armed Forces. Our goal was to evaluate behavioral responses in specific subtests and cortisol responses of candidate dogs. After dogs were rated as approved or nonapproved based on the test leader’s assessment of the full test result, we independently analyzed video recordings of 4 subtests. In addition, for 37 dogs, we analyzed pretest and posttest salivary cortisol levels. Dogs which were approved by the test leader for further training scored higher in the video recordings on emotionality and, in particular, fear-related behavior during a subset of the test and had higher levels of cortisol both before and after the test, than nonapproved dogs. Although this may actually reflect the desired traits, it could also indicate a bias in the selection procedure, which may pose limitations on the attempts to recruit the most suitable working dogs.

  • 9.
    Foyer, Pernilla
    et al.
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten. Department of Military Studies, Military-Technology Division, Swedish Defence University, Stockholm, Sweden.
    Svedberg, Anna-Maria
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Nilsson, Emma
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Wilsson, Erik
    Swedish Armed Forces Dog Training Unit, Märsta, Sweden.
    Olsen Faresjö, Åshild
    Linköpings universitet, Institutionen för medicin och hälsa, Avdelningen för samhällsmedicin. Linköpings universitet, Medicinska fakulteten.
    Jensen, Per
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    Behavior and cortisol responses of dogs evaluated in a standardized temperament test for military working dogs2016Inngår i: Journal of Veterinary Behavior: Clinical Applications and Research, ISSN 1558-7878, E-ISSN 1878-7517, Vol. 11, 7-12 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Military and police working dogs are often exposed to stressful or threatening events, and an improper response, e.g., fear, may implicate both reduced working efficiency and welfare. Therefore, identifying individuals that display a favorable response to potentially threatening situations is of great interest. In the present study, we investigated behavior responses of 85 prospective military working dogs in 4 subtests in a standardized temperament test used to select working dogs for the Swedish Armed Forces. Our goal was to evaluate behavioral responses in specific subtests and cortisol responses of candidate dogs. After dogs were rated as approved or nonapproved based on the test leader’s assessment of the full test result, we independently analyzed video recordings of 4 subtests. In addition, for 37 dogs, we analyzed pretest and posttest salivary cortisol levels. Dogs which were approved by the test leader for further training scored higher in the video recordings on emotionality and, in particular, fear-related behavior during a subset of the test and had higher levels of cortisol both before and after the test, than nonapproved dogs. Although this may actually reflect the desired traits, it could also indicate a bias in the selection procedure, which may pose limitations on the attempts to recruit the most suitable working dogs.

  • 10.
    Gavrilets, Sergey
    et al.
    Departments of Ecology and Evolutionary Biology and Mathematics, University of Tennessee, Knoxville,USA.
    Arnqvist, Göran
    Department of Ecology and Environmental Science, University of Umeå, Sweden.
    Friberg, Urban
    Department of Ecology and Environmental Science, University of Umeå, Sweden.
    The evolution of female mate choice by sexual conflict2001Inngår i: Proceedings of the Royal Society of London Series B, ISSN 0080-4649, Vol. 268, nr 1466, 531-539 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although empirical evidence has shown that many male traits have evolved via sexual selection by female mate choice, our understanding of the adaptive value of female mating preferences is still very incomplete. It has recently been suggested that female mate choice may result from females evolving resistance rather than attraction to males, but this has been disputed. Here, we develop a quantitative genetic model showing that sexual conflict over mating indeed results in the joint evolution of costly female mate choice and exaggerated male traits under a wide range of circumstances. In contrast to traditional explanations of costly female mate choice, which rely on indirect genetic benefits, our model shows that mate choice can be generated as a side–effect of females evolving to reduce the direct costs of mating.

