Orjan Carlborg

Summary

Country: Sweden

Publications

  1. pmc Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana
    Xia Shen
    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    PLoS Genet 8:e1002839. 2012
  2. pmc Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens
    Weronica Ek
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences Uppsala, Sweden
    Front Genet 3:29. 2012
  3. pmc Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross
    Zheya Sheng
    State Key Laboratory for Agro Biotechnology, China Agricultural University, Beijing, People s Republic of China
    BMC Genomics 14:151. 2013
  4. pmc A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed
    Jiazhong Guo
    College of Animal Science and Technology, Northwest A and F University, Yangling, Shaanxi 712100, People s Republic of China
    BMC Genet 13:82. 2012
  5. pmc An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden
    Genetics 178:2315-26. 2008
  6. pmc Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight
    Per Wahlberg
    Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden
    BMC Genomics 10:248. 2009
  7. doi request reprint Genetic analysis of metabolic traits in an intercross between body weight-selected chicken lines
    Weronica Ek
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Physiol Genomics 42:20-2. 2010
  8. pmc How to perform meaningful estimates of genetic effects
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    PLoS Genet 4:e1000062. 2008
  9. ncbi request reprint Major growth QTLs in fowl are related to fearful behavior: possible genetic links between fear responses and production traits in a red junglefowl x white leghorn intercross
    Karin E Schütz
    Department of Animal Environment and Health, Section of Ethology, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Behav Genet 34:121-30. 2004
  10. pmc Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens
    Lucy Crooks
    Department of Cell and Molecular Biology, Uppsala University, Uppsala, SE 75124, Sweden
    G3 (Bethesda) 3:1253-60. 2013

