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  • 1. Al Azzawi, Tiba Nazar Ibrahim
    et al.
    Khan, Murtaza
    Hussain, Adil
    Shahid, Muhammad
    Imran, Qari Muhammad
    Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics. School of Applied Biosciences, Kyungpook National University, Korea.
    Mun, Bong-Gyu
    Lee, Sang-Uk
    Yun, Byung-Wook
    Evaluation of Iraqi Rice Cultivars for Their Tolerance to Drought Stress2020In: Agronomy, E-ISSN 2073-4395, Vol. 10, no 11, article id 1782Article in journal (Refereed)
    Abstract [en]

    Drought stress is a serious problem around the globe and particularly in the Republic of Iraq. Rice is the third most consumed crop for the Iraqi people; however, its cultivation and production is very low due to several challenges including drought. The current study was performed to evaluate five Iraqi rice cultivars along with relevant (drought-tolerant and drought-susceptible) controls under drought stress, either by treatment with 10% PEG (polyethylene glycol) or through water withholding to induce natural drought stress. The phenotypes of all the cultivars were evaluated and the transcriptional responses of key drought-responsive candidate genes, identified through the EST-SSR marker-based approach, were studied. We also studied transcript accumulation of drought-related transcriptional factors, such as OsGRASS23, OsbZIP12, and OsDREB2A. Moreover, the reference cultivars also included a drought-tolerant inter-specific cultivar Nerica 7 (a cross between Oryza sativa ssp. indica X O. glaberrima). Among the cultivars, the more drought-tolerant phenotypic characteristics and higher transcript accumulation of drought-related marker genes OsE647 and OsE1899 and transcriptional factors OsGRASS23, OsbZIP12, and OsDREB2A were observed in four (out of five) significantly drought-tolerant Iraqi cultivars; Mashkab, followed by Furat, Yasmen, and Amber 33. On another note, Amber Barka was found to be significantly drought susceptible. Mashkab and Amber Barka were found to be the most drought-tolerant and-susceptible cultivars, respectively. The identified tolerant cultivars may potentially serve as a genetic source for the incorporation of drought-tolerant phenotypes in rice.

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  • 2. Almeida, Pedro
    et al.
    Proux-Wera, Estelle
    Churcher, Allison M
    Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology).
    Soler, Lucile
    Dainat, Jacques
    Pucholt, Pascal
    Nordlund, Jessica
    Martin, Tom
    Ronnberg-Wastljung, Ann-Christin
    Nystedt, Bjorn
    Berlin, Sofia
    Mank, Judith E.
    Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion2020In: BMC Biology, E-ISSN 1741-7007, Vol. 18, no 1, article id 78Article in journal (Refereed)
    Abstract [en]

    Background: Sex chromosomes have evolved independently multiple times in eukaryotes and are therefore considered a prime example of convergent genome evolution. Sex chromosomes are known to emerge after recombination is halted between a homologous pair of chromosomes, and this leads to a range of non-adaptive modifications causing gradual degeneration and gene loss on the sex-limited chromosome. However, the proximal causes of recombination suppression and the pace at which degeneration subsequently occurs remain unclear.

    Results: Here, we use long- and short-read single-molecule sequencing approaches to assemble and annotate a draft genome of the basket willow, Salix viminalis, a species with a female heterogametic system at the earliest stages of sex chromosome emergence. Our single-molecule approach allowed us to phase the emerging Z and W haplotypes in a female, and we detected very low levels of Z/W single-nucleotide divergence in the non-recombining region. Linked-read sequencing of the same female and an additional male (ZZ) revealed the presence of two evolutionary strata supported by both divergence between the Z and W haplotypes and by haplotype phylogenetic trees. Gene order is still largely conserved between the Z and W homologs, although the W-linked region contains genes involved in cytokinin signaling regulation that are not syntenic with the Z homolog. Furthermore, we find no support across multiple lines of evidence for inversions, which have long been assumed to halt recombination between the sex chromosomes.

    Conclusions: Our data suggest that selection against recombination is a more gradual process at the earliest stages of sex chromosome formation than would be expected from an inversion and may result instead from the accumulation of transposable elements. Our results present a cohesive understanding of the earliest genomic consequences of recombination suppression as well as valuable insights into the initial stages of sex chromosome formation and regulation of sex differentiation.

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  • 3.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Uppsala, Sweden;Texas A&M Univ, College Stn, TX 77843 USA.
    Fisher's quantitative genetic model and the molecular genetics of multifactorial traits2018In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 135, no 6, p. 391-392Article in journal (Other academic)
  • 4.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.;Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Mutations in Domestic Animals Disrupting or Creating Pigmentation Patterns2020In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 8, article id 116Article, review/survey (Refereed)
    Abstract [en]

    The rich phenotypic diversity in coat and plumage color in domestic animals is primarily caused by direct selection on pigmentation phenotypes. Characteristic features are selection for viable alleles with no or only minor negative pleiotropic effects on other traits, and that alleles often evolve by accumulating several consecutive mutations in the same gene. This review provides examples of mutations that disrupt or create pigmentation patterns. White spotting patterns in domestic animals are often caused by mutations in KIT, microphthalmia transcription factor (MITF), or endothelin receptor B (EDNRB), impairing migration or survival of melanoblasts. Wild boar piglets are camouflage-colored and show a characteristic pattern of dark and light longitudinal stripes. This pattern is disrupted by mutations in Melanocortin 1 receptor (MC1R), implying that a functional MC1R receptor is required for wild-type camouflage color in pigs. The great majority of pig breeds carry MC1R mutations disrupting wild-type color and different mutations causing dominant black color were independently selected in European and Asian domestic pigs. The European allele evolved into a new allele creating a pigmentation pattern, black spotting, after acquiring a second mutation. This second mutation, an insertion of two C nucleotides in a stretch of 6 Cs, is somatically unstable and creates black spots after the open reading frame has been restored by somatic mutations. In the horse, mutations located in an enhancer downstream of TBX3 disrupt the Dun pigmentation pattern present in wild equids, a camouflage color where pigmentation on the flanks is diluted. A fascinating example of the creation of a pigmentation pattern is Sex-linked barring in chicken which is caused by the combined effect of both regulatory and coding mutations affecting the function of CDKN2A, a tumor suppressor gene associated with familial forms of melanoma in human. These examples illustrate how evolution of pigmentation patterns in domestic animals constitutes a model for evolutionary change in natural populations.

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  • 5.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX 77843 USA..
    White horses - non-coding sequences drive premature hair greying and predisposition to melanoma2024In: Upsala Journal of Medical Sciences, ISSN 0300-9734, E-ISSN 2000-1967, Vol. 129, no S1, article id e10626Article, review/survey (Refereed)
    Abstract [en]

    The Grey allele in horses is causing premature hair greying and susceptibility to melanoma. The causal mutation is a 4.6 kb tandem duplication in intron 6 of the Syntaxin 17 gene. A recent study demonstrated that the most common allele at the Grey locus (G3) involves three tandem copies of this sequence, whilst a more rare allele (G2) has two tandem copies and the wild-type allele (G1) only one copy. The G3 allele is causing fast greying and high incidence of skin melanoma, whereas the G2 allele is causing slow greying and no obvious increase in melanoma incidence. Further somatic copy number expansion has been documented in melanoma tissue from Grey horses. Functional studies showed that this intronic sequence acts as a weak melanocyte-specific enhancer that becomes substantially stronger by the copy number expansion. The Grey mutation is associated with upregulated expression of both Syntaxin 17 and the neighbouring NR4A3 gene in Grey horse melanomas. It is still an open question which of these genes is most important for the phenotypic effects or if causality is due to the combined effect of upregulation of both genes. Interestingly, RNAseq data in the Human Protein Atlas give support for a possible role of NR4A3 because it is particularly upregulated in human skin cancer, and it belongs to a cluster of genes associated with skin cancer and melanin biosynthesis. The Grey mutation and its association with melanoma provide a possibility to study the path to tumour development in numerous Grey horses carrying exactly the same predisposing mutation.

