Comparative mapping in the Pinaceae

Abstract

A comparative genetic map was constructed between two important genera of the family Pinaceae. Ten homologous linkage groups in loblolly pine (Pinus taeda L.) and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco) were identified using orthologous expressed sequence tag polymorphism (ESTP) and restriction fragment length polymorphism (RFLP) markers. The comparative mapping revealed extensive synteny and colinearity between genomes of the Pinaceae, consistent with the hypothesis of conservative chromosomal evolution in this important plant family. This study reports the first comparative map in forest trees at the family taxonomic level and establishes a framework for comparative genomics in Pinaceae.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.

Figure 1.—

Genetic maps of loblolly pine (Pinus taeda L.), Pt, and Douglas fir (Pseudotsuga menziesii [Mirb.] Franco), Pm. Orthologous markers are highlighted by larger, boldface, italicized, and underlined type and are connected by lines, except four of them that were mapped in pine species other than loblolly, but in the same syntenic linkage group (LG) [estPpINR_RS01G05_a was mapped in LG1 in Pinus pinaster (Chagné et al. 2003), and estPmaLU_SB42_a, estPaTUM_PA0053_a, and estPmaLU_SB21_a were mapped in LG6, LG8, and LG10 in Picea abies, respectively (our unpublished data)]. The loci were named following guidelines for the TreeGenes genome database (http://dendrome.ucdavis.edu/Tree_Page.htm; see also materials and methods). Abbreviations placed after the underscore in some loblolly pine marker names show other conifer species and syntenic linkage groups in which these markers were also mapped. For instance, Pe1 in the PtIFG_2006_A/Pe1 marker name in the linkage group Pt-1 means that the PtIFG_2006_A marker was also mapped in the Pinus elliottii syntenic linkage group 1. Similarly, Pp stands for P. pinaster, Pr for P. radiata, Ps for P. sylvestris, and Pa for Picea abies.