Detail Information

Publications43

  1. pmc Inheritance beyond plain heritability: variance-controlling genes in Arabidopsis thaliana
    Xia Shen
    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
    PLoS Genet 8:e1002839. 2012
    ....
  2. pmc Generation of a multi-locus chicken introgression line to study the effects of genetic interactions on metabolic phenotypes in chickens
    Weronica Ek
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences Uppsala, Sweden
    Front Genet 3:29. 2012
    ..This confirmed introgression line will facilitate later detailed studies of the effects of genetic interactions on complex traits in this population, including growth, and body-composition traits...
  3. pmc Genetic dissection of growth traits in a Chinese indigenous × commercial broiler chicken cross
    Zheya Sheng
    State Key Laboratory for Agro Biotechnology, China Agricultural University, Beijing, People s Republic of China
    BMC Genomics 14:151. 2013
    ....
  4. pmc A genome-wide association study using international breeding-evaluation data identifies major loci affecting production traits and stature in the Brown Swiss cattle breed
    Jiazhong Guo
    College of Animal Science and Technology, Northwest A and F University, Yangling, Shaanxi 712100, People s Republic of China
    BMC Genet 13:82. 2012
    ....
  5. pmc An improved method for quantitative trait loci detection and identification of within-line segregation in F2 intercross designs
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, 75124 Uppsala, Sweden
    Genetics 178:2315-26. 2008
    ..Extensions of FIA and its applications on other intercross populations including backcrosses, advanced intercross lines, and heterogeneous stocks are also discussed...
  6. pmc Genetic analysis of an F(2) intercross between two chicken lines divergently selected for body-weight
    Per Wahlberg
    Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Uppsala, Sweden
    BMC Genomics 10:248. 2009
    ..Furthermore, we utilized genotype data from ~13,000 SNPs to search the genome for potential selective sweeps that have occurred in the selected lines...
  7. doi request reprint Genetic analysis of metabolic traits in an intercross between body weight-selected chicken lines
    Weronica Ek
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Physiol Genomics 42:20-2. 2010
    ....
  8. pmc How to perform meaningful estimates of genetic effects
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    PLoS Genet 4:e1000062. 2008
    ..We also discuss further implementations leading to a completely general genotype-phenotype map...
  9. ncbi request reprint Major growth QTLs in fowl are related to fearful behavior: possible genetic links between fear responses and production traits in a red junglefowl x white leghorn intercross
    Karin E Schütz
    Department of Animal Environment and Health, Section of Ethology, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Behav Genet 34:121-30. 2004
    ..The results show that loci affecting important production traits are located in the same chromosomal region as loci affecting different fear-related behaviors...
  10. pmc Identification of null alleles and deletions from SNP genotypes for an intercross between domestic and wild chickens
    Lucy Crooks
    Department of Cell and Molecular Biology, Uppsala University, Uppsala, SE 75124, Sweden
    G3 (Bethesda) 3:1253-60. 2013
    ..We suggest that our approach could be a useful complement to linkage analysis in experimental crosses. ..
  11. pmc Dissection of the genetic architecture of body weight in chicken reveals the impact of epistasis on domestication traits
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
    Genetics 179:1591-9. 2008
    ..Our results demonstrate that the effects of many genes are dependent on genetic interactions with other loci and how their involvement in the domestication process relies on these interactions...
  12. ncbi request reprint Chicken genomics: feather-pecking and victim pigmentation
    Linda Keeling
    Department of Animal Environment and Health, Swedish University of Agricultural Sciences, PO Box 234, 53223 Skara, Sweden
    Nature 431:645-6. 2004
    ....
  13. pmc Replication and explorations of high-order epistasis using a large advanced intercross line pedigree
    Mats Pettersson
    Department of Animal Breeding and Genetics, Swedish University of Agriculture Sciences SLU, Uppsala, Sweden
    PLoS Genet 7:e1002180. 2011
    ..Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait...
  14. pmc Fine mapping and replication of QTL in outbred chicken advanced intercross lines
    Francois Besnier
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Genet Sel Evol 43:3. 2011
    ..Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature...
  15. pmc Increasing the efficiency of variance component quantitative trait loci analysis by using reduced-rank identity-by-descent matrices
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    Genetics 176:1935-8. 2007
    ..The relative advantage of using our method increases with pedigree size, marker density, and linkage disequilibrium, indicating even greater improvements in the future...
  16. doi request reprint Modelling of genetic interactions improves prediction of hybrid patterns--a case study in domestic fowl
    José M Alvarez-Castro
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Genet Res (Camb) 94:255-66. 2012
    ..This observation coincides with the hypothesis that hybridization tends to break up co-adapted gene complexes, i.e. generate Bateson-Dobzhansky-Muller incompatibilities...
  17. pmc A genetic algorithm based method for stringent haplotyping of family data
    Francois Besnier
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    BMC Genet 10:57. 2009
    ..It is therefore important to only use haplotypes that are strongly supported by the available data for IBD estimation, to avoid introducing new errors due to erroneous linkage phases...
  18. pmc Phenotypic evolution from genetic polymorphisms in a radial network architecture
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    BMC Biol 5:50. 2007
    ..To date, most of our understanding comes from theoretical, model-based studies, and it remains difficult to assess how realistic their conclusions are as they lack empirical support...
  19. ncbi request reprint Epistasis and the release of genetic variation during long-term selection
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, Box 598, SE 75124 Uppsala, Sweden
    Nat Genet 38:418-20. 2006
    ..The interactions in this radial network mediate a considerably larger selection response than predicted by a single-locus model...
  20. doi request reprint How to deal with genotype uncertainty in variance component quantitative trait loci analyses
    Xia Shen
    The Linnaeus Centre for Bioinformatics, Uppsala University, Sweden
    Genet Res (Camb) 93:333-42. 2011
    ..Our simulations show that the bias of variance component estimates using traditional expected IBD matrix can be adjusted by accounting for the distribution and that the calculations are computationally feasible for large pedigrees...
  21. pmc A global search reveals epistatic interaction between QTL for early growth in the chicken
    Orjan Carlborg
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, S 751 24 Uppsala, Sweden
    Genome Res 13:413-21. 2003
