Alignment of a Salix linkage map to the Populus genomic sequence reveals macrosynteny between willow and poplar genomes
- 382 Downloads
Poplars (genus Populus) and willows (genus Salix) are members of the Salicaceae, a family of catkin-bearing trees, shrubs and sub-shrubs. Poplar is considered the model system for biological studies in trees and considerable genetic and genomic resources have become available in recent years. The transfer of information to research studies in willow, for which fewer resources are currently available, would be highly beneficial. However, the extent of conservation between poplar and willow genomes has not yet been extensively studied. To address this, we have constructed a linkage map of willow based on a large mapping population derived from a cross between two Salix viminalis × (S. viminalis × S. schwerinii) hybrid sibs, and aligned this to the publicly available poplar genome sequence. A set of genome-wide, expressed poplar sequences was selected and used to design primer sets that efficiently amplified homeologous regions in willow. Direct sequencing of the willow products confirmed homology with the poplar target in the majority of instances and allowed identification of single nucleotide polymorphisms (SNPs) that were used to map these loci. In total, 202 amplified fragment length polymorphisms (AFLPs), 75 microsatellites and 79 SNPs were used to construct a willow consensus map that spanned 1,856.7 cM with an average interval between markers of 6.3 cM. Poplar sequences homologous to those of the mapped willow microsatellite loci were identified and used in addition to the SNP markers to putatively align all but two minor linkage groups to the poplar genome sequence. A high degree of macrosynteny was revealed.
KeywordsWillow Poplar Synteny
This study is part of the BEGIN (Biomass for Energy Genetic Improvement Network) project (bioass4energy.org) funded by the Department of Environment, Food and Rural Affairs (DEFRA) (Project no. NF0424) and the Biotechnology and Biological Sciences Research Council of the United Kingdom. We would like to thank Prof Gail Taylor, University of Southampton, UK for helpful discussions and for providing the poplar leaf material used in this study. Rothamsted Research receives grant-aided support from the Biotechnology and Biological Sciences Research Council of the United Kingdom.
- 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 89:167–178Google Scholar
- Hanley SJ (2003) Genetic mapping of important agronomic traits in biomass willow. Ph.D. thesis, University of Bristol, UKGoogle Scholar
- Kruglyak L (1997) The use of a genetic map of biallelic markers in linkage studies. Nat Genet 138:499–510Google Scholar
- Rönnberg-Wästljung AC, Tsarouhas V, Semerikov V, Lagercrantz U (2003) A genetic linkage map of a tetraploid Salix viminalis × S. dasyclados hybrid based on AFLP markers. For Genet 10:185–194Google Scholar
- 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 95:13330–13335CrossRefGoogle Scholar
- Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar