| 1. |
- Munthe, Christian, 1962
(author)
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Precaution and Ethics: Handling risks, uncertainties and knowledge gaps in the regulation of new biotechnologies
- 2017
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Book (other academic/artistic)abstract
- This volume outlines and analyses ethical issues actualized by applying a precautionary approach to the regulation of new biotechnologies. It presents a novel way of categorizing and comparing biotechnologies from a precautionary standpoint. Based on this, it addresses underlying philosophical problems regarding the ethical assessment of decision-making under uncertainty and ignorance, and discusses how risks and possible benefits of such technologies should be balanced from an ethical standpoint. It argues on conceptual and ethical grounds for a technology neutral regulation as well as for a regulation that not only checks new technologies but also requires old, inferior ones to be phased out. It demonstrates how difficult ethical issues regarding the extent and ambition of precautionary policies need to be handled by such a regulation, and presents an overarching framework for doing so.
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| 2. |
- Sandin, Per, et al.
(author)
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Technology neutrality and regulation of agricultural biotechnology
- 2018
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In: Professionals in food chains: ethics, rules and responsibility. EurSafe 2018, Vienna, Austria 13 – 16 June 2018 / edited by: Svenja Springer, Herwig Grimm. - Wageningen, Netherlands : Wageningen Academic Publishers. - 9789086863211
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Conference paper (peer-reviewed)abstract
- Agricultural biotechnology, in particular genetically modified organisms (GMOs), is subject to regulation in many areas of the world, not least in the European Union (EU). A number of authors have argued that those regulatory processes are unfair, costly, and slow and that regulation therefore should move in the direction of increased ‘technology neutrality’. The issue is becoming more pressing, especially since new biotechnologies such as CRISPR increasingly blur the regulatory distinction between GMOs and non-GMOs. This paper offers a definition of technology neutrality, uses the EU GMO regulation as a starting point for exploring technology neutrality, and presents distinctions between variants of the call for technology neutral GMO regulation in the EU.
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| 3. |
- Sattar, Muhammad Naeem, et al.
(author)
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Cotton leaf curl disease - an emerging threat to cotton production worldwide
- 2013
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In: Journal of General Virology. - : Microbiology Society. - 0022-1317 .- 1465-2099. ; 94, s. 695-710
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Research review (peer-reviewed)abstract
- Cotton leaf curl disease (CLCuD) is a serious disease of cotton which has characteristic symptoms, the most unusual of which is the formation of leaf-like enations on the undersides of leaves. The disease is caused by whitefly-transmitted geminiviruses (family Geminiviridae, genus Begomovirus) in association with specific, symptom-modulating satellites (betasatellites) and an evolutionarily distinct group of satellite-like molecules known as alphasatellites. CLCuD occurs across Africa as well as in Pakistan and north-western India. Over the past 25 years, Pakistan and India have experienced two epidemics of the disease, the most recent of which involved a virus and satellite that are resistance breaking. Loss of this conventional host-plant resistance, which saved the cotton growers from ruin in the late 1990s, leaves farmers with only relatively poor host plant tolerance to counter the extensive losses the disease causes. There has always been the fear that CLCuD could spread from the relatively limited geographical range it encompasses at present to other cotton-growing areas of the world where, although the disease is not present, the environmental conditions are suitable for its establishment and the whitefly vector occurs. Unfortunately recent events have shown this fear to be well founded, with CLCuD making its first appearance in China. Here, we outline recent advances made in understanding the molecular biology of the components of the disease complex, their interactions with host plants, as well as efforts being made to control CLCuD.
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| 4. |
- Lindskog, Cecilia, et al.