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  • 6.
    Androsiuk, P.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. University of Warmia & Mazury, Poland.
    Shimono, A.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Westin, J.
    Lindgren, D.
    Fries, A.
    Wang, X. -R
    Genetic status of Norway spruce (Picea abies) breeding populations for northern Sweden2013In: Silvae Genetica, ISSN 0037-5349, Vol. 62, no 3, p. 127-136Article in journal (Refereed)
    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.

  • 7.
    Asdal, Åsmund
    et al.
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Brodal, Guro
    Norwegian Insititute of Bioeconomy Research, NIBIO.
    Solberg, Svein Øivind
    Inland Norway University of Applied Sciences.
    Yndgaard, Flemming
    von Bothmer, Roland
    Swedish University of Agricultural Sciences, SLU.
    Meen, Eivind
    Kimen Seed Laboratory.
    Seed Longevity and Survival of Seed Borne Diseases after 30 Years Conservation in Permafrost: Report from the 100 Year Storage experiment2019Report (Other academic)
    Abstract [en]

    The Nordic Gene bank established the 100 year seed storage experiment in Coal mine no. 3 outside Longyearbyen in 1986. Security duplicate samples of the Nordic seed collection had been deposited in permafrost in the coal mine since 1984. 

    The experiment was established with the aim to monitor the longevity of seeds in this Nordic back-up seed collection and to gain general knowledge about the longevity of seed stored under permafrost conditions, as well as studying the survival of seed borne plant pathogens.

    The experimental set up included in total 41 seed lots of 17 agricultural and horticultural crop species commonly grown in the Nordic countries. The seed germination experiment included two or three varieties of each crop. The experimental part dedicated to studies of pathogen survival included seeds from 11 crops naturally contaminated by pathogens.

    The test program comprises germination and pathogen survival tests every 2.5 years during the first 20 years and then every 5 years for the last 80 years. In total 25 identical sets of test seeds placed in sealed glass tubes were packed in wooden boxes, one box for each planned test year.

    The tests have been carried out according to schedule and this report sums up the results from the first 30 years of the experiment. All tests have been carried out in accordance with the same ISTA-protocols.

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  • 8.
    Atikuzzaman, Mohammad
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Sanz, Libia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Pla, Davinia
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Alvarez-Rodriguez, Manuel
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Rubér, Marie
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Wright, Dominic
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Calvete, Juan J.
    Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain.
    Rodriguez-Martinez, Heriberto
    Linköping University, Department of Clinical and Experimental Medicine, Division of Children's and Women's health. Linköping University, Faculty of Medicine and Health Sciences.
    Selection for higher fertility reflects in the seminal fluid proteome of modern domestic chicken2017In: Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics, ISSN 1744-117X, E-ISSN 1878-0407, Vol. 21, p. 27-40Article in journal (Refereed)
    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.

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  • 9.
    Axelsson, Erik
    et al.
    Uppsala University, Sweden.
    Ljungvall, Ingrid
    Swedish University of Agricultural Sciences, Sweden.
    Bhoumik, Priyasma
    Novartis Institutes for BioMedical Research, Switzerland.
    Bas Conn, Laura
    Uppsala University, Sweden.
    Muren, Eva
    Uppsala University, Sweden.
    Ohlsson, Åsa
    Swedish University of Agricultural Sciences, Sweden.
    Olsen, Lisbeth Høier
    University of Copenhagen, Denmark.
    Engdahl, Karolina
    Swedish University of Agricultural Sciences, Sweden.
    Hagman, Ragnvi
    Swedish University of Agricultural Sciences, Sweden.
    Hanson, Jeanette
    Swedish University of Agricultural Sciences, Sweden.
    Kryvokhyzha, Dmytro
    Uppsala University, Sweden.
    Pettersson, Mats
    Uppsala University, Sweden.
    Grenet, Olivier
    Novartis Institutes for BioMedical Research, Switzerland.
    Moggs, Jonathan
    Novartis Institutes for BioMedical Research, Switzerland.
    Del Rio-Espinola, Alberto
    Novartis Institutes for BioMedical Research, Switzerland.
    Epe, Christian
    Elanco Animal Health, USA.
    Taillon, Bruce
    Elanco Animal Health, USA.
    Tawari, Nilesh
    Elanco Animal Health, USA.
    Mane, Shrinivas
    Elanco Animal Health, USA.
    Hawkins, Troy
    Elanco Animal Health, USA.
    Hedhammar, Åke
    Swedish University of Agricultural Sciences, Sweden.
    Gruet, Philippe
    Novartis Animal Health, Switzerland.
    Häggström, Jens
    Swedish University of Agricultural Sciences, Sweden.
    Lindblad-Toh, Kerstin
    Uppsala University, Sweden.
    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 spaniels2021In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 17, no 9, article id e1009726Article in journal (Refereed)
    Abstract [en]

    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 ~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 heart-derived 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.
    Axelsson, Erik
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ljungvall, Ingrid
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Bhoumik, Priyasma
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland.;Swiss Fed Inst Technol, Sci & IT Serv, Basel Campus, Basel, Switzerland..
    Conn, Laura Bas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Murén, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ohlsson, Åsa
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Olsen, Lisbeth Hoier
    Univ Copenhagen, Dept Vet & Anim Sci, Copenhagen, Denmark..
    Engdahl, Karolina
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hagman, Ragnvi
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Hanson, Jeanette
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Kryvokhyzha, Dmytro
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Grenet, Olivier
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Moggs, Jonathan
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Del Rio-Espinola, Alberto
    Novartis Inst BioMed Res, Translat Med, Basel, Switzerland..
    Epe, Christian
    Elanco Anim Hlth, Greenfield, IN USA.;Boehringer Ingelheim Anim Hlth, Ingelheim, Germany..
    Taillon, Bruce
    Elanco Anim Hlth, Greenfield, IN USA..
    Tawari, Nilesh
    Elanco Anim Hlth, Greenfield, IN USA..
    Mane, Shrinivas
    Elanco Anim Hlth, Greenfield, IN USA..
    Hawkins, Troy
    Elanco Anim Hlth, Greenfield, IN USA..
    Hedhammar, Åke
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Gruet, Philippe
    Novartis Anim Hlth, St Aubin, Switzerland..
    Häggström, Jens
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA..
    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 spaniels2021In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 17, no 9, article id e1009726Article in journal (Refereed)
    Abstract [en]

    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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    FULLTEXT01
  • 11.
    Bianchi, Matteo
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Karlsson, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Murén, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sundberg, Katarina
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Andersson, Göran
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Kämpe, Olle
    Karolinska Inst, Dept Med Solna, Stockholm, Sweden..
    Hedhammar, Åke
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden..
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Broad Inst MIT & Harvard, Cambridge, MA 02142 USA..
    Rosengren Pielberg, Gerli
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs2020In: BMC Genomics, E-ISSN 1471-2164, Vol. 21, article id 307Article in journal (Refereed)
    Abstract [en]

    Background: Hypothyroidism is a common complex endocrinopathy that typically has an autoimmune etiology, and it affects both humans and dogs. Genetic and environmental factors are both known to play important roles in the disease development. In this study, we sought to identify the genetic risk factors potentially involved in the susceptibility to the disease in the high-risk Giant Schnauzer dog breed.

    Results: By employing genome-wide association followed by fine-mapping (top variant p-value=5.7x10(-6)), integrated with whole-genome resequencing and copy number variation analysis, we detected a similar to 8.9 kbp deletion strongly associated (p-value=0.0001) with protection against development of hypothyroidism. The deletion is located between two predicted Interferon alpha (IFNA) genes and it may eliminate functional elements potentially involved in the transcriptional regulation of these genes. Remarkably, type I IFNs have been extensively associated to human autoimmune hypothyroidism and general autoimmunity. Nonetheless, the extreme genomic complexity of the associated region on CFA11 warrants further long-read sequencing and annotation efforts in order to ascribe functions to the identified deletion and to characterize the canine IFNA gene cluster in more detail.

    Conclusions: Our results expand the current knowledge on genetic determinants of canine hypothyroidism by revealing a significant link with the human counterpart disease, potentially translating into better diagnostic tools across species, and may contribute to improved canine breeding strategies.

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  • 12.
    Biswas, M. K.
    et al.
    Huazhong Agricultural University, China.
    Ahmed, M. B.
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    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
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    In exploitation of genetic diversity in potato breeding2010In: Agronomski Glasnik (Agronomy Journal), ISSN 1848-8900, Vol. 72, no 4-5, p. 261-276Article in journal (Refereed)
    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.

  • 13.
    Braganca, F. M. Serra
    et al.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Broomé, Michael
    KTH, School of Electrical Engineering and Computer Science (EECS), Intelligent systems, Robotics, Perception and Learning, RPL.
    Rhodin, M.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Bjornsdottir, S.
    Agr Univ Iceland, Hvanneyri, Borgarnes, Iceland..
    Gunnarsson, V
    Holar Univ Coll, Dept Equine Sci, Holar, Iceland..
    Voskamp, J. P.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Persson-Sjödin, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Back, W.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands.;Univ Ghent, Fac Vet Med, Dept Surg & Anaesthesiol Domest Anim, B-9820 Merelbeke, Belgium..
    Lindgren, G.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, B-3001 Leuven, Belgium..
    Novoa-Bravo, M.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden.;Genet Anim Colombia Ltda, Bogota, Colombia..
    Roepstorff, C.
    Univ Zurich, Vetsuisse Fac, Equine Dept, Winterthurerstr 260, CH-8057 Zurich, Switzerland..
    van der Zwaag, B. J.
    Inertia Technol BV, Enschede, Netherlands..
    Van Weeren, P. R.
    Univ Utrecht, Fac Vet Med, Dept Clin Sci, NL-3584 CM Utrecht, Netherlands..
    Hernlund, E.
    Swedish Univ Agr Sci, Dept Anat Physiol & Biochem, Uppsala, Sweden..
    Improving gait classification in horses by using inertial measurement unit (IMU) generated data and machine learning2020In: Scientific Reports, E-ISSN 2045-2322, Vol. 10, no 1, article id 17785Article in journal (Refereed)
    Abstract [en]

    For centuries humans have been fascinated by the natural beauty of horses in motion and their different gaits. Gait classification (GC) is commonly performed through visual assessment and reliable, automated methods for real-time objective GC in horses are warranted. In this study, we used a full body network of wireless, high sampling-rate sensors combined with machine learning to fully automatically classify gait. Using data from 120 horses of four different domestic breeds, equipped with seven motion sensors, we included 7576 strides from eight different gaits. GC was trained using several machine-learning approaches, both from feature-extracted data and from raw sensor data. Our best GC model achieved 97% accuracy. Our technique facilitated accurate, GC that enables in-depth biomechanical studies and allows for highly accurate phenotyping of gait for genetic research and breeding. Our approach lends itself for potential use in other quadrupedal species without the need for developing gait/animal specific algorithms.

  • 14.
    Buinovskaja, Greta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Identifying structural variants from plant short-read sequencing data2022Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
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    Master_Thesis_Greta_Buinovskaja
  • 15. Capovilla, Giovanna
    et al.
    Symeonidi, Efthymia
    Wu, Rui
    Schmid, Markus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Max Planck Institute for Developmental Biology, Department of Molecular Biology, Spemannstr. 35, 72076 Tübingen, Germany.
    Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 18, p. 5117-5127Article in journal (Refereed)
    Abstract [en]

    FLOWERING LOCUS M (FLM), a component of the thermosensory flowering time pathway in Arabidopsis thaliana, is regulated by temperature-dependent alternative splicing (AS). The main splicing variant, FLM-beta, is a well-documented floral repressor that is down-regulated in response to increasing ambient growth temperature. Two hypotheses have been formulated to explain how flowering time is modulated by AS of FLM. In the first model a second splice variant, FLM-delta, acts as a dominant negative isoform that competes with FLM-beta at elevated ambient temperatures, thereby indirectly promoting flowering. Alternatively, it has been suggested that the induction of flowering at elevated temperatures is caused only by reduced FLM-beta expression. To better understand the role of the two FLM splice forms, we employed CRISPR/Cas9 technology to specifically delete the exons that characterize each splice variant. Lines that produced repressive FLM-beta but were incapable of producing FLM-delta were late flowering. In contrast, FLM-beta knockout lines that still produced FLM-delta flowered early, but not earlier than the flm-3 loss of function mutant, as would be expected if FLM-delta had a dominant-negative effect on flowering. Our data support the role of FLM-beta as a flower repressor and provide evidence that a contribution of FLM-delta to the regulation of flowering time in wild-type A. thaliana seems unlikely.

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    fulltext
  • 16. Carlson-Nilsson, Ulrika
    et al.
    Aloisi, Karolina
    NordGen.
    Cultivation Manual: Medicinal and Aromatic Plants in the Nordic and Baltic Region2022Report (Other (popular science, discussion, etc.))
    Abstract [en]

    The Nordic Genetic Resource Centre (NordGen) is the Nordic countries’ gene bank and knowledge center for genetic resources. NordGen is an organisation under the Nordic Council of Minister and works with the mission of conserving and facilitating the sustainable use of genetic resources linked to food, agriculture and forestry. 

    "Cultivation Manual: Medicinal and Aromatic Plants in the Nordic and Baltic Region" provides knowledge on cultivation of medicinal and aromatic plants. 

    Download full text (pdf)
    Cultivation Manual
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    omslag
  • 17.
    Chen, Zhi-Qiang
    et al.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Zan, Yanjun
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zhou, Linghua
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China..
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cui, BinBin
    Baoding Univ, Coll Biochem & Environm Engn, Baoding 071000, Hebei, Peoples R China..
    Niu, Shihui
    Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing, Peoples R China..
    Westin, Johan
    Skogforsk, Box 3, SE-91821 Savar, Sweden.;Swedish Univ Agr Sci, Unit Field Based Forest Res, SE-90183 Umeå, Sweden..
    Karlsson, Bo
    Skogforsk, Ekebo 2250, SE-26890 Svalov, Sweden..
    Garcia-Gil, Maria Rosario
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wu, Harry X.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden.;Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing, Peoples R China.;CSIRO Natl Collect Res Australia, Black Mt Lab, Canberra, ACT 2601, Australia..
    Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis2021In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 22, no 1, article id 179Article in journal (Refereed)
    Abstract [en]

    Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

    Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.

    Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.

