Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes

Tree Genetics and Genomes

Volumn 3, Issue 1, 2006, Pages 35-48

  Hanley, S J ^a   Mallott, M D ^a   Karp, A ^a  

^a ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

Poplar; Synteny; Willow

Indexed keywords

POPULUS; SALICACEAE; SALIX; SALIX ARBUSCULOIDES; SALIX SCHWERINII; SALIX VIMINALIS;

EID: 33751297219     PISSN: 16142942     EISSN: 16142950     Source Type: Journal    
DOI: 10.1007/s11295-006-0049-x     Document Type: Article

References (34)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. Barker JHA, Matthes M, Arnold GM, Edwards KJ, Åhman I, Larsson S, Karp A (1999) Characterisation of genetic diversity in potential biomass willows (Salix spp.) by RAPD and AFLP analyses. Genome 42:173-183
3. Barker JHA, Pahlich A, Trybush S, Edwards KJ, Karp A (2003) Microsatellite markers for diverse Salix species. Mol Ecol Notes 3:4-6
4. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12:1021-1029
5. Blanc G, Wolfe KH (2004) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667-1678
6. Bradshaw HD Jr, Villar M, Watson BD, Otto KG, Stewart S, Stettler RF (1994) Molecular genetics of growth and development in Populus. III. A genetic linkage map of hybrid poplar composed of RFLP, STS and RAPD markers. Theor Appl Genet 89:167-178
7. Bradshaw HD, Ceulemans R, Davis J, Stettler R (2000) Emerging model systems in plant biology: Poplar (Populus) as a model forest tree. J Plant Growth Regul 19:306-313
8. Cato SA, Gardner RC, Kent J, Richardson TE (2001) A rapid PCR-based method for genetically mapping ESTs. Theor Appl Genet 102:296-306
9. Cervera MT, Storme V, Ivens B, Gusmão J, Liu BH, Hostyn V, Van Slycken M, Van Montague M, Boerjan W (2001) Dense genetic linkage maps of three Populus species (Populus deltoides, P. nigra and P. trichocarpa) based on AFLP and microsatellite markers. Genetics 158:787-809
10. Chagné D, Brown G, Lalanne C, Madur D, Pot S, Neale D, Plomion C (2003) Comparative genome and QTL mapping between maritime and loblolly pines. Mol Breed 12:185-195
11. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758-760
12. Hanley SJ (2003) Genetic mapping of important agronomic traits in biomass willow. Ph.D. thesis, University of Bristol, UK
13. Hanley S, Barker JHA, Van Ooijen JW, Aldam C, Harris SL, Åhman I, Larsson S, Karp A (2002) A genetic linkage map of willow (Salix viminalis) based on AFLP and microsatellite markers. Theor Appl Genet 105:1087-1096
14. Hertzberg M, Aspeborg H, Schrader J, Andersson A, Erlansson R, Blomqvist K, Bhalerao R, Uhlén M, Teeri TT, Lundeberg J, Sundberg B, Nilsson P, Sandberg G (2001) A transcriptional roadmap to wood formation. Proc Natl Acad Sci U S A 98:14732-14737
15. Kruglyak L (1997) The use of a genetic map of biallelic markers in linkage studies. Nat Genet 138:499-510
16. Kwok PY, Deng Q, Zakeri H,Taylor SL, Nickerson DA (1996) Increasing the information content of STS-based genome maps: identifying polymorphisms in mapped STSs. Genomics 31:123-126
17. Maliepaard C, Jansen J, Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding species: overview and consequences for applications. Genet Res 70:237-250
18. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang C-X, Katsar CS, Lan T-H, Lin Y-R, Ming R, Wright RJ (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523-1539
19. Rönnberg-Wästljung AC, Tsarouhas V, Semerikov V, Lagercrantz U (2003) A genetic linkage map of a tetraploid Salix viminalis x S. dasyclados hybrid based on AFLP markers. For Genet 10:185-194
20. Smulders MJM, van der Schoot J, Arens P, Vosman B (2001) Trinucleotide repeat microsatellite markers for black poplar (Populus nigra L.). Mol Ecol Notes 1:188-190
21. Sterck L, Rombauts S, Jansson S, Sterky F, Rouzé P, Van de Peer Y (2005) EST data suggest that poplar is an ancient polyploid. New Phytol 167:165-170
22. Sterky F, Regan S, Karlsson J, Hertzberg M, Rohde A, Holmberg A, Amini B, Bhalerao R, Larsson M, Villarroel R, Van Montegu M, Sandberg G, Ollson O, Teeri TT, Boerjan W, Gustafsson P, Uhlén M, Sundberg B, Lundeberg J (1998) Gene discovery in the wood-forming tissues of poplar: analysis of 5,692 expressed sequence tags. P Natl Acad Sci U S A 95:13330-13335
23. Stirling B, Koo Yang Z, Gunter LE, Tuskan GA, Bradshaw HD Jr (2003) Comparative sequence analysis between orthologous regions of the Arabidopsis and Populus genomes reveals substantial synteny and microcollinearity. Can J For Res 33:2245-2251
24. Taylor G (2002) Populus: Arabidopsis for forestry. Do we need a model tree? Ann Bot 90:681-689
25. Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967-981
26. Tsarouhas V, Gullberg U, Lagercrantz (2002) An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix. Theor Appl Genet 105:277-288
27. Tuskan GA, Gunter LE, Yang ZK, Yin TM, Sewell MM, DiFazio SP (2004) Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Can J For Res 34:85-93
28. van der Schoot J, Popiskova M, Vosman B, Smulders MJM (2000) Development and characterization of microsatellite markers in black poplar (Populus nigra L.). Theor Appl Genet 101:317-322
29. Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
30. Voorrips RE (2002) MapChart: software for the graphical representation of linkage maps and QTLs. J Hered 93:77-78
31. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP - a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
32. Wu RL, Han YF, Hu JJ, Fang KK, Li L, Li ML, Zeng ZB (2000) An integrated genetic map of Populus deltoides based on amplified fragment length polymorphisms. Theor Appl Genet 100:1249-1256
33. Wullschleger SD, Jansson S, Taylor G (2002) Genomics and forest trees: Populus emerges as the perennial favourite. Plant Cell 14:2651-2655
34. Yin TM, DiFazio SP, Gunter LE, Riemenschneider S, Tuskan GA (2004) Large-scale heterospecific segregation distortion in Populus revealed by a dense genetic map. Theor Appl Genet 109:451-463