(author)
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The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling
- 2015
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In: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Journal article (peer-reviewed)abstract
- Background: To understand cardiac and skeletal muscle function, it is important to define and explore their molecular constituents and also to identify similarities and differences in the gene expression in these two different striated muscle tissues. Here, we have investigated the genes and proteins with elevated expression in cardiac and skeletal muscle in relation to all other major human tissues and organs using a global transcriptomics analysis complemented with antibody-based profiling to localize the corresponding proteins on a single cell level. Results: Our study identified a comprehensive list of genes expressed in cardiac and skeletal muscle. The genes with elevated expression were further stratified according to their global expression pattern across the human body as well as their precise localization in the muscle tissues. The functions of the proteins encoded by the elevated genes are well in line with the physiological functions of cardiac and skeletal muscle, such as contraction, ion transport, regulation of membrane potential and actomyosin structure organization. A large fraction of the transcripts in both cardiac and skeletal muscle correspond to mitochondrial proteins involved in energy metabolism, which demonstrates the extreme specialization of these muscle tissues to provide energy for contraction. Conclusions: Our results provide a comprehensive list of genes and proteins elevated in striated muscles. A number of proteins not previously characterized in cardiac and skeletal muscle were identified and localized to specific cellular subcompartments. These proteins represent an interesting starting point for further functional analysis of their role in muscle biology and disease.
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| 5. |
- Mascher, Martin, et al.
(author)
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A chromosome conformation capture ordered sequence of the barley genome
- 2017
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In: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 544:7651, s. 427-433
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Journal article (peer-reviewed)abstract
- Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
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| 6. |
- Lillie, Mette, et al.
(author)
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Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens
- 2018
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In: Poultry Science. - : Elsevier BV. - 0032-5791 .- 1525-3171. ; 97:3, s. 781-790
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Journal article (peer-reviewed)abstract
- Sixty years, constituting 60 generations, have passed since the founding of the Virginia body weight lines, an experimental population of White Plymouth Rock chickens. Using a stringent breeding scheme for divergent 8-week body weight, the lines, which originated from a common founder population, have responded to bidirectional selection with an approximate 15-fold difference in the selected trait. They provide a model system to study the genetics of complex traits in general and the influences of artificial selection on quantitative genetic architectures in particular. As we reflect on the 60th anniversary of the initiation of the Virginia body weight lines, there is opportunity to discuss the findings obtained using different analytical and experimental genetic and genomic strategies and integrate them with a recent pooled genome resequencing dataset. Hundreds of regions across the genome show differentiation between the 2 lines, reinforcing previous findings that response to selection relied on standing variation across many genes and giving insights into the haplotype complexity underlying regions associated with body weight.
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| 7. |
- Ek, Weronica, et al.
(author)
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Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens.
- 2012
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In: Developmental and comparative immunology. - : Elsevier BV. - 1879-0089 .- 0145-305X. ; 38:2, s. 352-9
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Journal article (peer-reviewed)abstract
- Systemic sclerosis (SSc) or scleroderma is a rare, autoimmune, multi-factorial disease characterized by early microvascular alterations, inflammation, and fibrosis. Chickens from the UCD-200 line develop a hereditary SSc-like disease, showing all the hallmarks of the human disorder, which makes this line a promising model to study genetic factors underlying the disease. A backcross was generated between UCD-200 chickens and its wild ancestor - the red jungle fowl and a genome-scan was performed to identify loci affecting early (21 days of age) and late (175 days of age) ischemic lesions of the comb. A significant difference in frequency of disease was observed between sexes in the BC population, where the homogametic males were more affected than females, and there was evidence for a protective W chromosome effect. Three suggestive disease predisposing loci were mapped to chromosomes 2, 12 and 14. Three orthologues of genes implicated in human SSc are located in the QTL region on chromosome 2, TGFRB1, EXOC2-IRF4 and COL1A2, as well as CCR8, which is more generally related to immune function. IGFBP3 is also located within the QTL on chromosome 2 and earlier studies have showed increased IGFBP3 serum levels in SSc patients. To our knowledge, this study is the first to reveal a potential genetic association between IGFBP3 and SSc. Another gene with an immunological function, SOCS1, is located in the QTL region on chromosome 14. These results illustrate the usefulness of the UCD-200 chicken as a model of human SSc and motivate further in-depth functional studies of the implicated candidate genes.