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  • 18.
    Cope, Jonathan E.
    et al.
    Swedish Univ Agr Sci, Dept Crop Prod Ecol, S-75007 Uppsala, Sweden..
    Berckx, Fede
    Swedish Univ Agr Sci, Dept Crop Prod Ecol, S-75007 Uppsala, Sweden..
    Lundmark, Johan
    Lantmannen Lantbruk, Udda Lundkvists Vag 11, S-26881 Svalov, Sweden..
    Henriksson, Tina
    Lantmannen Lantbruk, Udda Lundkvists Vag 11, S-26881 Svalov, Sweden..
    Karlsson, Ida
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Swedish Univ Agr Sci, Dept Crop Prod Ecol, S-75007 Uppsala, Sweden.
    Weih, Martin
    Swedish Univ Agr Sci, Dept Crop Prod Ecol, S-75007 Uppsala, Sweden..
    Clear effects on root system architecture of winter wheat cultivars (Triticum aestivum L.) from cultivation environment and practices2024In: Scientific Reports, E-ISSN 2045-2322, Vol. 14, no 1, article id 11099Article in journal (Refereed)
    Abstract [en]

    Roots play a pivotal role in the adaption of a plant to its environment, with different root traits adapting the plant to different stresses. The environment affects the Root System Architecture (RSA), but the genetic factors determine to what extent, and whether stress brought about by extreme environmental conditions is detrimental to a specific crop. This study aimed to identify differences in winter wheat RSA caused by cultivation region and practice, in the form of preceding crop (precrop), and to identify if modern cultivars used in Sweden differ in their reaction to these environments. This was undertaken using high-throughput phenotyping to assess the RSA. Clear differences in the RSA were observed between the Swedish cultivation regions, precrop treatments, and interaction of these conditions with each other and the genetics. Julius showed a large difference between cultivars, with 9.3-17.1% fewer and 12-20% narrower seminal roots. Standardized yield decreased when grown after wheat, 23% less compared to oilseed rape (OSR), and when grown in the Southern region, 14% less than the Central region. Additionally, correlations were shown between the root number, angle, and grain yield, with different root types being correlated depending on the precrop. Cultivars on the Swedish market show differences that can be adapted to the region-precrop combinations. The differences in precrop effect on RSA between regions show global implications and a need for further assessment. Correlations between RSA and yield, based on root-typexprecrop, indicate different needs of the RSA depending on the management practices and show the potential for improving crop yield through targeting genotypic and environmental conditions in a holistic manner. Understanding this RSA variance, and the mechanisms of conditional response, will allow targeted cultivar breeding for specific environments, increasing plant health and food security.

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    FULLTEXT01
  • 19.
    Danielsson-Tham, Marie-Louise
    et al.
    Department of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Tham, WilhelmDepartment of Food Hygiene, Faculty of Veterinary Medicine, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Nordic PFGE meeting January 27–28, 2000, Uppsala, Sweden2000Conference proceedings (editor) (Refereed)
  • 20. Deane, C. S.
    et al.
    Borg, J.
    Cahill, T.
    Carnero-Diaz, E.
    Etheridge, T.
    Hardiman, G.
    Leys, N.
    Madrigal, P.
    Manzano, A.
    Mastroleo, F.
    Medina, F. J.
    Fernandez-Rojo, M. A.
    Siew, K.
    Szewczyk, N. J.
    Villacampa, A.
    Walsh, S. B.
    Weging, S.
    Bezdan, D.
    Giacomello, Stefania
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    da Silveira, W. A.
    Herranz, R.
    Team, Space Omics Topical
    Space omics research in Europe: Contributions, geographical distribution and ESA member state funding schemes2022In: iScience, ISSN 2589-0042, Vol. 25, no 3, p. 103920-, article id 103920Article in journal (Refereed)
    Abstract [en]

    The European research community, via European Space Agency (ESA) spaceflight opportunities, has significantly contributed toward our current understanding of spaceflight biology. Recent molecular biology experiments include “omic” analysis, which provides a holistic and systems level understanding of the mechanisms underlying phenotypic adaptation. Despite vast interest in, and the immense quantity of biological information gained from space omics research, the knowledge of ESA-related space omics works as a collective remains poorly defined due to the recent exponential application of omics approaches in space and the limited search capabilities of pre-existing records. Thus, a review of such contributions is necessary to clarify and promote the development of space omics among ESA and ESA state members. To address this gap, in this review, we i) identified and summarized omics works led by European researchers, ii) geographically described these omics works, and iii) highlighted potential caveats in complex funding scenarios among ESA member states.

  • 21.
    Denoyes-Rothan, B.
    et al.
    INRA, Bordeaux, France.
    Lerceteau-Köhler, Estelle
    University of Graz, Austria.
    Guerin, G.
    Baudry, A.
    Moliner, V.
    Navatel, J. C.
    Anthracnose on strawberry in France: Situation and perspectives2006In: Proceedings of the Vth International Strawberry Symposium, INTERNATIONAL SOCIETY HORTICULTURAL SCIENCE , 2006, p. 277-280Conference paper (Refereed)
    Abstract [en]

    Anthracnose, caused by Colletotrichum acutatum, on strawberry (Fragaria x ananassa) was first reported on fruit in France in 1981. Damage was later recorded on runners, petioles, foliage and crowns. The evolution of a disease control method, the molecular variability of C acutatum, the study of the interaction between pathogen and host, the different techniques of inoculation, and the last results concerning QTLs linked to resistance to C acutatum are reported, which cover 10 years of research in France.

  • 22.
    Denoyes-Rothan, B
    et al.
    INRA, Bordeaux, France.
    Lerceteau-Köhler, Estelle
    Centre Interregional de Recherche & d'Experimentation de la Fraise, France.
    Guerin, G
    Bosseur, S
    Bariac, J
    Martin, E
    Roudeillac, P
    QTL analysis for resistances to Colletotrichum acutatum and Phytophthora cactorum in octoploid strawberry (Fragaria x ananassa)2004In: Proceedings of the XIth Eucarpia Symposium on Fruit Breeding and Genetics, Vols 1 and 2, INTERNATIONAL SOCIETY HORTICULTURAL SCIENCE , 2004, p. 147-151Conference paper (Refereed)
    Abstract [en]

    Colletotrichum acutatum and Phytophthora cactorum are two of the most important pathogens of strawberry in Europe, and particularly in France. The characterization of quantitative trait loci (QTL) controlling resistances to these two pathogens would allow a better knowledge of the genetic architecture of these resistances in order to develop durable resistance. A pseudo-testcross strawberry population derived from the cross between Capitola and CF1116 was used for detecting QTLs associated with C. acutatum and P cactorum resistances. One hundred and eighty five individuals were inoculated with C. acutatum by dipping cold stored plants in a conidial suspension adjusted to 2.10(6) conidia per ml. They were also inoculated separately with P cactorum by inserting an agar disk containing mycelium into the crown. Each inoculation was conducted twice. Putative QTLs for resistance to C acutatum and P cactorum were identified by Interval Mapping (Mapmaker-QTL) using a LOD threshold of 2.

  • 23.
    Druid, Linnea
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Thiele, David
    Linköping University, Department of Physics, Chemistry and Biology, Biology.
    Vilda kulturväxtsläktingar: för framtidens föda2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Agriculture is facing several great challenges. The crops need, among other things, to be adapted to a changing climate. Here, the wild relatives of the crops, the crop wild relatives, are important since they carry a vast amount of genetic diversity. For the crop wild relatives to be used in the process of adapting and improving today’s crops, it is essential that they are conserved. This literature review aims to make a survey of the previous conservation efforts and the work that remains, as well as presenting the conservation efforts in Sweden. The review shows that several international conventions, conservation strategies, and collaborations have been significant for the conservation efforts. Some large seed collecting projects have been completed and, in some places, protected areas for crop wild relatives have been established. However, extensive conservation efforts are still required. Plans need to be actualized, projects funded, and political incentive increased. The Swedish conservation efforts are still at an early stage, but some progress has been made and work is in ongoing. Increasing awareness about crop wild relatives could result in their conservation receiving a higher status and increased funds. Biology teachers can make an important contribution to this by including crop wild relatives and their significance in class, for example by letting students work with questions concerning the security of the futures food production.

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    Druid och Thiele (2022) - Vilda kulturväxtsläktingar - för framtidens föda
  • 24.
    Edvardsson Björnberg, Karin
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Philosophy and History, Philosophy.
    Jonas, E.
    Marstorp, H.
    Tidåker, P.
    The Role of Biotechnology in Sustainable Agriculture: Views and Perceptions Among Key Actors in the Swedish Food Supply Chain2016In: Sustainable Agriculture and Food Supply: Scientific, Economic, and Policy Enhancements, Apple Academic Press , 2016, p. 315-336Chapter in book (Other academic)
  • 25.
    Eriksson, Camilla
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research.
    Petitt, Andrea
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research. Uppsala Univ, Ctr Gender Res, Uppsala, Sweden.
    Designing Cattle: The Social Practice of Constructing Breeds2020In: Anthrozoos, ISSN 0892-7936, E-ISSN 1753-0377, Vol. 33, no 2, p. 175-190Article in journal (Refereed)
    Abstract [en]

    This paper explores how cattle breeds are constructed through social practice-which we conceptually develop as "designing" cattle. We show how breed varieties are designed, informed by the social, material and moral embeddedness of cattle breeding associations' visions of the future and how they draw on science and technology in their breeding strategies. Based on an analysis of the trade magazines of three different breeding associations, we illustrate how breeding associations are working to establish four different varieties of Swedish Mountain Cattle (SMC). We conclude that the concept of designing cattle enables us to unpack how breeds are socially constructed and institutionally stabilized through sociotechnical imaginaries.

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    fulltext
  • 26.
    Fagerheim White, Ellen-Louisa
    et al.
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Honkatukia, Mervi
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Peippo, Jaana
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Kjetså, Maria
    Nordic Council of Ministers, The Nordic Genetic Resource Centre (NordGen).
    Equines in the Nordics: History, status and genetics2024Report (Other (popular science, discussion, etc.))
    Abstract [en]

    With roots as far as the Bronze age, equines have played an invaluable role in history, both with regards to agriculture and forestry, warfare, transportation and leisure, and therefore hold important cultural signi icance in the Nordics. The link between horses and the welfare bene its of their caregivers makes the species an important part of society as well. Since the agricultural and industrial revolution, the equine sector has been in luenced by a range of challenges due to the dramatic change in the role of horses in society, especially for the Nordic native breeds.

    However, as society adapts and finds new ways to use and protect them, there is a hope for the future. Although there has been cooperation between the Nordic countries in the horse sector, a collective report of the status of all the Nordic countries has been missing. This report marks a start for this type of effort by considering both commercial and native breeds. Further, it comprises the horse sector in the Nordics, with a special focus on the native horse breeds and the possibilities they carry for environmental sustainability, their socio-economic importance, their genetics as well as their risk status.

    The report further evaluates the Domestic Animal Diversity Information System (DAD-IS) maintained and developed by FAO as a tool for gathering information about the development and current status of the native breeds. The goal of this report is to identify knowledge gaps and areas of improvement for the Nordic equine sector and the collected data of the native horse breeds. One of the biggest challenges has been to find validated information sources for the population numbers of the breeds in each country – there are varying estimates for both commercial and native breeds. The numbers have significant impact for the determination of managing strategies of the populations.

    Reports for each of the countries (Denmark, Finland, the Faroe Islands, Iceland, Norway and Sweden) are presented, and depict the current role of horses, breeding, population development and economic values of the equine sector are listed in each of the country-reports. The information in the country reports were derived from a questionnaire and by using DAD-IS.

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  • 27.
    Fagerlind, Magnus
    et al.
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Stålhammar, Hans
    VikingGenetics, Skara.
    Olsson, Björn
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Klinga-Levan, Karin
    University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Bioscience.
    Expression of miRNAs in Bull Spermatozoa Correlates with Fertility Rates2015In: Reproduction in domestic animals, ISSN 0936-6768, E-ISSN 1439-0531, Vol. 50, no 4, p. 587-594Article in journal (Refereed)
    Download full text (pdf)
    fulltext
  • 28.
    Fallahshahroudi, Amir
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Domestication Effects on the Stress Response in Chickens: Genetics, Physiology, and Behaviour2017Doctoral thesis, comprehensive summary (Other academic)
    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.

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    Domestication Effects on the Stress Response in Chickens: Genetics, Physiology, and Behaviour
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  • 29.
    Fegraeus, Kim Jaederkvist
    et al.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Velie, Brandon D.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Axelsson, Jeanette
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Ang, Rachel
    Univ Sydney, Fac Sci, Sydney, NSW, Australia.
    Hamilton, Natasha A.
    Univ Sydney, Fac Sci, Sydney, NSW, Australia.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden; Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX USA.
    Meadows, Jennifer R. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindgren, Gabriella
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    A potential regulatory region near the EDN3 gene may control both harness racing performance and coat color variation in horses2018In: Physiological Reports, E-ISSN 2051-817X, Vol. 6, no 10, article id e13700Article in journal (Refereed)
    Abstract [en]

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

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  • 30.
    Fegraeus, Kim
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Molecular Precision Medicine.
    Rosengren, Maria K.
    Swedish Univ Agr Sci Uppsala, Dept Anim Biosci, Uppsala, Sweden..
    Naboulsi, Rakan
    Swedish Univ Agr Sci Uppsala, Dept Anim Biosci, Uppsala, Sweden.;Karolinska Inst, Dept Womens & Childrens Hlth, Childhood Canc Res Unit, Stockholm, Sweden..
    Orlando, Ludovic
    Univ Paul Sabatier, Ctr Anthropobiol & Genom Toulouse, CNRS, UMR 5288, Toulouse, France..
    Åbrink, Magnus
    Swedish Univ Agr Sci, Dept Biomed Sci & Vet Publ Hlth, Uppsala, Sweden..
    Jouni, Ahmad
    Swedish Univ Agr Sci Uppsala, Dept Anim Biosci, Uppsala, Sweden..
    Velie, Brandon D.
    Univ Sydney, Sch Life & Environm Sci, Sydney, Australia..
    Raine, Amanda
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Egner, Beate
    Vet Acad Higher Learning, Dept Cardiovasc Res, Babenhausen, Germany..
    Mattsson, C. Mikael
    Silicon Valley Exercise Analyt Svexa, Menlopark, CA USA..
    Lång, Karin
    Karolinska Univ Hosp, Karolinska Inst, Ctr Mol Med, Dept Med,Div Cardiovasc Med, Solna, Sweden..
    Zhigulev, Artemy
    KTH Royal Inst Technol, Sch Chem Biotechnol & Hlth, Sci Life Lab, Stockholm, Sweden..
    Björck, Hanna M.
    Karolinska Univ Hosp, Karolinska Inst, Ctr Mol Med, Dept Med,Div Cardiovasc Med, Solna, Sweden..
    Franco-Cereceda, Anders
    Karolinska Inst, Dept Mol Med & Surg, Sect Cardiothorac Surg, Stockholm, Sweden..
    Eriksson, Per
    Karolinska Univ Hosp, Karolinska Inst, Ctr Mol Med, Dept Med,Div Cardiovasc Med, Solna, Sweden..
    Andersson, Göran
    Swedish Univ Agr Sci Uppsala, Dept Anim Biosci, Uppsala, Sweden..
    Sahlén, Pelin
    KTH Royal Inst Technol, Sch Chem Biotechnol & Hlth, Sci Life Lab, Stockholm, Sweden..
    Meadows, Jennifer R. S.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindgren, Gabriella
    Swedish Univ Agr Sci Uppsala, Dept Anim Biosci, Uppsala, Sweden.;Katholieke Univ Leuven, Ctr Anim Breeding & Genet, Dept Biosyst, Leuven, Belgium..
    An endothelial regulatory module links blood pressure regulation with elite athletic performance2024In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 20, no 6, article id e1011285Article in journal (Refereed)
    Abstract [en]

    The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.

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  • 31.
    Feiner, Nathalie
    et al.
    Lund Univ, Dept Biol, Lund, Sweden..
    Yang, Weizhao
    Lund Univ, Dept Biol, Lund, Sweden.;Chengdu Inst Biol, Chinese Acad Sci, Chengdu, Peoples R China..
    Bunikis, Ignas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.
    While, Geoffrey M.
    Univ Tasmania, Sch Nat Sci, Sandy Bay, Tas, Australia..
    Uller, Tobias
    Lund Univ, Dept Biol, Lund, Sweden..
    Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards2024In: Science Advances, E-ISSN 2375-2548, Vol. 10, no 14, article id eadk9315Article in journal (Refereed)
    Abstract [en]

    The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such "phenotypic syndromes" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a similar to 400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.

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  • 32.
    Felkel, S.
    et al.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria.;Vienna Grad Sch Populat Genet, Vienna, Austria..
    Vogl, C.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Rigler, D.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Jagannathan, V.
    Univ Bern, Inst Genet, Vetsuisse Fac, Bern, Switzerland..
    Leeb, T.
    Univ Bern, Inst Genet, Vetsuisse Fac, Bern, Switzerland..
    Fries, R.
    Tech Univ Munich, Lehrstuhl Tierzucht, Freising Weihenstephan, Germany..
    Neuditschko, M.
    Agroscope, Swiss Natl Stud Farm, Avenches, Switzerland..
    Rieder, S.
    Agroscope, Swiss Natl Stud Farm, Avenches, Switzerland..
    Velie, B.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Lindgren, G.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Rubin, Carl-Johan
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Schlötterer, C.
    Univ Vet Med Vienna, Inst Populat Genet, Vienna, Austria..
    Rattei, T.
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Div Computat Syst Biol, Vienna, Austria..
    Brem, G.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Wallner, B.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, Vienna, Austria..
    Asian horses deepen the MSY phylogeny2018In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 49, no 1, p. 90-93Article in journal (Refereed)
    Abstract [en]

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

  • 33.
    Felkel, Sabine
    et al.
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria;Vienna Grad Sch Populat Genet, Vienna, Austria.
    Vogl, Claus
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria.
    Rigler, Doris
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria.
    Dobretsberger, Viktoria
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria.
    Chowdhary, Bhanu P.
    United Arab Emirates Univ, Al Ain 15551, U Arab Emirates.
    Distl, Ottmar
    Univ Vet Med Hannover, Inst Anim Breeding & Genet, D-30559 Hannover, Germany.
    Fries, Ruedi
    Tech Univ Muenchen, Lehrstuhl Tierzucht, D-85354 Freising Weihenstephan, Germany.
    Jagannathan, Vidhya
    Univ Bern, Vetsuisse Fac, Inst Genet, CH-3001 Bern, Switzerland.
    Janecka, Jan E.
    Duquesne Univ, Dept Biol Sci, Pittsburgh, PA 15282 USA.
    Leeb, Tosso
    Univ Bern, Vetsuisse Fac, Inst Genet, CH-3001 Bern, Switzerland.
    Lindgren, Gabriella
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden;Katholieke Univ Leuven, Dept Biosyst, B-3001 Leuven, Belgium.
    McCue, Molly
    Univ Minnesota, Vet Populat Med Dept, St Paul, MN 55108 USA.
    Metzger, Julia
    Univ Vet Med Hannover, Inst Anim Breeding & Genet, D-30559 Hannover, Germany.
    Neuditschko, Markus
    Agroscope, Swiss Natl Stud Farm, CH-1580 Avenches, Switzerland.
    Rattei, Thomas
    Univ Vienna, Dept Microbiol & Ecosyst Sci, Div Computat Syst Biol, Althanstr 14, A-1090 Vienna, Austria.
    Raudsepp, Terje
    Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.
    Rieder, Stefan
    Agroscope, Swiss Natl Stud Farm, CH-1580 Avenches, Switzerland.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Schaefer, Robert
    Agroscope, Swiss Natl Stud Farm, CH-1580 Avenches, Switzerland.
    Schloetterer, Christian
    Univ Vet Med Vienna, Inst Populat Genet, A-1210 Vienna, Austria.
    Thaller, Georg
    Univ Kiel, Inst Anim Breeding & Husb, D-24098 Kiel, Germany.
    Tetens, Jens
    Univ Kiel, Inst Anim Breeding & Husb, D-24098 Kiel, Germany;Georg August Univ Gottingen, Dept Anim Sci, Funct Breeding Grp, D-37077 Gottingen, Germany.
    Velie, Brandon
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, S-75007 Uppsala, Sweden;Univ Sydney, Sch Life & Environm Sci, Sydney, NSW 2006, Australia.
    Brem, Gottfried
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria.
    Wallner, Barbara
    Univ Vet Med Vienna, Inst Anim Breeding & Genet, A-1210 Vienna, Austria.
    The horse Y chromosome as an informative marker for tracing sire lines2019In: Scientific Reports, E-ISSN 2045-2322, Vol. 9, article id 6095Article in journal (Refereed)
    Abstract [en]

    Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'crown haplogroup' in Central European and North American breeds. Within the crown, we distinguished 58 haplotypes based on 211 variants, forming three major haplogroups. In addition to two previously characterised haplogroups, one observed in Arabian/Coldblooded and the other in Turkoman/Thoroughbred horses, we uncovered a third haplogroup containing Iberian lines and a North African Barb Horse. In a genealogical showcase, we distinguished the patrilines of the three English Thoroughbred founder stallions and resolved a historic controversy over the parentage of the horse 'Galopin', born in 1872. We observed two nearly instantaneous radiations in the history of Central and Northern European Y-chromosomal lineages that both occurred after domestication 5,500 years ago.

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  • 34.
    Fountain, Toby
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Helsinki, Dept Biosci, Helsinki, Finland.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield, S Yorkshire, England..
    Ravinet, Mark
    Natl Inst Genet, Ecol Genet Div, Mishima, Shizuoka, Japan..
    Naylor, Richard
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Reinhardt, Klaus
    Tech Univ Dresden, Appl Zool, Dept Biol, D-01069 Dresden, Germany..
    Butlin, Roger K.
    Univ Gothenburg, Dept Marine Sci, Gothenburg, Sweden.;Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    A Linkage Map and QTL Analysis for Pyrethroid Resistance in the Bed Bug Cimex lectularius2016In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 6, no 12, p. 4059-4066Article in journal (Refereed)
    Abstract [en]

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

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  • 35.
    Foyer, Pernilla
    et al.
    Swedish Defence University, Department of Military Studies, Military-Technology Division. 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 dogs2016In: Journal of Veterinary Behavior: Clinical Applications and Research, ISSN 1558-7878, E-ISSN 1878-7517, Vol. 11, p. 7-12Article in journal (Refereed)
    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.

  • 36.
    Foyer, Pernilla
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering. Department of Military Studies, Military-Technology Division, Swedish Defence University, Stockholm, Sweden.
    Svedberg, Anna-Maria
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Nilsson, Emma
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Wilsson, Erik
    Swedish Armed Forces Dog Training Unit, Märsta, Sweden.
    Olsen Faresjö, Åshild
    Linköping University, Department of Medical and Health Sciences, Division of Community Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Jensen, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    Behavior and cortisol responses of dogs evaluated in a standardized temperament test for military working dogs2016In: Journal of Veterinary Behavior: Clinical Applications and Research, ISSN 1558-7878, E-ISSN 1878-7517, Vol. 11, p. 7-12Article in journal (Refereed)
    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.