  • 11. Hjalten, Joakim
    et al.
    Axelsson, E. Petter
    Julkunen-Tiitto, Riitta
    Wennström, Anders
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap.
    Pilate, Gilles
    Innate and Introduced Resistance Traits in Genetically Modified Aspen Trees and Their Effect on Leaf Beetle Feeding2013Inngår i: PLoS ONE, ISSN 1932-6203, Vol. 8, nr 9, e73819- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genetic modifications of trees may provide many benefits, e. g. increase production, and mitigate climate change and herbivore impacts on forests. However, genetic modifications sometimes result in unintended effects on innate traits involved in plant-herbivore interactions. The importance of intentional changes in plant defence relative to unintentional changes and the natural variation among clones used in forestry has not been evaluated. By a combination of biochemical measurements and bioassays we investigated if insect feeding on GM aspens is more affected by intentional (induction Bt toxins) than of unintentional, non-target changes or clonal differences in innate plant defence. We used two hybrid wildtype clones (Populus tremula x P. tremuloides and Populus tremula x P. alba) of aspen that have been genetically modified for 1) insect resistance (two Bt lines) or 2) reduced lignin properties (two lines COMT and CAD), respectively. Our measurements of biochemical properties suggest that unintended changes by GM modifications (occurring due to events in the transformation process) in innate plant defence (phenolic compounds) were generally smaller but fundamentally different than differences seen among different wildtype clones (e. g. quantitative and qualitative, respectively). However, neither clonal differences between the two wildtype clones nor unintended changes in phytochemistry influenced consumption by the leaf beetle (Phratora vitellinae). By contrast, Bt induction had a strong direct intended effect as well as a post experiment effect on leaf beetle consumption. The latter suggested lasting reduction of beetle fitness following Bt exposure that is likely due to intestinal damage suffered by the initial Bt exposure. We conclude that Bt induction clearly have intended effects on a target species. Furthermore, the effect of unintended changes in innate plant defence traits, when they occur, are context dependent and have in comparison to Bt induction probably less pronounced effect on targeted herbivores.

  • 12.
    Imsland, Freyja
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Monogenic Traits Associated with Structural Variants in Chicken and Horse: Allelic and Phenotypic Diversity of Visually Appealing Traits2015Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 13.
    Johnsson, Martin
    et al.
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Jonsson, Kenneth B.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kirurgiska vetenskaper, Ortopedi.
    Andersson, Leif
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    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 Chicken2016Inngår i: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, nr 2, 311-319 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 14.
    Krappmann, K
    et al.
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Wurmser, C
    Chair of Animal Breeding, Technische Universität München, Freising, Germany.
    Repsilber, Dirk
    Research Unit Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Fries, R
    Chair of Animal Breeding, Technische Universität München, Freising, Germany.
    Weikard, R
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Kesting, U
    Landeskontrollverband für Leistungs- und Qualitätsprüfung Mecklenburg, Güstrow, Germany.
    Kühn, Christa
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Short communication: evaluation of bovine milk residues from routine milk testing programs as DNA source for genotyping2012Inngår i: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 95, nr 9, 5436-41 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Genome-wide association studies and genomic evaluation using a dense set of genetic markers both require a large number of genotyped individuals. Collection of the respective samples contributes substantially to the cost of the approach. In dairy cattle research, the use of residues from routine milk recording would be a cost-saving alternative to obtain samples for an appropriate number of individuals with specific phenotypes in a very short time. To assess the suitability of milk recording residues, we concurrently investigated milk residues obtained after standardized milk recording procedures and blood samples from 115 cows originating from 3 farms with different milking systems by genotyping 15 microsatellite markers. We found that 4% of the milk samples were possibly assigned to the wrong animal (i.e., conflicts) and that at least 27% of the milk residues were contaminated, as indicated by an extra allele not present in the blood sample. These additional alleles primarily originated from a sample with a higher somatic cell score that went through the milk sample analyzer in the milk laboratory before the target sample. Furthermore, additional allele carryover was observed across more than one sample, when the difference in somatic cell count between samples exceeded 100,000 cells/mL. Finally, in several samples, the extra allele could not be traced back to previous samples passing through the milk sample analyzer. One source of those contaminations might be sample collection on-farm due to milk traces from the previously milked cow in the hose. No correlation was found between the farm management and conflicts or contaminations. We conclude that residues from routine milk recording are not suitable for genomic evaluation or genome-wide association studies because of the high prevalence of contamination generated at several steps during the collection and processing of milk residual samples.

  • 15.
    Lamichhaney, Sangeet
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    The genetic basis for adaptation in natural populations2016Doktoravhandling, med artikler (Annet vitenskapelig)
    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.

  • 16.
    Lamichhaney, Sangeet
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Han, Fan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Berglund, Jonas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Wang, Chao
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Sällman Almen, Markus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    T. Webster, Matthew
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    A beak size locus in Darwin’s finches facilitated character displacement during a drought2016Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, nr 6284, 470-474 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 17.
    Martínez Barrio, Álvaro
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lamichhaney, Sangeet
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, 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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Pettersson, Mats
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Zhang, He
    BGI-Shenzhen, Shenzen, China; College of Physics, Qingdao University, Qingdao, China.
    Dainat, Jacques
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ekman, Diana
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Höppner, Marc P.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Martin, Marcel
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Nystedt, Björn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, 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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Gustafson, Ulla
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    Rubin, Carl-Johan
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sällman Almén, Markus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, 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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, 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 sequencing2016Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 5, e12081Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 18.
    Mehrabi, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och botanik.
    Candidate genes for resistance and susceptibility to the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley (Hordeum vulgare L.)2016Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Bird cherry-oat aphid (Rhopalosiphum padi L.) is an important pest on spring-sown cereals. The aphid reduces yield and can act as a vector of barley yellow dwarf virus. R. padi does not give visible symptoms, but heavy infestation can reduce the yield substantially. R. padi is one of the most important pests of barley, which has the fourth rank among the cereals in global production. In order to overcome this problem, the plants are treated with pesticides. However, some of the pesticides are no longer permitted to use due to their negative environmental effects. Another problem is that the aphids develop resistance against them. Therefore, a new approach is to identify genetic factors that could be used in breeding host plants for resistance. There are many examples of successful plant breeding for resistance to aphids, but in the case of R. padi and barley, no resistant cultivar is commercially available. The aim of this thesis was to identify and characterise aphid resistance and susceptibility factors in barley. This was done using two major approaches. Firstly, constitutive and aphid-induced gene expression was studied in a large number of barley genotypes with known levels of resistance. Secondly, two cDNAs putatively adding to aphid resistance were transformed to Arabidopsis and barley and the effect of transformation on aphid performance and behaviour was evaluated.

         The study of constitutive transcript abundance in 23 barley genotypes gave suggestive evidence that two genes might be related to aphid resistance; a thionin and a proteinase inhibitor gene, and that a lipoxygenase gene might be related to aphid susceptibility.The study of both constitutive and aphid-induced transcript abundances of three glucanase genes, gave support to the idea that two of them might be susceptibility factors. The cDNA of the proteinase inhibitor mentioned above was expressed in Arabidopsis, under control of either a constitutive or a phloem-specific promoter and the effects were evaluated using the green peach aphid, Myzus persicae Sulzer. This aphid is a generalist, feeding on many different plant species, both monocot (such as barley) and dicot (such as Arabidopsis).  The results showed lower settling and fecundity on some of the transgenic lines as compared to on controls.  

         In conclusion, the thesis suggests a role in resistance against R. padi in barley for two genes encoding a thionin and a proteinase inhibitor. It has also given support for a role in susceptibility against R. padi of genes encoding a lipoxygenase and two glucanases. The work further shows that a cDNA from barley, selected based on the interaction between a monocot plant and an essentially monocot specialist aphid, affected the resistance of the dicot Arabidopsis against a generalist aphid.

     

     

  • 19.
    Melzer, Nina
    et al.
    FBN Dummerstorf, Dummerstorf, Germany.
    Jakubowski, S
    LKV, Güstrow, Germany.
    Hartwig, S
    LKV, Güstrow, Germany.
    Kesting, U
    LKV, Güstrow, Germany.
    Wolf, S
    LKV, Güstrow, Germany.
    Nürnberg, Gerd
    FBN Dummerstorf, Dummerstorf, Germany.
    Reinsch, Norbert
    FBN Dummerstorf, Dummerstorf, Germany.
    Repsilber, Dirk
    FBN Dummerstorf, Dummerstorf, Germany.
    Design, infrastructure and database structure for a study on predicting milk phenotypes from genome-wide SNP markers and metabolite profiles2010Inngår i: 9th World Congress on Genetics Applied to Livestock Production, 2010, 427-431 s.Konferansepaper (Fagfellevurdert)
  • 20.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Including metabolomic profiles to improve genetic value prediction: an integrated bioinformatics approach using weighted genome-wide marker information2011Inngår i: 12th Day of the Doctoal Student: abstracts; 19 May 2011, Dummerstorf / [ed] Seyfert, H.-M., Viereck, G., Dummerstorf, Germany: FBN , 2011, 55-58 s.Konferansepaper (Fagfellevurdert)
  • 21.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Metabolites as new molecular traits and their role for genetic evaluation of traditional milk traits2012Inngår i: Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science: Bratislava, Slovakia, 27 - 31 August 2012, Wageningen: Wageningen Academic Publishers , 2012, 88-88 s.Konferansepaper (Fagfellevurdert)
  • 22.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany..
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Simulating SNP data: influence of simulation design on the extent of linkage disequilibrium2010Inngår i: 11th Day of the Doctoral Student: abstracts; 19 May 2010, Dummerstorf / [ed] Seyfert, H.-M., Viereck, G., Dummerstorf, Germany: FBN , 2010, 19-22 s.Konferansepaper (Fagfellevurdert)
  • 23.
    Pavani, Krishna Chaitanya
    University of the Azores.
    Optimization of a specific messenger RNA extraction protocol for fresh and vitrified bovine oocytes to gene expression studies: Specific mRNA extraction protocol for bovine oocytes.2012Independent thesis Advanced level (degree of Master (One Year)), 20 poäng / 30 hpOppgave
    Abstract [en]

    To understand bovine oocytes meiotic maturation, developmental potential, gene expression is required. The gene expression studies in the preimplantation bovine oocytes has been difficult, because the procedures that are being employed for extracting total RNA are not specific for bovine oocytes and so far is not providing the required amount for further procedures. Quantification of genes generally requires large amounts of total RNA in order to overcome the problem of low amount of mRNA present, so a standardized specific protocol is recommended. These days most of the researchers are using commercial Kit protocols without knowing the significance of chemicals and how they are acting on cells. In present project a standardized protocol (modified trizol) was designed for bovine oocytes, which was specific and less expensive. The efficiency of this protocol compared with Pure Link (Kit Protocol), GNTC (Guanidinium thiocyanate) for extraction of total RNA from fresh oocytes, vitrified oocytes with PROH (1,2 propanediol) and DMSO (dimethylsulfoxide) cryoprotectans was much better. The RNA (absorbance 260/280) purity levels of the standardized protocol was ranging (1.50-2.10), whereas for GNTC protocol (1.05-1.36), Pure Link (kit protocol) (2.05-2.7). Amplification of housekeeping genes (SDHA and GAPDH gene) showed the specificity and efficiency of the standardized protocol over other protocols.

  • 24.
    Rozpadek, Piotr
    et al.
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland; Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland.
    Rapala-Kozik, Maria
    Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
    Wezowicz, Katarzyna
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.
    Grandin, Anna
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Karlsson, Stefan
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Wazny, Rafal
    Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
    Anielska, Teresa
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.
    Turnau, Katarzyna
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
    Arbuscular mycorrhiza improves yield and nutritional properties of onion (Allium cepa)2016Inngår i: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 107, 264-272 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Improving the nutritional value of commonly cultivated crops is one of the most pending problems for modern agriculture. In natural environments plants associate with a multitude of fungal microorganisms that improve plant fitness. The best described group are arbuscular mycorrhizal fungi (AMF). These fungi have been previously shown to improve the quality and yield of several common crops. In this study we tested the potential utilization of Rhizophagus irregularis in accelerating growth and increasing the content of important dietary phytochemicals in onion (Allium cepa). Our results clearly indicate that biomass production, the abundance of vitamin B1 and its analogs and organic acid concentration can be improved by inoculating the plant with AM fungi. We have shown that improved growth is accompanied with up-regulated electron transport in PSII and antioxidant enzyme activity.

  • 25. Sorahinobar, Mona
    et al.
    Niknam, Vahid
    Ebrahimzadeh, Hassan
    Soltanloo, Hassan
    Moradi, Babak
    Bahram, Mohammad
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Lack of association between Fusarium graminearum resistance in spike and crude extract tolerance in seedling of wheat2016Inngår i: European journal of plant pathology, ISSN 0929-1873, E-ISSN 1573-8469, Vol. 144, nr 3, 525-538 s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 26.
    Sullivan, Alexis R.
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för ekologi, miljö och geovetenskap. School of Forest Resources and Environmental Science, Michigan Technological Universi ty, 1400 Townsend Drive, Houghton, MI 49931, USA.
    Owusu, Sandra A.
    Weber, Jaime A.
    Hipp, Andrew L.
    Gailing, Oliver
    Hybridization and divergence in multi-species oak (Quercus) communities2016Inngår i: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 181, nr 1, 99-114 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oaks (Quercus: Fagaceae) commonly interbreed yet retain their morphological, genetic and ecological distinctiveness. Post-zygotic isolation mechanisms, such as ecologically dependent selection on adaptive loci, may therefore limit introgression. To test this hypothesis, we quantified hybridization and genetic divergence across the contact zone of four red oaks (Quercus section Lobatae) in the Great Lakes region of North America using a suite of 259 amplified fragment length polymorphisms and 27 genic and genomic microsatellite markers. First, we identified hybrids using genetic structure analysis and confirmed the reliability of our assignments via simulations. Then, we identified candidate loci for species maintenance with three complementary tests for selection and obtained partial gene sequences linked to an outlier locus and three other loci. We detected evidence of recent hybridization among all species and considerable gene flow between Q.ellipsoidalis and Q.velutina. Overall, c.20% of Q.velutina had recent ancestry from Q.ellipsoidalis, whereas nearly 30% of Q.ellipsoidalis had a Q.velutina ancestor. Most loci were negligibly to weakly differentiated among species, but two gene-linked microsatellites deviated significantly from neutral expectations in multiple, complementary outlier tests. Both outlier loci were located in the same 15-cM bin on an existing Q.robur linkage map, a region under divergent selection in other oak species. Adaptive loci in this highly differentiated genomic region may contribute to ecological divergence among species and limit introgression.

  • 27.
    Sundström, Elisabeth
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Imsland, Freyja
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Mikko, Sofia
    Wade, Claire
    Sigurdsson, Snaevar
    Pielberg, Gerli R
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Golovko, Anna
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Curik, Ino
    Seltenhammer, Monika H.
    Soelkner, Johann
    Lindblad-Toh, Kerstin
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Andersson, Leif
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses2012Inngår i: BMC Genomics, ISSN 1471-2164, Vol. 13, 365- s.Artikkel i tidsskrift (Fagfellevurdert)
    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.