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| 8. |
- Tengvall, Katarina, 1980-, et al.
(author)
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Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis
- 2022
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In: Communications Biology. - : Springer Nature. - 2399-3642. ; 5:1
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Journal article (peer-reviewed)abstract
- Canine atopic dermatitis is an inflammatory skin disease with clinical similarities to human atopic dermatitis. Several dog breeds are at increased risk for developing this disease but previous genetic associations are poorly defined. To identify additional genetic risk factors for canine atopic dermatitis, we here apply a Bayesian mixture model adapted for mapping complex traits and a cross-population extended haplotype test to search for disease-associated loci and selective sweeps in four dog breeds at risk for atopic dermatitis. We define 15 associated loci and eight candidate regions under selection by comparing cases with controls. One associated locus is syntenic to the major genetic risk locus (Filaggrin locus) in human atopic dermatitis. One selection signal in common type Labrador retriever cases positions across the TBC1D1 gene (body weight) and one signal of selection in working type German shepherd controls overlaps the LRP1B gene (brain), near the KYNU gene (psoriasis). In conclusion, we identify candidate genes, including genes belonging to the same biological pathways across multiple loci, with potential relevance to the pathogenesis of canine atopic dermatitis. The results show genetic similarities between dog and human atopic dermatitis, and future across-species genetic comparisons are hereby further motivated.
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| 9. |
- Axelsson, Erik, et al.
(author)
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The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
- 2021
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In: PLOS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 17:9
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Journal article (peer-reviewed)abstract
- Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a similar to 10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heartderived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.
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| 10. |
- Kolseth, Anna-Karin, et al.
(author)
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Influence of genetically modified organisms on agro-ecosystem processes
- 2015
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In: Agriculture, Ecosystems & Environment. - Amsterdam : Elsevier BV. - 1873-2305 .- 0167-8809. ; 214, s. 96-106
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Journal article (peer-reviewed)abstract
- Biotechnology offers extensive possibilities to incorporate new traits into organisms. Genetically modified (GM) traits relevant for agro-ecosystems include traits such as pest resistance and herbicide tolerance in crop plants, increased growth rate in fish and livestock, and enhanced nitrogen-fixation capabilities of soil microbes. In this review, we evaluated the direct and indirect trait-specific effects of GM plants, microbes, and animals on ecosystem processes and found that most of the effects of genetically modified organisms (GMOs) on ecosystem processes are indirect and are the result of associated changes in management strategy rather than a direct effect of the GMOs. Conflicting results on the performance and effects of GMOs are frequently reported, especially regarding crop yield and impacts on soil organisms. This is partly because methods with different levels of resolution have been used in different ecological contexts. Overall, there is little evidence that the effects of GM traits on ecosystem processes act with different mechanisms from those of traits modified using conventional methods. However, little is known about trait-specific effects of GMOs on ecosystem processes even though GMOs have been used for more than three decades. In particular, studies linking genetically modified traits to ecosystem processes at longer time scales are rare, but needed for evaluating trait effects, especially in an evolutionary context. In addition, biotechnology may provide a unique tool for gaining insights into the links between traits and ecosystem processes when integrated into basic ecological research. (C) 2015 Elsevier B.V. All rights reserved.
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| 11. |
- Weston, David J., et al.
(author)
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The Sphagnome Project : enabling ecological and evolutionary insights through a genus-level sequencing project
- 2018
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In: New Phytologist. - : Wiley. - 0028-646X .- 1469-8137. ; 217:1, s. 16-25
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Journal article (other academic/artistic)abstract
- 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.
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| 12. |
- Svensson, Catarina, et al.
(author)
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Dairy farmer and farm staff attitudes and perceptions regarding daily milk allowance to calves
- 2023
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In: Journal of Dairy Science. - : Elsevier. - 0022-0302 .- 1525-3198. ; 106:10, s. 7220-7239
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Journal article (peer-reviewed)abstract
- The benefits of feeding calves more milk are increasingly being recognized by dairy farmers. However, most producers have still not implemented higher feeding plans. The aim of the present study was to gain a deeper understanding of farmer and farm staff attitudes, and the perceptions and factors considered in their decision-making regarding daily milk allowances. We collected data through focus group interviews with dairy farmers, farm managers, and calf-care workers who were selected using purposive and snowball sampling. In total, 40 persons (24 women and 16 men) joined a focus group interview (6 in all, each with 5–8 participants). Interviews were recorded, and recordings were transcribed and analyzed thematically. Participants had contrasting opinions about the minimum, maximum, and recommended daily milk allowances to their calves. Their suggested lowest daily milk allowance to sustain animal welfare ranged from 4 to 8–10 L and the maximum allowance from 6 to 15 L. We found that farmers' and farm staff's choices and recommendations of milk-feeding protocols were influenced by a large number of factors that could be grouped into 4 themes: (1) Life beyond work, (2) Farm facilities and equipment, (3) Care of the calves, and (4) Profitability and production. Participants' considerations were similar and aimed to maximize daily milk allowance based on farm conditions. However, the allowances they described as optimal for their calves often differed from what they considered practically feasible. We found that the care of the calves and the well-being of the owners and the staff was central in the participants' decision-making, but that this care perspective was challenged by the social and economic sustainability of the farm. Most participants fed their calves twice daily and did not think that increasing that number would be practically feasible. Our results indicate that the participants' viewpoints regarding calves were important for their decision-making about milk allowances. We suggest that a more holistic perspective should be used when advising farmers about milk allowances, putting particular emphasis on the caring and social sustainability aspects of the individual farm.
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| 13. |
- Björnberg, K. E., et al.
(author)
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The role of biotechnology in sustainable agriculture : Views and perceptions among key actors in the Swedish food supply chain
- 2015
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In: Sustainability. - : MDPI AG. - 2071-1050. ; 7:6, s. 7512-7529
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Journal article (peer-reviewed)abstract
- Researchers have put forward agricultural biotechnology as one possible tool for increasing food production and making agriculture more sustainable. In this paper, it is investigated how key actors in the Swedish food supply chain perceive the concept of agricultural sustainability and the role of biotechnology in creating more sustainable agricultural production systems. Based on policy documents and semi-structured interviews with representatives of five organizations active in producing, processing and retailing food in Sweden, an attempt is made to answer the following three questions: How do key actors in the Swedish food supply chain define and operationalize the concept of agricultural sustainability? Who/what influences these organizations' sustainability policies and their respective positions on agricultural biotechnology? What are the organizations' views and perceptions of biotechnology and its possible role in creating agricultural sustainability? Based on collected data, it is concluded that, although there is a shared view of the core constituents of agricultural sustainability among the organizations, there is less explicit consensus on how the concept should be put into practice or what role biotechnology can play in furthering agricultural sustainability.
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| 14. |
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| 15. |
- Guo, Ying, et al.
(author)
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Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens
- 2024
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In: Poultry Science. - : Elsevier. - 0032-5791 .- 1525-3171. ; 103:1
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Journal article (peer-reviewed)abstract
- We compared the genomes of multiple domestic chicken breeds with red and white earlobes to identify the differentiated regions between groups of breeds differing in earlobe color. This was done using a selective sweep mapping approach based on whole-genome sequence data. The most significant selective sweep was identified on chromosome 11, where the white earlobe chicken breeds originated from Mediterranean share a common haplotype, and where multiple candidate genes are located. The most plausible functional candidate gene is the Melanocor-tin 1 Receptor (MC1R), a receptor known to regulate pigmentation in the skin and hair, and it is also the gene with the strongest positional support from the haplotype-based analyses. It, however, still needs to be explored experimentally to identify effects also on chicken earlobe color variation. Our study is the first exploration of the genetic basis of white earlobe color in Mediterranean chickens using a selective sweep mapping method based on whole-genome sequencing data and shows its value for identifying likely func-tional genes mediating the pigmentation in earlobe. It also indicates a potential novel role of MC1R in birds and exemplifies how selection on fancy traits has influenced the genome during formation of the modern chicken breeds.
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| 16. |
- Felleki, Majbritt
(author)
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Genetic Heteroscedasticity for Domestic Animal Traits
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Animal traits differ not only in mean, but also in variation around the mean. For instance, one sire’s daughter group may be very homogeneous, while another sire’s daughters are much more heterogeneous in performance. The difference in residual variance can partially be explained by genetic differences. Models for such genetic heterogeneity of environmental variance include genetic effects for the mean and residual variance, and a correlation between the genetic effects for the mean and residual variance to measure how the residual variance might vary with the mean.The aim of this thesis was to develop a method based on double hierarchical generalized linear models for estimating genetic heteroscedasticity, and to apply it on four traits in two domestic animal species; teat count and litter size in pigs, and milk production and somatic cell count in dairy cows.The method developed is fast and has been implemented in software that is widely used in animal breeding, which makes it convenient to use. It is based on an approximation of double hierarchical generalized linear models by normal distributions. When having repeated observations on individuals or genetic groups, the estimates were found to be unbiased.For the traits studied, the estimated heritability values for the mean and the residual variance, and the genetic coefficients of variation, were found in the usual ranges reported. The genetic correlation between mean and residual variance was estimated for the pig traits only, and was found to be favorable for litter size, but unfavorable for teat count.
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| 17. |
- Martínez Barrio, Álvaro, et al.
(author)
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The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing
- 2016
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In: eLIFE. - 2050-084X. ; 5
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Journal article (peer-reviewed)abstract
- 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.
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| 18. |
- Lethin, Johanna, et al.
(author)
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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines
- 2020
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In: Bmc Plant Biology. - : Springer Science and Business Media LLC. - 1471-2229. ; 20:1
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Journal article (peer-reviewed)abstract
- Background Triticum aestivum (wheat) is one of the world's oldest crops and has been used for >8000 years as a food crop in North Africa, West Asia and Europe. Today, wheat is one of the most important sources of grain for humans, and is cultivated on greater areas of land than any other crop. As the human population increases and soil salinity becomes more prevalent, there is increased pressure on wheat breeders to develop salt-tolerant varieties in order to meet growing demands for yield and grain quality. Here we developed a mutant wheat population using the moderately salt-tolerant Bangladeshi variety BARI Gom-25, with the primary goal of further increasing salt tolerance. Results After titrating the optimal ethyl methanesulfonate (EMS) concentration, ca 30,000 seeds were treated with 1% EMS, and 1676 lines, all originating from single seeds, survived through the first four generations. Most mutagenized lines showed a similar phenotype to BARI Gom-25, although visual differences such as dwarfing, giant plants, early and late flowering and altered leaf morphology were seen in some lines. By developing an assay for salt tolerance, and by screening the mutagenized population, we identified 70 lines exhibiting increased salt tolerance. The selected lines typically showed a 70% germination rate on filter paper soaked in 200 mM NaCl, compared to 0-30% for BARI Gom-25. From two of the salt-tolerant OlsAro lines (OA42 and OA70), genomic DNA was sequenced to 15x times coverage. A comparative analysis against the BARI Gom-25 genomic sequence identified a total of 683,201 (OA42), and 768,954 (OA70) SNPs distributed throughout the three sub-genomes (A, B and D). The mutation frequency was determined to be approximately one per 20,000 bp. All the 70 selected salt-tolerant lines were tested for root growth in the laboratory, and under saline field conditions in Bangladesh. The results showed that all the lines selected for tolerance showed a better salt tolerance phenotype than both BARI Gom-25 and other local wheat varieties tested. Conclusion The mutant wheat population developed here will be a valuable resource in the development of novel salt-tolerant varieties for the benefit of saline farming.
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| 19. |
- Ramesh, Vetukuri, et al.