  • 37.
    Garkava-Gustavsson, L.
    et al.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Sätra, J. Skytte af
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Odilbekov, F.
    Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
    Abreu, I.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Johansson, Annika I.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    van de Weg, E.
    Plant Breeding, Wageningen University & Research, Wageningen, Netherlands.
    Zhebentyayeva, T.
    Department of Ecosystem Science and Management, University Park, The Pennsylvania State University, PA, United States.
    Resistance to Neonectria ditissima in apple: insights from metabolomics and lipidomics analyses2023In: Xxxi international horticultural congress (ihc2022): International symposium on breeding and effective use of biotechnology and molecular tools in horticultural crops / [ed] V. Bus; M. Causse, International Society for Horticultural Science , 2023, p. 329-335Conference paper (Refereed)
    Abstract [en]

    European canker, caused by the necrotrophic fungus Neonectria ditissima, is the most serious disease in apple production in Sweden. The disease is favored by a relatively cool and rainy climate. The canker damages have a significant economic impact due to reduced bearing surface and increased orchard management costs. The possibilities for chemical and biological control are very limited. Therefore, directed breeding for new resistant cultivars is urgently needed. Knowledge of inheritance of canker resistance and understanding of molecular mechanisms involved in resistant and susceptible responses to fungal attacks would facilitate breeding. In this study, we evaluated the tempo-spatial differences in plant-pathogen interactions in a set of partially resistant and susceptible cultivars by conducting metabolomic and lipidomic analyses. The major trends in metabolomics and lipidomic profiles were common among cultivars, irrespective of the degree of susceptibility. Several metabolites and lipids varied with time point and cultivar under N. ditissima infection. Putative key metabolites such as suberic acid and jasmonic acid were upregulated in all cultivars upon infection. Additionally, several lipids exhibited changes 30 to 45 days post-inoculation. Thus, the approach used seems to have resulted in a rich data set to be further analyzed in light of ongoing QTL-mapping efforts.

  • 38.
    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 conflict2001In: Proceedings of the Royal Society of London Series B, ISSN 0080-4649, Vol. 268, no 1466, p. 531-539Article in journal (Refereed)
    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.

  • 39.
    Gholami, Soheila
    et al.
    Univ Kurdistan, Fac Agr, Dept Hort Sci & Engn, Sanandaj 6617715175, Iran..
    Vafaee, Yavar
    Univ Kurdistan, Fac Agr, Dept Hort Sci & Engn, Sanandaj 6617715175, Iran.;Univ Kurdistan, Med Plants Breeding & Dev Res Inst, Sanandaj 6617715175, Iran..
    Nazari, Farzad
    Univ Kurdistan, Fac Agr, Dept Hort Sci & Engn, Sanandaj 6617715175, Iran..
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Molecular characterization of endangered Iranian terrestrial orchids using ISSR markers and association with floral and tuber-related phenotypic traits2021In: PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS, ISSN 0971-5894, Vol. 27, no 1, p. 53-68Article in journal (Refereed)
    Abstract [en]

    We aimed to study the genetic diversity, population structure, and phylogeny of Iranian orchids using inter-simple sequence repeat (ISSR) markers to find markers associated with phenotypic traits. Based on the phenotypic analysis, the inflorescence length and the flower number of studied accessions ranged from 3.92 to 27.13 cm and 5 to 50, respectively. On the other hand, the tuber length ranged from 1.80 to 9.35 cm. A total of 310 reproducible ISSR fragments with a size range of 150 to 3000 bp were amplified. ISSR primers provided an average polymorphism information content of 0.391, varied from 0.488 for UBC-876 to 0.351 for UBC-842. Os.J population showed the lowest genetic diversity (H = 0.057 and I = 0.075), while Oyst.JA population showed the highest genetic diversity (H = 0.114 and I = 0.158). At species level, the average coefficient of genetic differentiation (G(ST)) ranged from 0.265 for Orchis simia to 0.587 for Himantoglossum affine. Gene flow (Nm) varied from 1.38 (O. simia) to 0.756 (Anacamptis collina). The UPGMA genetic similarity dendrogram using Jaccard coefficients (r = 0.973) revealed six main clusters. Based on the Bayesian clustering method, the highest probability of the data was achieved when accessions were divided into eight groups. Floral and tuber-related phenotypic traits represented high correlations together, and they were associated with some ISSR bands based on the multiple association analysis. Altogether, ISSR markers proved to be useful for discrimination and clarification of the relationships among species and populations collected from geographically different locations. Furthermore, it could identify the polymorphism among accessions within each population and species.

  • 40.
    Guo, Ying
    et al.
    State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China;Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China;Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden.
    Ou, Jen‐Hsiang
    Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden.
    Zan, Yanjun
    Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden.
    Wang, Yuzhe
    State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China.
    Li, Huifang
    Jiangsu Institute of Poultry Science Yangzhou China.
    Zhu, Chunhong
    Jiangsu Institute of Poultry Science Yangzhou China.
    Chen, Kuanwei
    Jiangsu Institute of Poultry Science Yangzhou China.
    Zhou, Xin
    Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China.
    Hu, Xiaoxiang
    State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China;National Engineering Laboratory for Animal Breeding China Agricultural University Beijing China.
    Carlborg, Örjan
    Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden.
    Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history2021In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 15, no 4, p. 553-564Article in journal (Refereed)
  • 41.
    Guo, Ying
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. China Agr Univ, State Key Lab Anim Biotech Breeding, Beijing, Peoples R China.;China Agr Univ, Natl Engn Lab Anim Breeding, Beijing, Peoples R China.;Yazhouwan Natl Lab, Sanya 572025, Peoples R China..
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Rönneburg, Tilman
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wang, Shouzhi
    Minist Agr & Rural Affairs, Key Lab Chicken Genet & Breeding, Harbin, Peoples R China..
    Li, Hui
    Educ Dept Heilongjiang Prov, Key Lab Anim Genet Breeding & Reprod, Harbin, Peoples R China.;Northeast Agr Univ, Coll Anim Sci & Technol, Harbin, Peoples R China..
    Hu, Xiaoxiang
    China Agr Univ, Natl Engn Lab Anim Breeding, Beijing, Peoples R China..
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens2024In: Poultry Science, ISSN 0032-5791, E-ISSN 1525-3171, Vol. 103, no 1, article id 103232Article in journal (Refereed)
    Abstract [en]

    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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  • 42.
    Guo, Ying
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. China Agr Univ, State Key Lab Anim Biotech Breeding, CN-100193 Beijing, Peoples R China.;China Agr Univ, Natl Engn Lab Anim Breeding, CN-100193 Beijing, Peoples R China.;Yazhouwan Natl Lab, CN-572024 Sanya, Peoples R China..
    Tian, Jing
    China Agr Univ, State Key Lab Anim Biotech Breeding, CN-100193 Beijing, Peoples R China.;China Agr Univ, Natl Engn Lab Anim Breeding, CN-100193 Beijing, Peoples R China.;Inner Mongolia Acad Agr & Anim Husb Sci, CN-010031 Hohhot, Peoples R China..
    Song, Chi
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Han, Wei
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Zhu, Chunhong
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Li, Huifang
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Zhang, Shuangjie
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Chen, Kuanwei
    Jiangsu Inst Poultry Sci, Natl Chickens Genet Resources, CN-225125 Yangzhou, Jiangsu, Peoples R China..
    Li, Ning
    China Agr Univ, State Key Lab Anim Biotech Breeding, CN-100193 Beijing, Peoples R China.;China Agr Univ, Natl Engn Lab Anim Breeding, CN-100193 Beijing, Peoples R China..
    Carlborg, Örjan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hu, Xiaoxiang
    China Agr Univ, State Key Lab Anim Biotech Breeding, CN-100193 Beijing, Peoples R China.;China Agr Univ, Natl Engn Lab Anim Breeding, CN-100193 Beijing, Peoples R China..
    Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum2023In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 12, article id msad273Article in journal (Refereed)
    Abstract [en]

    Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.

