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  • 1.
    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)
  • 2.
    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.

  • 3.
    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.

  • 4.
    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.

  • 5. 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.

  • 6.
    Danielsson-Tham, Marie-Louise
    et al.
    Örebro University, School of Hospitality, Culinary Arts & Meal Science.
    Tham, WilhelmÖrebro University, School of Hospitality, Culinary Arts & Meal Science.
    Nordic PFGE meeting January 27–28, 2000, Uppsala, Sweden2000Conference proceedings (editor) (Refereed)
  • 7.
    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)
  • 8.
    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.

  • 9.
    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.

  • 10.
    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.

  • 11.
    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, ISSN 2045-2322, 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.

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

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

  • 13.
    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.

  • 14.
    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.

  • 15.
    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.

  • 16.
    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.

  • 17. 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, ISSN 1932-6203, 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.

  • 18.
    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.

  • 19.
    Johnsson, Martin
    et al.
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Jonsson, Kenneth B.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences, Orthopaedics.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jensen, Per
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Wright, Dominic
    Linkoping Univ, Dept Biol, AVIAN Behav Genom & Physiol Grp, S-58183 Linkoping, Sweden..
    Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 2, p. 311-319Article in journal (Refereed)
    Abstract [en]

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

  • 20.
    Krappmann, K
    et al.
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany .
    Wurmser, C
    Chair of Animal Breeding, Technische Universität München, Freising, Germany.
    Repsilber, Dirk
    Research Unit Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Fries, R
    Chair of Animal Breeding, Technische Universität München, Freising, Germany.
    Weikard, R
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Kesting, U
    Landeskontrollverband für Leistungs- und Qualitätsprüfung Mecklenburg-Vorpommern, Güstrow, Germany.
    Kühn, Christa
    Research Unit Molecular Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Short communication: evaluation of bovine milk residues from routine milk testing programs as DNA source for genotyping2012In: Journal of Dairy Science, ISSN 0022-0302, E-ISSN 1525-3198, Vol. 95, no 9, p. 5436-41Article in journal (Refereed)
    Abstract [en]

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

  • 21.
    Lamichhaney, Sangeet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    The genetic basis for adaptation in natural populations2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

  • 22.
    Lamichhaney, Sangeet
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Han, Fan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Berglund, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wang, Chao
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sällman Almen, Markus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    T. Webster, Matthew
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Grant, B. Rosemary
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA..
    R. Grant, Peter
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    A beak size locus in Darwin’s finches facilitated character displacement during a drought2016In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 352, no 6284, p. 470-474Article in journal (Refereed)
    Abstract [en]

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

  • 23.
    Li, Faji
    et al.
    Xinjiang Agr Univ, Coll Agron, Urumqi 830052, Xinjiang, Peoples R China.;CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Wen, Weie
    Xinjiang Agr Univ, Coll Agron, Urumqi 830052, Xinjiang, Peoples R China.;CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Liu, Jindong
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Zhang, Yong
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Cao, Shuanghe
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    He, Zhonghu
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China.;CAAS, Int Maize & Wheat Improvement Ctr CIMMYT China Of, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Rasheed, Awais
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China.;CAAS, Int Maize & Wheat Improvement Ctr CIMMYT China Of, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Jin, Hui
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China.;Heilongjiang Acad Agr Sci, Sinorussia Agr Sci & Technol Cooperat Ctr, 368 Xuefu St, Harbin 150086, Heilongjiang, Peoples R China..
    Zhang, Chi
    KTH, School of Chemical Science and Engineering (CHE).
    Yan, Jun
    CAAS, Inst Cotton Res, 38 Huanghe St, Anyang 455000, Henan, Peoples R China..
    Zhang, Pingzhi
    Anhui Acad Agr Sci, Crop Res Inst, 40 Nongke South St, Hefei 230001, Anhui, Peoples R China..
    Wan, Yingxiu
    Anhui Acad Agr Sci, Crop Res Inst, 40 Nongke South St, Hefei 230001, Anhui, Peoples R China..
    Xia, Xianchun
    CAAS, Natl Wheat Improvement Ctr, Inst Crop Sci, 12 Zhongguancun South St, Beijing 100081, Peoples R China..
    Genetic architecture of grain yield in bread wheat based on genome-wide association studies2019In: BMC Plant Biology, ISSN 1471-2229, E-ISSN 1471-2229, Vol. 19, article id 168Article in journal (Refereed)
    Abstract [en]

    BackgroundIdentification of loci for grain yield (GY) and related traits, and dissection of the genetic architecture are important for yield improvement through marker-assisted selection (MAS). Two genome-wide association study (GWAS) methods were used on a diverse panel of 166 elite wheat varieties from the Yellow and Huai River Valleys Wheat Zone (YHRVWD) of China to detect stable loci and analyze relationships among GY and related traits.ResultsA total of 326,570 single nucleotide polymorphism (SNP) markers from the wheat 90K and 660K SNP arrays were chosen for GWAS of GY and related traits, generating a physical distance of 14,064.8Mb. One hundred and twenty common loci were detected using SNP-GWAS and Haplotype-GWAS, among which two were potentially functional genes underpinning kernel weight and plant height (PH), eight were at similar locations to the quantitative trait loci (QTL) identified in recombinant inbred line (RIL) populations in a previous study, and 78 were potentially new. Twelve pleiotropic loci were detected on eight chromosomes; among these the interval 714.4-725.8Mb on chromosome 3A was significantly associated with GY, kernel number per spike (KNS), kernel width (KW), spike dry weight (SDW), PH, uppermost internode length (UIL), and flag leaf length (FLL). GY shared five loci with thousand kernel weight (TKW) and PH, indicating significantly affected by two traits. Compared with the total number of loci for each trait in the diverse panel, the average number of alleles for increasing phenotypic values of GY, TKW, kernel length (KL), KW, and flag leaf width (FLW) were higher, whereas the numbers for PH, UIL and FLL were lower. There were significant additive effects for each trait when favorable alleles were combined. UIL and FLL can be directly used for selecting high-yielding varieties, whereas FLW can be used to select spike number per unit area (SN) and KNS.ConclusionsThe loci and significant SNP markers identified in the present study can be used for pyramiding favorable alleles in developing high-yielding varieties. Our study proved that both GWAS methods and high-density genetic markers are reliable means of identifying loci for GY and related traits, and provided new insight to the genetic architecture of GY.

  • 24.
    Li, Jingyi
    et al.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA USA;Texas A&M Univ, Coll Vet Med & Biomed Sci, Dept Vet Integrat Biosci, College Stn, TX USA.
    Bed'hom, Bertrand
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Marthey, Sylvain
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Valade, Mathieu
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Dureux, Audrey
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Moroldo, Marco
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Pechoux, Christine
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Coville, Jean-Luc
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Gourichon, David
    INRA, PEAT, Nouzilly, France.
    Vieaud, Agathe
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    Dorshorst, Ben
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA USA.
    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 USA; Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Tixier-Boichard, Michele
    Univ Paris Saclay, INRA, AgroParisTech, GABI, Jouy En Josas, France.
    A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome structure2019In: Pigment Cell & Melanoma Research, ISSN 1755-1471, E-ISSN 1755-148X, Vol. 32, no 3, p. 381-390Article in journal (Refereed)
    Abstract [en]

    The chocolate plumage color in chickens is due to a sex-linked recessive mutation, choc, which dilutes eumelanin pigmentation. Because TYRP1 is sex-linked in chickens, and TYRP1 mutations determine brown coat color in mammals, TYRP1 appeared as the obvious candidate gene for the choc mutation. By combining gene mapping with gene capture, a complete association was identified between the chocolate phenotype and a missense mutation leading to a His214Asn change in the ZnA zinc-binding domain of the protein. A diagnostic test confirmed complete association by screening 428 non-chocolate chickens of various origins. This is the first TYRP1 mutation described in the chicken. Electron microscopy analysis showed that melanosomes were more numerous in feather follicles of chocolate chickens but exhibited an abnormal structure characterized by a granular content and an irregular shape. A similar altered morphology was observed on melanosomes of another TYRP1 mutant in birds, the roux mutation of the quail.

  • 25.
    Li, Jinxiu
    et al.
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China;Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci & Informat, Beijing, Peoples R China.
    Hu, Yiqing
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Li, Li
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Wang, Yuzhe
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Li, Qinghe
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Feng, Chungang
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Lan, He
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Gu, Xiaorong
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Zhao, Yiqiang
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Larsson, Mårten
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Hu, Xiaoxiang
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China.
    Li, Ning
    China Agr Univ, Coll Biol Sci, State Key Labs Agrobiotechnol, Beijing, Peoples R China;China Agr Univ, Natl Engn Lab Anim Breeding, Beijing, Peoples R China;Yunnan Agr Univ, Coll Anim Sci & Technol, Kunming, Yunnan, Peoples R China.
    A Discovery of a Genetic Mutation Causing Reduction of Atrogin-1 Expression in Broiler Chicken Muscle2019In: Frontiers in Genetics, ISSN 1664-8021, E-ISSN 1664-8021, Vol. 10, article id 716Article in journal (Refereed)
    Abstract [en]

    Chickens are bred all over the world and have significant economic value as one of the major agricultural animals. The growth rate of commercial broiler chickens is several times higher than its Red Jungle fowl (RJF) ancestor. To further improve the meat production of commercial chickens, it is quite important to decipher the genetic mechanism of chicken growth traits. In this study, we found that broiler chickens exhibited lower levels of E3 ubiquitin ligase muscle atrophy F-box (MAFbx or Atrogin-1) relative to its RJF ancestor. As a ubiquitin ligase, Atrogin-1 plays a crucial role in muscle development in which its up-regulation often indicates the activation of muscle atrophic pathways. Here, we showed that the Atrogin-1 expression variance partly affects chicken muscle growth rates among different breeds. Furthermore, we demonstrated that the reduced expression of Atrogin-1 in broiler chickens was ascribed to a single nucleotide polymorphism (SNP), which inhibited the binding of transcription regulators and attenuated the enhancer activity. The decreased Atrogin-1 in broiler chickens suppresses the catabolism of muscle protein and preserves muscle mass. Our study facilitates the understanding of the molecular mechanism of chicken muscle development and has a high translational impact in chicken breeding.

  • 26.
    Martínez Barrio, Álvaro
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lamichhaney, Sangeet
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fan, Guangyi
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China; BGI-Shenzhen, Shenzen, China; 5 College of Physics, Qingdao University, Qingdao, China .
    Rafati, Nima
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pettersson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zhang, He
    BGI-Shenzhen, Shenzen, China; College of Physics, Qingdao University, Qingdao, China.
    Dainat, Jacques
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ekman, Diana
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Höppner, Marc P.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jern, Patric
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Martin, Marcel
    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Liu, Xin
    BGI-Shenzhen, Shenzen, China.
    Chen, Wenbin
    BGI-Shenzhen, Shenzhen, China.
    Liang, Xinming
    BGI-Shenzhen, Shenzhen, China.
    Shi, Chengcheng
    BGI-Shenzhen, Shenzhen, China.
    Fu, Yuanyuan
    BGI-Shenzhen, Shenzhen, China.
    Ma, Kailong
    BGI-Shenzhen, Shenzhen, China.
    Zhan, Xiao
    BGI-Shenzhen, Shenzhen, China.
    Feng, Chungang
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Gustafson, Ulla
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sällman Almén, Markus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Blass, Martina
    Department of Aquatic Resources, Institute of Coastal Research, Swedish University of Agricultural Sciences, Öregrund, Sweden.
    Casini, Michele
    Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Marine Research.
    Folkvord, Arild
    Department of Biology, University of Bergen, Bergen, Norway; Hjort Center of Marine Ecosystem Dynamics, Bergen, Norway; Institute of Marine Research, Bergen, Norway .
    Laikre, Linda
    Department of Zoology, Stockholm University.
    Ryman, Nils
    Department of Zoology, Stockholm University, Stockholm, Sweden.
    Lee, Simon Ming-Yuen Lee
    State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao.
    Xu, Xun
    BGI-Shenzhen, Shenzhen, China.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab. Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, Texas, United States.
    The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e12081Article in journal (Refereed)
    Abstract [en]

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

  • 27.
    McCoy, Annette M.
    et al.
    Univ Illinois, Dept Vet Clin Med, Urbana, IL 61801 USA.
    Beeson, Samantha K.
    Univ Minnesota, Vet Populat Med Dept, St Paul, MN 55108 USA.
    Rubin, Carl-Johan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Texas A&M Univ, Dept Vet Integrat Biosci, College Stn, TX USA.
    Caputo, Paul
    Paul Caputo, DVM, Pompano Beach, FL USA.
    Lykkjen, Sigrid
    Norwegian Univ Life Sci, Fac Vet Med, Oslo, Norway.
    Moore, Alison
    Moore Equine Serv, Cambridge, ON, Canada.
    Piercy, Richard J.
    Royal Vet Coll, Dept Clin Sci & Serv, London, England.
    Mickelson, James R.
    Univ Minnesota, Vet & Biomed Sci Dept, St Paul, MN 55108 USA.
    McCue, Molly E.
    Univ Minnesota, Vet Populat Med Dept, St Paul, MN 55108 USA.
    Identification and validation of genetic variants predictive of gait in standardbred horses2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008146Article in journal (Refereed)
    Abstract [en]

    Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature stop codon in the gene DMRT3 is permissive for gaitedness across breeds. However, this mutation is nearly fixed in both American Standardbred trotters and pacers, which perform a diagonal and lateral gait, respectively, during harness racing. This suggests that modifying alleles must influence the preferred gait at racing speeds in these populations. A genome-wide association analysis for the ability to pace was performed in 542 Standardbred horses (n = 176 pacers, n = 366 trotters) with genotype data imputed to similar to 74,000 single nucleotide polymorphisms (SNPs). Nineteen SNPs on nine chromosomes (ECA1, 2, 6, 9, 17, 19, 23, 25, 31) reached genome-wide significance (p < 1.44 x 10(-6)). Variant discovery in regions of interest was carried out via whole-genome sequencing. A set of 303 variants from 22 chromosomes with putative modifying effects on gait was genotyped in 659 Standardbreds (n = 231 pacers, n = 428 trotters) using a high-throughput assay. Random forest classification analysis resulted in an out-of-box error rate of 0.61%. A conditional inference tree algorithm containing seven SNPs predicted status as a pacer or trotter with 99.1% accuracy and subsequently performed with 99.4% accuracy in an independently sampled population of 166 Standardbreds (n = 83 pacers, n = 83 trotters). This highly accurate algorithm could be used by owners/trainers to identify Standardbred horses with the potential to race as pacers or as trotters, according to the genotype identified, prior to initiating training and would enable fine-tuning of breeding programs with designed matings. Additional work is needed to determine both the algorithm's utility in other gaited breeds and whether any of the predictive SNPs play a physiologically functional role in the tendency to pace or tag true functional alleles.

  • 28.
    Mehrabi, Sara
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Candidate genes for resistance and susceptibility to the bird cherry-oat aphid (Rhopalosiphum padi L.) in barley (Hordeum vulgare L.)2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

     

     

  • 29.
    Melzer, Nina
    et al.
    FBN Dummerstorf, Dummerstorf, Germany.
    Jakubowski, S
    LKV, Güstrow, Germany.
    Hartwig, S
    LKV, Güstrow, Germany.
    Kesting, U
    LKV, Güstrow, Germany.
    Wolf, S
    LKV, Güstrow, Germany.
    Nürnberg, Gerd
    FBN Dummerstorf, Dummerstorf, Germany.
    Reinsch, Norbert
    FBN Dummerstorf, Dummerstorf, Germany.
    Repsilber, Dirk
    FBN Dummerstorf, Dummerstorf, Germany.
    Design, infrastructure and database structure for a study on predicting milk phenotypes from genome-wide SNP markers and metabolite profiles2010In: Proceedings of the 9th World Congress on Genetics Applied to Livestock Production, German Society for Animal Science , 2010, p. 427-431Conference paper (Refereed)
  • 30.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Including metabolomic profiles to improve genetic value prediction: an integrated bioinformatics approach using weighted genome-wide marker information2011In: 12th Day of the Doctoal Student: abstracts; 19 May 2011, Dummerstorf / [ed] Seyfert, H.-M., Viereck, G., Dummerstorf, Germany: FBN , 2011, p. 55-58Conference paper (Refereed)
  • 31.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Metabolites as new molecular traits and their role for genetic evaluation of traditional milk traits2012In: Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science: Bratislava, Slovakia, 27 - 31 August 2012, Wageningen: Wageningen Academic Publishers , 2012, p. 88-88Conference paper (Refereed)
  • 32.
    Melzer, Nina
    et al.
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany..
    Wittenburg, Dörte
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Repsilber, Dirk
    Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.
    Simulating SNP data: influence of simulation design on the extent of linkage disequilibrium2010In: 11th Day of the Doctoral Student: abstracts; 19 May 2010, Dummerstorf / [ed] Seyfert, H.-M., Viereck, G., Dummerstorf, Germany: FBN , 2010, p. 19-22Conference paper (Refereed)
  • 33.
    Pavani, Krishna Chaitanya
    University of the Azores.
    Optimization of a specific messenger RNA extraction protocol for fresh and vitrified bovine oocytes to gene expression studies: Specific mRNA extraction protocol for bovine oocytes.2012Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

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

  • 34.
    Qanbari, Saber
    et al.
    Univ Gottingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, Germany;AREEO, ABRII, Dept Anim Biotechnol, Karaj, Iran.
    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.
    Maqbool, Khurram
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Weigend, Steffen
    Friedrich Loeffler Inst, Neustadt, Germany;Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany.
    Weigend, Annett
    Friedrich Loeffler Inst, Neustadt, Germany.
    Geibel, Johannes
    Univ Gottingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, Germany;Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany.
    Kerje, Susanne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wurmser, Christine
    Tech Univ Munich, Chair Anim Breeding, Freising Weihenstephan, Germany.
    Peterson, Andrew Townsend
    Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA.
    Brisbi, I. Lehr, Jr.
    Univ Georgia, Savannah River Ecol Lab, Odum Sch Ecol, Aiken, SC USA.
    Preisinger, Ruedi
    Lohmann Tierzucht GmbH, Cuxhaven, Germany.
    Fries, Ruedi
    Tech Univ Munich, Chair Anim Breeding, Freising Weihenstephan, Germany.
    Simianer, Henner
    Univ Gottingen, Dept Anim Sci, Anim Breeding & Genet Grp, Gottingen, Germany;Univ Gottingen, Ctr Integrated Breeding Res, Gottingen, Germany.
    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.
    Genetics of adaptation in modern chicken2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 4, article id e1007989Article in journal (Refereed)
    Abstract [en]

    We carried out whole genome resequencing of 127 chicken including red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken (Gallus gallus domesticus). We uncovered >21 million high quality SNPs of which 34% are newly detected variants. This panel comprises >115,000 predicted amino-acid altering substitutions as well as 1,100 SNPs predicted to be stop-gain or -loss, several of which reach high frequencies. Signatures of selection were investigated both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during domestication and breed development. Contrasting wild and domestic chicken we confirmed selection at the BCO2 and TSHR loci and identified 34 putative sweeps co-localized with ALX1, KITLG, EPGR, IGF1, DLK1, JPT2, CRAMP1, and GLI3, among others. Analysis of enrichment between groups of wild vs. commercials and broilers vs. layers revealed a further panel of candidate genes including CORIN, SKIV2L2 implicated in pigmentation and LEPR, MEGF10 and SPEF2, suggestive of production-oriented selection. SNPs with marked allele frequency differences between wild and domestic chicken showed a highly significant deficiency in the proportion of amino-acid altering mutations (P<2.5x10(-6)). The results contribute to the understanding of major genetic changes that took place during the evolution of modern chickens and in poultry breeding. Author summary Domestic chickens (Gallus gallus domesticus) provide a critical resource for animal proteins for human nutrition worldwide. Chickens were primarily domesticated from the red jungle fowl (Gallus gallus gallus), a bird that still runs wild in most of Southeast Asia. Human driven selection during domestication and subsequent specialization into meat type (broilers) and egg layer (layers) birds has left detectable signatures of selection within the genome of modern chicken. In this study, we performed whole genome sequencing of 127 chicken including the red jungle fowl and multiple populations of commercial broilers and layers to perform a systematic screening of adaptive changes in modern chicken. Analysis of selection provided a comprehensive list of several tens of independent loci that are likely to have contributed to domestication or improving production. SNP by SNP comparison of allele frequency between groups of wild and domestic chicken showed a highly significant deficiency of the proportion of amino acid altering mutations. This implies that commercial birds have undergone purifying selection reducing the frequency of deleterious variants.

  • 35.
    Reimer, C.
    et al.
    Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany;Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany.
    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.
    Sharifi, A. R.
    Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany;Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany.
    Ha, N. -T
    Weigend, S.
    Friedrich Loeffler Inst, Inst Farm Anim Genet, Holtystr 10, D-31535 Neustadt, Germany;Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany.
    Waldmann, K. -H
    Distl, O.
    Univ Vet Med Fdn, Inst Anim Breeding & Genet, Bunteweg 17p, D-30559 Hannover, Germany.
    Pant, S. D.
    Charles Sturt Univ, Sch Anim & Vet Sci, Graham Ctr Agr Innovat, Locked Bag 588,Boorooma St, Wagga Wagga, NSW, Australia.
    Fredholm, M.
    Univ Copenhagen, Dept Vet & Anim Sci, Gronnegardsvej 3, DK-1870 Frederiksberg C, Denmark.
    Schlather, M.
    Univ Mannheim, Sch Business Informat & Math, A5 6, D-68131 Mannheim, Germany;Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany.
    Simianer, H.
    Univ Goettingen, Dept Anim Sci, Anim Breeding & Genet Grp, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany;Univ Goettingen, Ctr Integrated Breeding Res, Albrecht Thaer Weg 3, D-37075 Gottingen, Germany.
    Analysis of porcine body size variation using re-sequencing data of miniature and large pigs2018In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 687Article in journal (Refereed)
    Abstract [en]

    Background: Domestication has led to substantial phenotypic and genetic variation in domestic animals. In pigs, the size of so called minipigs differs by one order of magnitude compared to breeds of large body size. We used biallelic SNPs identified from re-sequencing data to compare various publicly available wild and domestic populations against two minipig breeds to gain better understanding of the genetic background of the extensive body size variation. We combined two complementary measures, expected heterozygosity and the composite likelihood ratio test implemented in "SweepFinder", to identify signatures of selection in Minipigs. We intersected these sweep regions with a measure of differentiation, namely F-ST, to remove regions of low variation across pigs. An extraordinary large sweep between 52 and 61 Mb on chromosome X was separately analyzed based on SNP-array data of F-2 individuals from a cross of Goettingen Minipigs and large pigs. Results: Selective sweep analysis identified putative sweep regions for growth and subsequent gene annotation provided a comprehensive set of putative candidate genes. A long swept haplotype on chromosome X, descending from the Goettingen Minipig founders was associated with a reduction of adult body length by 3% in F-2 cross-breds. Conclusion: The resulting set of genes in putative sweep regions implies that the genetic background of body size variation in pigs is polygenic rather than mono-or oligogenic. Identified genes suggest alterations in metabolic functions and a possible insulin resistance to contribute to miniaturization. A size QTL located within the sweep on chromosome X, with an estimated effect of 3% on body length, is comparable to the largest known in pigs or other species. The androgen receptor AR, previously known to influence pig performance and carcass traits, is the most obvious potential candidate gene within this region.

  • 36.
    Rozpadek, Piotr
    et al.
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland; Institute of Plant Physiology, Polish Academy of Sciences, Kraków, Poland.
    Rapala-Kozik, Maria
    Department of Comparative Biochemistry and Bioanalytics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
    Wezowicz, Katarzyna
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.
    Grandin, Anna
    Örebro University, School of Science and Technology.
    Karlsson, Stefan
    Örebro University, School of Science and Technology.
    Wazny, Rafal
    Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
    Anielska, Teresa
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland.
    Turnau, Katarzyna
    Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
    Arbuscular mycorrhiza improves yield and nutritional properties of onion (Allium cepa)2016In: Plant physiology and biochemistry (Paris), ISSN 0981-9428, E-ISSN 1873-2690, Vol. 107, p. 264-272Article in journal (Refereed)
    Abstract [en]

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

  • 37.
    Silva, C. N. S.
    et al.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;James Cook Univ, Coll Marine & Environm Sci, Ctr Sustainable Trop Fisheries & Aquaculture, Townsville, Qld, Australia.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Hagen, I. J.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronnegard, L.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Dalarna Univ, Sch Technol & Business Studies, Falun, Sweden.
    Billing, A. M.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kvalnes, T.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Kemppainen, P.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ronning, B.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Ringsby, T. H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Saether, B-E
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Jensen, H.
    Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Husby, A.
    Univ Helsinki, Dept Biosci, Metapopulat Res Ctr, Helsinki, Finland;Norwegian Univ Sci & Technol, Dept Biol, Ctr Biodivers Dynam, Trondheim, Norway.
    Insights into the genetic architecture of morphological traits in two passerine bird species2017In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 119, no 3, p. 197-205Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 39.
    Sullivan, Alexis R.
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. School of Forest Resources and Environmental Science, Michigan Technological Universi ty, 1400 Townsend Drive, Houghton, MI 49931, USA.
    Owusu, Sandra A.
    Weber, Jaime A.
    Hipp, Andrew L.
    Gailing, Oliver
    Hybridization and divergence in multi-species oak (Quercus) communities2016In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 181, no 1, p. 99-114Article in journal (Refereed)
    Abstract [en]

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

  • 40.
    Sundström, Elisabeth
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Imsland, Freyja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mikko, Sofia
    Wade, Claire
    Sigurdsson, Snaevar
    Pielberg, Gerli R
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Golovko, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Curik, Ino
    Seltenhammer, Monika H.
    Soelkner, Johann
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 365-Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 41.
    Sutherland, D. A. T.
    et al.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Honaker, C. F.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Dorshorst, B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Siegel, P. B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Asymmetries, heterosis, and phenotypic profiles of red junglefowl, White Plymouth Rocks, and F-1 and F-2 reciprocal crosses2018In: Journal of Applied Genetics, ISSN 1234-1983, E-ISSN 2190-3883, Vol. 59, no 2, p. 193-201Article in journal (Refereed)
    Abstract [en]

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

  • 42.
    Sutherland, Dez-Ann Antoinette Therese
    et al.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Honaker, Christa Ferst
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Dorshorst, Ben
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Brisbin, I. Lehr, Jr.
    Univ Georgia, Savannah River Ecol Lab, Odum Sch Ecol, Aiken, SC USA.
    Siegel, Paul B.
    Virginia Tech, Dept Anim & Poultry Sci, Blacksburg, VA 24061 USA.
    Growth patterns for three generations of an intercross between red junglefowl and chickens selected for low body weight2018In: Journal of Animal Breeding and Genetics, ISSN 0931-2668, E-ISSN 1439-0388, Vol. 135, no 4, p. 300-310Article in journal (Refereed)
    Abstract [en]

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

  • 43. Torkzaban, Bahareh
    et al.
    Kayvanjoo, Amir Hossein
    Ardalan, Arman
    KTH, School of Biotechnology (BIO), Gene Technology. Natl Inst Genet Engn & Biotechnol, Iran.
    Mousavi, Soraya
    Mariotti, Roberto
    Baldoni, Luciana
    Ebrahimie, Esmaeil
    Ebrahimi, Mansour
    Hosseini-Mazinani, Mehdi
    Machine Learning Based Classification of Microsatellite Variation: An Effective Approach for Phylogeographic Characterization of Olive Populations2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 11, article id e0143465Article in journal (Refereed)
    Abstract [en]

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

  • 44.
    Vargas, Alexander O
    et al.
    Laboratorio de Ontogenia y Filogenia, Departamento de Biología, Facultad de Ciencias Universidad de Chile, Las Palermas, Ñuñoa, Santiago, Chile.
    Krabichler, Quirin
    TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
    Guerrero-Bosagna, Carlos
    Linköping University, Department of Physics, Chemistry and Biology, Biology. Linköping University, Faculty of Science & Engineering.
    An Epigenetic Perspective on the Midwife Toad Experiments of Paul Kammerer (1880-1926)2017In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, ISSN 1552-5007, E-ISSN 1552-5015, Vol. 328, no 1-2, p. 179-192Article, review/survey (Refereed)
    Abstract [en]

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

  • 45.
    Velie, Brandon D.
    et al.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Univ Sydney, Sch Life & Environm Sci, Sydney, NSW, Australia.
    Lillie, Mette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Fegraeus, Kim Jaderkvist
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Rosengren, Maria K.
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Sole, Marina
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden.
    Wiklund, Maja
    Swedish Univ Agr Sci, Dept Clin Sci, Uppsala, Sweden.
    Ihler, Carl-Fredrik
    Norwegian Univ Life Sci, Dept Compan Anim Clin Sci, Oslo, Norway.
    Strand, Eric
    Norwegian Univ Life Sci, Dept Compan Anim Clin Sci, Oslo, Norway.
    Lindgren, Gabriella
    Swedish Univ Agr Sci, Dept Anim Breeding & Genet, Uppsala, Sweden;Katholieke Univ Leuven, Dept Biosyst, Livestock Genet, Leuven, Belgium.
    Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model2019In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 20, article id 104Article in journal (Refereed)
    Abstract [en]