(author)
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Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans
- 2012
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In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 7:12, s. e51399-
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Journal article (peer-reviewed)abstract
- Phytophthora infestans is the oomycete pathogen responsible for the devastating late blight disease on potato and tomato. There is presently an intense research focus on the role(s) of effectors in promoting late blight disease development. However, little is known about how they are regulated, or how diversity in their expression may be generated among different isolates. Here we present data from investigation of RNA silencing processes, characterized by non-coding small RNA molecules (sRNA) of 19-40 nt. From deep sequencing of sRNAs we have identified sRNAs matching numerous RxLR and Crinkler (CRN) effector protein genes in two isolates differing in pathogenicity. Effector gene-derived sRNAs were present in both isolates, but exhibited marked differences in abundance, especially for CRN effectors. Small RNAs in P. infestans grouped into three clear size classes of 21, 25/26 and 32 nt. Small RNAs from all size classes mapped to RxLR effector genes, but notably 21 nt sRNAs were the predominant size class mapping to CRN effector genes. Some effector genes, such as PiAvr3a, to which sRNAs were found, also exhibited differences in transcript accumulation between the two isolates. The P. infestans genome is rich in transposable elements, and the majority of sRNAs of all size classes mapped to these sequences, predominantly to long terminal repeat (LTR) retrotransposons. RNA silencing of Dicer and Argonaute genes provided evidence that generation of 21 nt sRNAs is Dicer-dependent, while accumulation of longer sRNAs was impacted by silencing of Argonaute genes. Additionally, we identified six microRNA (miRNA) candidates from our sequencing data, their precursor sequences from the genome sequence, and target mRNAs. These miRNA candidates have features characteristic of both plant and metazoan miRNAs.
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| 20. |
- Roos, Jonas
(author)
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Verticillium longisporum and plant immunity responses in Arabidopsis
- 2014
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Doctoral thesis (other academic/artistic)abstract
- Verticillium spp. are soil-borne ascomycete fungi belonging to a subgroup of Sordariomycetes, and the three major plant pathogens Verticillium longisporum, V. dahliae and V. albo-atrum cause disease on numerous plant species worldwide. In Sweden, V. longisporum poses a threat to Brassica oilseed crops, and is thus emphasized in this thesis. Here the early immune responses to V. longisporum in the model plant Arabidopsis and recent data on the V. longisporum genome are presented. Three genes of importance in the Arabidopsis–V. longisporum interaction were studied. The genes were identified via transcriptome and single nucleotide polymorphism (SNP) analysis. RabGAP22, a RabGTPase-regulating protein, was found to contribute to V. longisporum resistance. Pull-down assays revealed SERINE:GLYOXYLATE AMINOTRANSFERASE (AGT1) as an interacting partner during V. longisporum infection and the two proteins were shown to co-localize in the peroxisomes. Unexpectedly, a role for RabGAP22 was also found in stomatal immunity. The monoterpene synthase TPS23/27 was on the other hand found to contribute to fungal invasion, by triggering germination of V. longisporum conidia. The third gene codes for a nitrate/peptide transporter, NPF5.12. Pull-down experiments and fluorescent imaging revealed interaction between NPF5.12 and a major latex protein family member, NPFBP1. Implications in plant immunity processes of these three genes are further discussed. The genomes of two Swedish V. longisporum isolates were sequenced and found to have a size of approximately 70 Mb and harbor ~21,000 protein-coding genes. Initial analyses revealed that 86% of the V. longisporum genomes are shared with V. dahliae and V. albo-atrum, with a high extent of gene duplications. Large numbers of proteins were predicted to contain secretion motifs, and this group of proteins is presumed to play major roles in the interactions with V. longisporum host plants. In conclusion, this thesis work has revealed new fungal and plant host genes and thereby laid the basis for new plant breeding and disease protection strategies.
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| 21. |
- Truvé, Katarina, et al.
(author)
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Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus
- 2016
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In: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7404 .- 1553-7390. ; 12:5
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Journal article (peer-reviewed)abstract
- Gliomas are the most common form of malignant primary brain tumors in humans and second most common in dogs, occurring with similar frequencies in both species. Dogs are valuable spontaneous models of human complex diseases including cancers and may provide insight into disease susceptibility and oncogenesis. Several brachycephalic breeds such as Boxer, Bulldog and Boston Terrier have an elevated risk of developing glioma, but others, including Pug and Pekingese, are not at higher risk. To identify glioma-associated genetic susceptibility factors, an across-breed genome-wide association study (GWAS) was performed on 39 dog glioma cases and 141 controls from 25 dog breeds, identifying a genome-wide significant locus on canine chromosome (CFA) 26 (p = 2.8 x 10(-8)). Targeted re-sequencing of the 3.4 Mb candidate region was performed, followed by genotyping of the 56 SNVs that best fit the association pattern between the re-sequenced cases and controls. We identified three candidate genes that were highly associated with glioma susceptibility: CAMKK2, P2RX7 and DENR. CAMKK2 showed reduced expression in both canine and human brain tumors, and a non-synonymous variant in P2RX7, previously demonstrated to have a 50% decrease in receptor function, was also associated with disease. Thus, one or more of these genes appear to affect glioma susceptibility.
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| 22. |
- Guschanski, Katerina, et al.
(author)
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The evolution of duplicate gene expression in mammalian organs
- 2017
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In: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 27:9, s. 1461-1474
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Journal article (peer-reviewed)abstract
- 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.
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| 23. |
- Niazi, Adnan, et al.
(author)
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Genome Analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: A Rhizobacterium That Improves Plant Growth and Stress Management
- 2014
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9
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Journal article (peer-reviewed)abstract
- The Bacillus amyloliquefaciens subsp. plantarum strain UCMB5113 is a Gram-positive rhizobacterium that can colonize plant roots and stimulate plant growth and defense based on unknown mechanisms. This reinforcement of plants may provide protection to various forms of biotic and abiotic stress. To determine the genetic traits involved in the mechanism of plantbacteria association, the genome sequence of UCMB5113 was obtained by assembling paired-end Illumina reads. The assembled chromosome of 3,889,532 bp was predicted to encode 3,656 proteins. Genes that potentially contribute to plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis and siderophore production were identified. Moreover, annotation identified putative genes responsible for non-ribosomal synthesis of secondary metabolites and genes supporting environment fitness of UCMB5113 including drug and metal resistance. A large number of genes encoding a diverse set of secretory proteins, enzymes of primary and secondary metabolism and carbohydrate active enzymes were found which reflect a high capacity to degrade various rhizosphere macromolecules. Additionally, many predicted membrane transporters provides the bacterium with efficient uptake capabilities of several nutrients. Although, UCMB5113 has the possibility to produce antibiotics and biosurfactants, the protective effect of plants to pathogens seems to be indirect and due to priming of plant induced systemic resistance. The availability of the genome enables identification of genes and their function underpinning beneficial interactions of UCMB5113 with plants.
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| 24. |
- Fallahshahroudi, Amir, 1981-
(author)
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Domestication Effects on the Stress Response in Chickens : Genetics, Physiology, and Behaviour
- 2017
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 25. |
- Negro, S., et al.
(author)
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Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses
- 2017
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In: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 48:3, s. 349-352
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Journal article (peer-reviewed)abstract
- Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P<0.05) and with total white markings (P<0.05) in PRMe horses. The relative contribution of this variant to white markings in PRMe horses was estimated at 47.6% (head) and 43.4% (total score). In PRE horses, this variant was also associated with hindlimb scores (P<0.05) with a relative contribution of 41.2%. The g.20147039C>T intronic variant located 29.9kb downstream from the transcription start site of the MITF gene was associated with less white markings on forelimbs (P<0.05) in PRMe horses, with a relative contribution of 63.9%, whereas in PRE horses this variant was associated with white facial markings (P<0.05), with a relative contribution of 63.9%. No significant associations were found for PAX3 variants in these breeds. These results show that KIT and MITF variants are involved in the white marking patterns of both PRMe and PRE horses, providing breeders with an opportunity to use genetic testing to aid in breeding for their desired level of white markings.
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