    ..Several of the detected loci affected either early or late growth but not both. Very few loci affected the entire growth process, which points out that early and late growth, at least to some extent, have different genetic regulation...
  22. ncbi request reprint Epistasis: too often neglected in complex trait studies?
    Orjan Carlborg
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE 751 24 Uppsala, Sweden
    Nat Rev Genet 5:618-25. 2004
  23. pmc A unified model for functional and statistical epistasis and its application in quantitative trait Loci analysis
    José M Alvarez-Castro
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    Genetics 176:1151-67. 2007
    ..Furthermore, we use our theoretical foundations to conceptually clarify functional and statistical epistasis, discuss the advantages of NOIA over previous theory, and stress the importance of linking functional and statistical models...
  24. pmc Genetic architecture of tameness in a rat model of animal domestication
    Frank W Albert
    Department of Genetics and Pathology, Uppsala University, 75123 Uppsala, Sweden
    Genetics 182:541-54. 2009
    ..The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general...
  25. pmc SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools
    Stefan Marklund
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE 750 07 Uppsala, Sweden
    BMC Genomics 11:665. 2010
    ....
  26. doi request reprint Higher order interactions: detection of epistasis using machine learning and evolutionary computation
    Ronald M Nelson
    Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Methods Mol Biol 1019:499-518. 2013
    ..Here we show that evolutionary algorithms are a useful tool in high-dimensional analyses designed to identify gene-gene interactions in current large-scale genotypic data...
  27. doi request reprint Selection on variance-controlling genes: adaptability or stability
    Mats E Pettersson
    Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Evolution 66:3945-9. 2012
    ....
  28. pmc Genome-wide effects of long-term divergent selection
    Anna M Johansson
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    PLoS Genet 6:e1001188. 2010
    ....
  29. doi request reprint Whole-genome resequencing reveals loci under selection during chicken domestication
    Carl Johan Rubin
    Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE 75123 Uppsala, Sweden
    Nature 464:587-91. 2010
    ..This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research...
  30. pmc Separation of base allele and sampling term effects gives new insights in variance component QTL analysis
    Lars Rönnegård
    Linnaeus Centre for Bioinformatics, Uppsala University, BMC, Box 598, SE 75124 Uppsala, Sweden
    BMC Genet 8:1. 2007
    ..In the traditional VC model, each individual has a unique QTL effect and the relationship between these random effects is given as a covariance structure (known as the identity-by-descent (IBD) matrix)...
  31. pmc Strong signatures of selection in the domestic pig genome
    Carl Johan Rubin
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE 751 23 Uppsala, Sweden
    Proc Natl Acad Sci U S A 109:19529-36. 2012
    ....
  32. ncbi request reprint Efficient algorithms for quantitative trait loci mapping problems
    Kajsa Ljungberg
    Department of Scientific Computing, Information Technology, Uppsala University, Box 337, SE 751 05 Uppsala, Sweden
    J Comput Biol 9:793-804. 2002
    ..For example, using the new algorithms, it is reasonable to perform permutation testing using exhaustive search on populations of 200 individuals using an epistatic two-QTL model...
  33. doi request reprint Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens
    Weronica Ek
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
    Dev Comp Immunol 38:352-9. 2012
    ..These results illustrate the usefulness of the UCD-200 chicken as a model of human SSc and motivate further in-depth functional studies of the implicated candidate genes...
  34. ncbi request reprint QTL analysis of a red junglefowl x White Leghorn intercross reveals trade-off in resource allocation between behavior and production traits
    Karin Schutz
    Swedish University of Agricultural Sciences, Department of Animal Environment and Health, Section of Ethology, POB 234, SE 532 23 Skara, Sweden
    Behav Genet 32:423-33. 2002
    ..The results suggest a trade-off between energy-demanding behavior and high production and that some of this may be caused by genetic linkage or pleiotropic gene effects...
  35. pmc Dynamics of adaptive alleles in divergently selected body weight lines of chickens
    Mats E Pettersson
    Department of Clinical Sciences, Swedish University of Agricultural Sciences, 750 07, Uppsala, Sweden
    G3 (Bethesda) 3:2305-12. 2013
    ..This result illustrates the dependence of continued long-term selection response on standing genetic variation at many loci as well as strong, novel, beneficial mutations. ..
  36. pmc Variance heterogeneity in Saccharomyces cerevisiae expression data: trans-regulation and epistasis
    Ronald M Nelson
    Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
    PLoS ONE 8:e79507. 2013
    ....
  37. ncbi request reprint Evolutionary potential of hidden genetic variation
    Arnaud Le Rouzic
    Linnaeus Centre for Bioinformatics, Biomedical Centre, Box 598, Uppsala University, SE 751 24 Uppsala, Sweden
    Trends Ecol Evol 23:33-7. 2008
    ..We introduce the 'genetic charge' concept, to describe how the architecture of a trait can be 'charged' with potential for evolutionary change that can later be 'discharged' in response to selection...
  38. pmc A general and efficient method for estimating continuous IBD functions for use in genome scans for QTL
    Francois Besnier
    Linnaeus Centre for Bioinformatics, Uppsala University, SE 75124 Uppsala, Sweden
    BMC Bioinformatics 8:440. 2007
    ..Here, we propose a new approach to estimate IBD as continuous functions rather than as discrete values...
  39. pmc Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis
    Katarina Tengvall
    Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
    PLoS Genet 9:e1003475. 2013
    ..Our results may yield further insight into the genetics behind both canine and human AD...
  40. pmc Hierarchical likelihood opens a new way of estimating genetic values using genome-wide dense marker maps
    Xia Shen
    The Linnaeus Centre for Bioinformatics, Uppsala University, Uppsala, Sweden
    BMC Proc 5:S14. 2011
    ..We propose the use of hierarchical likelihood to solve such problems...
  41. pmc PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties
    Xidan Li
    Division of Computational Genetics, Department of Clinical Sciences, Swedish University of Agricultural Sciences Uppsala, Sweden
    Front Genet 4:21. 2013
    ....
  42. pmc qtl.outbred: Interfacing outbred line cross data with the R/qtl mapping software
    Ronald M Nelson
    Department of Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE 75007 Uppsala, Sweden
    BMC Res Notes 4:154. 2011
    ..abstract:..
  43. ncbi request reprint Use of randomization testing to detect multiple epistatic QTLs
    Orjan Carlborg
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, BMC, Box 597, S 751 24 Uppsala, Sweden
    Genet Res 79:175-84. 2002
    ..We believe that this method will facilitate the evaluation of the importance at epistatic interaction among QTLs controlling multifactorial traits and disorders...