  • 28. Torkzaban, Bahareh
    et al.
    Kayvanjoo, Amir Hossein
    Ardalan, Arman
    KTH, Skolan för bioteknologi (BIO), Genteknologi. Natl Inst Genet Engn & Biotechnol, Iran.
    Mousavi, Soraya
    Mariotti, Roberto
    Baldoni, Luciana
    Ebrahimie, Esmaeil
    Ebrahimi, Mansour
    Hosseini-Mazinani, Mehdi
    Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations2015Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, nr 11, e0143465Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Finding efficient analytical techniques is overwhelmingly turning into a bottleneck for the effectiveness of large biological data. Machine learning offers a novel and powerful tool to advance classification and modeling solutions in molecular biology. However, these methods have been less frequently used with empirical population genetics data. In this study, we developed a new combined approach of data analysis using microsatellite marker data from our previous studies of olive populations using machine learning algorithms. Herein, 267 olive accessions of various origins including 21 reference cultivars, 132 local ecotypes, and 37 wild olive specimens from the Iranian plateau, together with 77 of the most represented Mediterranean varieties were investigated using a finely selected panel of 11 microsatellite markers. We organized data in two '4-targeted' and '16-targeted' experiments. A strategy of assaying different machine based analyses (i.e. data cleaning, feature selection, and machine learning classification) was devised to identify the most informative loci and the most diagnostic alleles to represent the population and the geography of each olive accession. These analyses revealed microsatellite markers with the highest differentiating capacity and proved efficiency for our method of clustering olive accessions to reflect upon their regions of origin. A distinguished highlight of this study was the discovery of the best combination of markers for better differentiating of populations via machine learning models, which can be exploited to distinguish among other biological populations.

  • 29.
    Vargas, Alexander O
    et al.
    Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias Universidad de Chile, Las Palermas, Ñuñoa, Santiago, Chile.
    Krabichler, Quirin
    TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
    Guerrero-Bosagna, Carlos
    Linköpings universitet, Institutionen för fysik, kemi och biologi, Biologi. Linköpings universitet, Tekniska fakulteten.
    An Epigenetic Perspective on the Midwife Toad Experiments of Paul Kammerer (1880-1926)2017Inngår i: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, ISSN 1552-5007, E-ISSN 1552-5015, Vol. 328, nr 1-2, 179-192 s.Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Paul Kammerer was the most outstanding neo-Lamarckian experimentalist of the early 20th century. He reported spectacular results in the midwife toad, including crosses of environmentally modified toads with normal toads, where acquired traits were inherited in Mendelian fashion. Accusations of fraud generated a great scandal, ending with Kammerer's suicide. Controversy reignited in the 1970s, when journalist Arthur Koestler argued against these accusations. Since then, others have argued that Kammerer's results, even if real, were not groundbreaking and could be explained by somatic plasticity, inadvertent selection, or conventional genetics. More recently, epigenetics has uncovered mechanisms by which inheritance can respond directly to environmental change, inviting a reanalysis of Kammerer's descriptions. Previous arguments for mere somatic plasticity have ignored the description of experiments showing heritable germ line modification. Alleged inadvertent selection associated with egg mortality can be discarded, since mortality decreased in a single generation, upon repeated exposures. The challenging implications did not escape the attention of Kammerer's noted contemporary, William Bateson, but he reacted with disbelief, thus encouraging fraud accusations. Nowadays, formerly puzzling phenomena can be explained by epigenetic mechanisms. Importantly, Kammerer described parent-of-origin effects, an effect of parental sex on dominance. Epigenetic mechanisms underlie these effects in genomic imprinting and experiments of transgenerational epigenetic inheritance. In the early 20th century, researchers had no reason to link them with the inheritance of acquired traits. Thus, the parent-of-origin effects in Kammerer's experiments specifically suggest authenticity. Ultimate proof should come from renewed experimentation. To encourage further research, we present a model of possible epigenetic mechanisms.

  • 30.
    Wittenburg, Dörte
    et al.
    Leibniz Institute for Farm Animal Biology, Genetics and Biometry, Dummersdorf, Germany.
    Melzer, Nina
    Leibniz Institute for Farm Animal Biology, Genetics and Biometry, Dummersdorf, Germany.
    Reinsch, Norbert
    Leibniz Institute for Farm Animal Biology, Genetics and Biometry, Dummersdorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Genetics and Biometry, Dummersdorf, Germany.
    Milk metabolites and their genetic variability2012Inngår i: Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science: Bratislava, Slovakia, 27 - 31 August 2012, Wageningen: Wageningen Academic Publishers, 2012, 94-94 s.Konferansepaper (Fagfellevurdert)
  • 31.
    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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, 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 universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. 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 buffalo2015Inngår i: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 46, nr 6, 676-682 s.Artikkel i tidsskrift (Fagfellevurdert)
    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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