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  • 43.
    Guschanski, Katerina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Warnefors, Maria
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    Kaessmann, Henrik
    Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance.
    The evolution of duplicate gene expression in mammalian organs2017In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 27, no 9, p. 1461-1474Article in journal (Refereed)
    Abstract [en]

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

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  • 44.
    Hagberg, Kajsa
    et al.
    Jönköping University, Jönköping International Business School, JIBS, Business Administration.
    Stakston, Emma
    Jönköping University, Jönköping International Business School, JIBS, Business Administration.
    Tebaay, Annika
    Jönköping University, Jönköping International Business School, JIBS, Business Administration.
    Harvesting Innovation: Strategic Planning for Technological Advancements and Regulatory Changes in Swedish Agriculture2023Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Strategic management is crucial for organizational success in today's volatile business environment, and yet, underutilized within agricultural businesses. The agricultural industry is facing rapid change with the introduction of new GM technologies, such as CRISPR-Cas9, and following regulations. Although these technologies have the potential to provide farmers with improved crops containing desired traits, excessive regulations and obstacles hinder its implementation in European agricultural practices. If the upcoming decision regarding CRISPR-Cas9 allows the technology to not be treated under GMO regulations, European agriculture is faced with a major opportunity. However, as procedures are unexplored, organizations are left unprepared.  

    This study investigates the optimal strategic planning approach for Swedish agricultural businesses wanting to efficiently implement new technologies and adjust to regulatory changes. The research is based on a qualitative study that incorporates deductive methodology. It follows a multiple case study research design with eight semi-structured interviews from six Swedish and American case companies as the primary data collection method. By taking inspiration from experienced companies’ planning strategies and including European values, Swedish agricultural companies wanting to implement CRISPR-Cas9 can efficiently navigate changes within the industry while maintaining a competitive advantage. A simple model combining parts from short- and long-term planning frameworks with communication and value creation can guide companies entering the upcoming field.

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    Harvesting Innovation
  • 45.
    Han, Fan
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jamsandekar, Minal
    Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA..
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Su, Leyi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Fuentes Pardo, Angela P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Davis, Brian W.
    Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA..
    Bekkevold, Dorte
    Tech Univ Denmark, Natl Inst Aquat Resources, Silkeborg, Denmark..
    Berg, Florian
    Univ Bergen, Dept Biol Sci, Bergen, Norway.;Inst Marine Res, Bergen, Norway..
    Casini, Michele
    Swedish Univ Agr Sci, Inst Marine Res, Dept Aquat Resources, Lysekil, Sweden.;Univ Bologna, Dept Biol Geol & Environm Sci, Bologna, Italy..
    Dahle, Geir
    Inst Marine Res, Bergen, Norway..
    Farrell, Edward D.
    Univ Coll Dublin, Sci Ctr West, Sch Biol & Environm Sci, Dublin, Ireland..
    Folkvord, Arild
    Univ Bergen, Dept Biol Sci, Bergen, Norway.;Inst Marine Res, Bergen, Norway..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.;Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden..
    Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci2020In: eLIFE, E-ISSN 2050-084X, Vol. 9, article id e61076Article in journal (Refereed)
    Abstract [en]

    Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.

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  • 46.
    Hill, Jason
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Enbody, Erik D.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sprehn, Charlotte Grace
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Bekkevold, Dorte
    Tech Univ Denmark, Natl Inst Aquat Resources, DK-8600 Silkeborg, Denmark.
    Folkvord, Arild
    Univ Bergen, Dept Biol Sci, N-5020 Bergen, Norway;Inst Marine Res, N-5018 Bergen, Norway.
    Laikre, Linda
    Stockholm Univ, Div Populat Genet, Dept Zool, SE-10691 Stockholm, Sweden.
    Kleinau, Gunnar
    Charite Univ Med Berlin, Inst Med Phys & Biophys, Grp Prot Xray Crystallog & Signal Transduct, Charitepl 1, D-10117 Berlin, Germany;Free Univ Berlin, Charitepl 1, D-10117 Berlin, Germany;Humboldt Univ, Charitepl 1, D-10117 Berlin, Germany;Berlin Inst Hlth, Charitepl 1, D-10117 Berlin, Germany.
    Scheerer, Patrick
    Charite Univ Med Berlin, Inst Med Phys & Biophys, Grp Prot Xray Crystallog & Signal Transduct, Charitepl 1, D-10117 Berlin, Germany;Free Univ Berlin, Charitepl 1, D-10117 Berlin, Germany;Humboldt Univ, Charitepl 1, D-10117 Berlin, Germany;Berlin Inst Hlth, Charitepl 1, D-10117 Berlin, Germany.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX 77843 USA.
    Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 37, p. 18473-18478Article in journal (Refereed)
    Abstract [en]

    The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (10(12)) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.

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  • 47. Hjalten, Joakim
    et al.
    Axelsson, E. Petter
    Julkunen-Tiitto, Riitta
    Wennström, Anders
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Pilate, Gilles
    Innate and Introduced Resistance Traits in Genetically Modified Aspen Trees and Their Effect on Leaf Beetle Feeding2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 9, p. e73819-Article in journal (Refereed)
    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.

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  • 48.
    Hong, Jun
    et al.
    Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci, Shanghai 200240, Peoples R China..
    Shi, Qian
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Materials Science and Engineering, Microsystems Technology.
    Biswas, Sukumar
    Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci, Shanghai 200240, Peoples R China..
    Jiang, Shang-Chuan
    Food & Agr Org United Nations, Plant Prod & Protect Div, Rural & Urban Crop & Mechanizat Syst, I-00153 Rome, Italy..
    Shi, Jianxin
    Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, Joint Int Res Lab Metab & Dev Sci, Shanghai 200240, Peoples R China.;Food & Agr Org United Nations, Plant Prod & Protect Div, Rural & Urban Crop & Mechanizat Syst, I-00153 Rome, Italy..
    Moving genome edited crops forward from the laboratory bench to the kitchen table2021In: Food Control, ISSN 0956-7135, E-ISSN 1873-7129, Vol. 122, article id 107790Article, review/survey (Refereed)
    Abstract [en]

    Targeted nuclease based genome editing technology particularly clustered regularly interspaced short palindromic repeats (CRISPR) that allows to manipulate virtually almost any genomic sequences has greatly facilitated both basic and applied researches in plants. However, so far, very few of them has entered to the field and much less to the kitchen table. This review starts with a brief summary of current status of the application of genome editing in crop science and crop breeding and, then identifies technical, ethical, intellectual and other challenges for the commercialization of genome edited crops. This review explores further advances in the specificity and the prediction and detection of off-targets of CRISPR system, and highlights the importance of molecular characterization and the introduction of novel techniques such as nanotechnology to CRISPR system. Finally, this review calls for collaborative efforts in proposing principles and guidelines for moving genome edited crops forward from the laboratory bench to the kitchen table, and emphasizes the equal importance of public outreach.

  • 49.
    Imsland, Freyja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Monogenic Traits Associated with Structural Variants in Chicken and Horse: Allelic and Phenotypic Diversity of Visually Appealing Traits2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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  • 50.
    Johnsson, Martin
    et al.
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Jonsson, Kenneth B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jensen, Per
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Wright, Dominic
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken2016In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 6, no 2, p. 311-319Article in journal (Refereed)
    Abstract [en]

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

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