Population structure and linkage disequilibrium in barley assessed by DArT markers

Theoretical and Applied Genetics

Volumn 119, Issue 1, 2009, Pages 43-52

  Zhang, Li Yi ^a   Marchand, Suzanne ^a   Tinker, Nicholas A ^b   Belzile, François ^a  

^a UNIVERSITÉ LAVAL   (Canada)

^b OTTAWA RESEARCH AND DEVELOPMENT CENTRE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF MOLECULAR VARIANCES; ASSOCIATION MAPPING; BREEDING LINES; COMPLEX TRAITS; GENETIC DISTANCES; GENETIC DIVERSITY; GENETIC VARIANCE; GEOGRAPHIC CLUSTERING; HIGH CONFIDENCE; HORDEUM VULGARE; INFORMATION CONTENTS; LARGE GROUPS; LINKAGE DISEQUILIBRIUM; MEAN VALUES; POPULATION STRUCTURES; PRINCIPAL COORDINATE ANALYSIS; REPRODUCIBILITY; ROW LINE;

CHROMOSOMES; CLUSTER ANALYSIS; FORESTRY; PLANTS (BOTANY);

LADDER NETWORKS;

ARTICLE; BARLEY; CANADA; CHROMOSOME MAP; CLASSIFICATION; CLUSTER ANALYSIS; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; METHODOLOGY; PHYLOGENY; PLANT GENOME; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS;

CANADA; CHROMOSOME MAPPING; CLUSTER ANALYSIS; GENETIC MARKERS; GENETICS, POPULATION; GENOME, PLANT; GENOTYPE; HORDEUM; LINKAGE DISEQUILIBRIUM; PHYLOGENY; POLYMORPHISM, GENETIC; PRINCIPAL COMPONENT ANALYSIS;

HORDEUM; HORDEUM VULGARE SUBSP. VULGARE;

EID: 67349119868     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-009-1015-4     Document Type: Article

References (23)

1. YP Bao M Huber TF Wei SS Marla JJ Storhoff UR Müller 2005 SNP identification in unamplified human genomic DNA with gold nanoparticle probes Nucleic Acids Res 33 2 e15
2. D Botstein RL White M Skolnick RW Davis 1980 Construction of a genetic linkage map in man using restriction fragment length polymorphisms Am J Hum Genet 32 314 331 (Pubitemid 11105557)
3. KS Caldwell J Russell P Langridge W Powell 2006 Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare Genetics 172 557 567 (Pubitemid 43345515)
4. J Felsenstein 1985 Confidence-limits on phylogenies-an approach using the bootstrap Evolution 39 783 791
5. SA Flint-Garcia JM Thornsberry ES Buckler 2003 Structure of linkage disequilibrium in plants Annu Rev Plant Biol 54 357 374 (Pubitemid 37399998)
6. P Hayes P Szucs 2006 Disequilibrium and association in barley: thinking outside the glass Proc Natl Acad USA 103 49 18385 18386 (Pubitemid 44913418)
7. WG Hill A Robertson 1968 The effects of inbreeding at loci with heterozygote advantage Genetics 60 3 615 628
8. WG Hill BS Weir 1988 Variances and covariances of squared linkage disequilibria in finite populations Theor Popul Biol 33 1 54 78
9. H Iwata Y Uga Y Yoshioka K Ebana T Hayashi 2007 Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms Theor Appl Genet 114 1437 1449 (Pubitemid 46733385)
10. D Jaccoud K Peng D Feinstein A Kilian 2001 Diversity arrays: a solid state technology for sequence information independent genotyping Nucleic Acids Res 29 e25
11. G Jander SR Norris SD Rounsley DF Bush IM Levin RL Last 2002 Arabidopsis map-based cloning in the post-genome era Plant Physiol 129 440 450 (Pubitemid 34689134)
12. ATW Kraakman RE Niks PMMM Van den Berg P Stam FA Van Eeuwijk 2004 Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars Genetics 168 345 446
13. LV Maliysheva-Otto MW Ganal MS Roder 2006 Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.) BMC Genet 7 1 14
14. M Nei W Li 1979 Mathematical model for studying genetic variation in terms of restriction endonuleases Proc Natl Acad USA 76 5269 5273 (Pubitemid 10236121)
15. M Nordborg JO Borevitz J Bergelson CC Berry J Chory J Hagenblad M Kreitman JN Maloof T Noyes PJ Oefner EA Stahl D Weigel 2002 The extent of linkage disequilibrium in Arabidopsis thaliana Nat Genet 30 190 193 (Pubitemid 34887714)
16. DL Remington JM Thornsberry Y Matsuoka LM Wilson SR Whitt J Doebley S Kresovich MM Goodman ES Buckler 2001 Structure of linkage disequilibrium and phenotypic associations in the maize genome Proc Natl Acad USA 98 20 11479 11484 (Pubitemid 32928754)
17. N Rostoks L Ramsay K MacKenzie L Cardle PR Bhat 2006 Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties Proc Natl Acad USA 103 49 18656 18661 (Pubitemid 44913466)
18. J Russell A Booth J Fuller B Harrower P Hedley G Machray W Powell 2004 A comparison of sequence-based polymorphism and haplotype content in transcribed and anonymous regions of the barley genome Genome 47 2 389 398 (Pubitemid 38673769)
19. Swofford DL (2003) PAUP*. Phylogenetic analysis using parsimony (*and other methods), vol 4. Sinauer Associates, Sunderland, MA
20. NA Tinker A Kilian CP Wight K Heller-Uszynska P Wenzl HW Rines A Bjornstad CJ Howarth JL Jannink JM Anderson BG Rossnagel DD Stuthman ME Sorrells EW Jackson S Tuvesson FL Kolb O Olsson LC Federizzi ML Carson HH Ohm SJ Molnar GJ Scoles PE Eckstein JM Bonman A Ceplitis T Langdon 2009 New DArT markers for oat provide enhanced map coverage and global germplasm characterization BMC Genom 10 39
21. BS Weir WG Hill 1986 Nonuniform recombination within the human beta-globin gene cluster Am J Hum Genet 38 5 776 781
22. P Wenzl J Carling D Kudrna D Jaccoud E Huttner A Kleinhofs A Kilian 2004 Diversity Arrays Technology (DArT) for whole-genome profiling of barley Proc Natl Acad Sci USA 101 26 9915 9920 (Pubitemid 38869336)
23. P Wenzl H Li J Carling M Zhou H Raman E Paul P Hearnden C Maier L Xia V Caig J Ovesna M Cakir D Poulsen J Wang R Raman KP Smith GJ Muehlbauer KJ Chalmers A Kleinhofs E Huttner A Kilian 2006 A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits BMC Genom 7 206