    BackgroundHorses have been strongly selected for speed, strength, and endurance-exercise traits since the onset of domestication. As a result, highly specialized horse breeds have developed with many modern horse breeds often representing closed populations with high phenotypic and genetic uniformity. However, a great deal of variation still exists between breeds, making the horse particularly well suited for genetic studies of athleticism. To identify genomic regions associated with athleticism as it pertains to trotting racing ability in the horse, the current study applies a pooled sequence analysis approach using a unique Nordic horse model.ResultsPooled sequence data from three Nordic horse populations were used for F-ST analysis. After strict filtering, F-ST analysis yielded 580 differentiated regions for trotting racing ability. Candidate regions on equine chromosomes 7 and 11 contained the largest number of SNPs (n=214 and 147, respectively). GO analyses identified multiple genes related to intelligence, energy metabolism, and skeletal development as potential candidate genes. However, only one candidate region for trotting racing ability overlapped a known racing ability QTL.ConclusionsNot unexpected for genomic investigations of complex traits, the current study identified hundreds of candidate regions contributing to trotting racing ability in the horse. Likely resulting from the cumulative effects of many variants across the genome, racing ability continues to demonstrate its polygenic nature with candidate regions implicating genes influencing both musculature and neurological development.

  • 46.
    Weston, David J.
    et al.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA; Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA.
    Turetsky, Merritt R.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Johnson, Matthew G.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX USA.
    Granath, Gustaf
    Uppsala universitet, Växtekologi och evolution.
    Lindo, Zoe
    Univ Western Ontario, Dept Biol, London, ON, Canada.
    Belyea, Lisa R.
    Queen Mary Univ London, Sch Geog, London, England.
    Rice, Steven K.
    Union Coll, Dept Biol Sci, Schenectady, NY USA.
    Hanson, David T.
    Univ New Mexico, Dept Biol, Albuquerque, NM USA.
    Engelhardt, Katharina A. M.
    Univ Maryland, Appalachian Lab, Ctr Environm Sci, Frostburg, MD USA.
    Schmutz, Jeremy
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA; Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
    Dorrepaal, Ellen
    Ume Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, Abisko, Sweden.
    Euskirchen, Eugenie S.
    Univ Alaska, Inst Arctic Biol, Fairbanks, AK USA.
    Stenoien, Hans K.
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Trondheim, Norway.
    Szovenyi, Peter
    Univ Zurich, Dept Systemat & Evolutionary Bot, Zurich, Switzerland.
    Jackson, Michelle
    Duke Univ, Dept Biol, Durham, NC USA.
    Piatkowski, Bryan T.
    Duke Univ, Dept Biol, Durham, NC USA.
    Muchero, Wellington
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Norby, Richard J.
    Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA ;Oak Ridge Natl Lab, Environm Sci Div, Oak Ridge, TN USA.
    Kostka, Joel E.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Glass, Jennifer B.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Rydin, Håkan
    Uppsala universitet, Växtekologi och evolution.
    Limpens, Juul
    Wageningen Univ, Dept Environm Sci, Plant Ecol & Nat Conservat Grp, Wageningen, Netherlands.
    Tuittila, Eeva-Stiina
    Univ Eastern Finland, Sch Forest Sci, Peatland & Soil Ecol Grp, Joensuu, Finland.
    Ullrich, Kristian K.
    Max Planck Inst Evolutionary Biol, Plon, Germany.
    Carrell, Alyssa
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Benscoter, Brian W.
    Florida Atlantic Univ, Dept Biol Sci, Davie, FL USA.
    Chen, Jin-Gui
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Oke, Tobi A.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Nilsson, Mats B.
    Swedish Univ Agr Sci, Dept Forest Ecol & Management, Umeå, Sweden.
    Ranjan, Priya
    Univ Tennessee, Dept Plant Sci, Knoxville, TN USA.
    Jacobson, Daniel
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Lilleskov, Erik A.
    US Forest Serv, Res Stn, Houghton, MI USA.
    Clymo, R. S.
    Queen Mary Univ London, Sch Biol & Chem Sci, London, England.
    Shaw, A. Jonathan
    Duke Univ, Dept Biol, Durham, NC USA.
    The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 1, p. 16-25Article in journal (Refereed)
    Abstract [en]

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

  • 47.
    Weston, David J.
    et al.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA; Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA.
    Turetsky, Merritt R.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Johnson, Matthew G.
    Texas Tech Univ, Dept Biol Sci, Lubbock, TX USA.
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lindo, Zoe
    Univ Western Ontario, Dept Biol, London, ON, Canada.
    Belyea, Lisa R.
    Queen Mary Univ London, Sch Geog, London, England.
    Rice, Steven K.
    Union Coll, Dept Biol Sci, Schenectady, NY USA.
    Hanson, David T.
    Univ New Mexico, Dept Biol, Albuquerque, NM USA.
    Engelhardt, Katharina A. M.
    Univ Maryland, Appalachian Lab, Ctr Environm Sci, Frostburg, MD USA.
    Schmutz, Jeremy
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA; Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
    Dorrepaal, Ellen
    Ume Univ, Dept Ecol & Environm Sci, Climate Impacts Res Ctr, Abisko, Sweden.
    Euskirchen, Eugenie S.
    Univ Alaska, Inst Arctic Biol, Fairbanks, AK USA.
    Stenoien, Hans K.
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Trondheim, Norway.
    Szovenyi, Peter
    Univ Zurich, Dept Systemat & Evolutionary Bot, Zurich, Switzerland.
    Jackson, Michelle
    Duke Univ, Dept Biol, Durham, NC USA.
    Piatkowski, Bryan T.
    Duke Univ, Dept Biol, Durham, NC USA.
    Muchero, Wellington
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Norby, Richard J.
    Oak Ridge Natl Lab, Climate Change Sci Inst, Oak Ridge, TN USA ;Oak Ridge Natl Lab, Environm Sci Div, Oak Ridge, TN USA.
    Kostka, Joel E.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Glass, Jennifer B.
    Georgia Inst Technol, Sch Biol, Atlanta, GA USA; Georgia Inst Technol, Sch Earth & Atmospher Sci, Atlanta, GA USA.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Limpens, Juul
    Wageningen Univ, Dept Environm Sci, Plant Ecol & Nat Conservat Grp, Wageningen, Netherlands.
    Tuittila, Eeva-Stiina
    Univ Eastern Finland, Sch Forest Sci, Peatland & Soil Ecol Grp, Joensuu, Finland.
    Ullrich, Kristian K.
    Max Planck Inst Evolutionary Biol, Plon, Germany.
    Carrell, Alyssa
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Benscoter, Brian W.
    Florida Atlantic Univ, Dept Biol Sci, Davie, FL USA.
    Chen, Jin-Gui
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Oke, Tobi A.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Nilsson, Mats B.
    Swedish Univ Agr Sci, Dept Forest Ecol & Management, Umeå, Sweden.
    Ranjan, Priya
    Univ Tennessee, Dept Plant Sci, Knoxville, TN USA.
    Jacobson, Daniel
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN USA.
    Lilleskov, Erik A.
    US Forest Serv, Res Stn, Houghton, MI USA.
    Clymo, R. S.
    Queen Mary Univ London, Sch Biol & Chem Sci, London, England.
    Shaw, A. Jonathan
    Duke Univ, Dept Biol, Durham, NC USA.
    The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 1, p. 16-25Article in journal (Other academic)
    Abstract [en]

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

  • 48.
    Wetterskog, Robert
    Linnaeus University, Faculty of Technology, Department of Forestry and Wood Technology.
    Somatiska embryogenes-plantors överlevnad och höjdtillväxt vid fyra ljusförhållanden2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Somatiska embryogenes är en mikroförökningsmetod som med hjälp av tillväxtreglerande medel får en växtdel att bilda skott och rötter i ett speciellt odlingssubstrat sterila förhållanden. Kunskapen vad gäller förutsättningar för groning och plantetablering efter detta laboratoriestudium är dock begränsad. I denna studie undersökte hur två kloner av SE-groddar av gran etablerade sig i olika ljusförhållanden avseende våglängd och intensitet i fyra växtmiljöer. Etableringen bedömdes utifrån plantornas överlevnad och höjdtillväxt. Vid sista inventeringstillfället var 62 SE-plantor vid liv och 18 plantor var döda. Ingen signifikant skillnad kunde påvisas i överlevnad mellan de olika växtmiljöerna, inte heller mellan klonerna i respektive miljö eller oberoende av miljö. Signifikant skillnad i höjdtillväxten mellan klonerna kunde påvisas inom alla växtmiljöer, men inte mellan växtmiljöerna oberoende av klon. Det fanns en tendens att ljusförhållanden med en ljusintensitet på 100 μmol och rött ljus inom våglängderna 610-760 nm gav bäst etablering för SE-groddarna. Studien visade också att det var skillnad i etablering mellan de två kloner som användes.

  • 49.
    Wittenburg, Dörte
    et al.
    Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummersdorf, Germany.
    Melzer, Nina
    Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummersdorf, Germany.
    Reinsch, Norbert
    Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummersdorf, Germany.
    Repsilber, Dirk
    Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummersdorf, Germany.
    Milk metabolites and their genetic variability2012In: Book of Abstracts of the 63rd Annual Meeting of the European Federation of Animal Science: Bratislava, Slovakia, 27 - 31 August 2012, Wageningen: Wageningen Academic Publishers, 2012, p. 94-94Conference paper (Refereed)
  • 50.
    Yusnizar, Y.
    et al.
    Bogor Agr Univ IPB, Grad Sch, Bogor 16680, Indonesia.;Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden.;Indonesian Inst Sci LIPI, Biotechnol Res Ctr, Cibinong 16912, Indonesia..
    Wilbe, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medicinsk genetik och genomik. Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Herlino, A. O.
    Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Sumantri, C.
    Bogor Agr Univ IPB, Fac Anim Sci, Dept Anim Prod & Technol, Bogor 16680, Indonesia..
    Noor, R. Rachman
    Bogor Agr Univ IPB, Fac Anim Sci, Dept Anim Prod & Technol, Bogor 16680, Indonesia..
    Boediono, A.
    Bogor Agr Univ IPB, Fac Vet Med, Dept Anat Physiol & Pharmacol, Bogor 16680, Indonesia..
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Andersson, G.
    Swedish Univ Agr Sci SLU, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Microphthalmia-associated transcription factor mutations are associated with white-spotted coat color in swamp buffalo2015In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 46, no 6, p. 676-682Article in journal (Refereed)
    Abstract [en]

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

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