Comparative genome mapping among Picea glauca, P. mariana × P. rubens and P. abies, and correspondence with other Pinaceae

Abstract

A composite linkage map was constructed from four individual maps for the conifer Picea glauca (Moench) Voss, from anonymous and gene-specific markfers (714 AFLPs, 38 SSRs, and 53 ESTPs). A total of 12 linkage groups were delineated with an average marker density of 2.7 cM. Macro-synteny and macro-colinearity comparisons with two other composite linkage maps developed for the species complex P. mariana (Mill.) B.S.P. x P. rubens Sarg., and for P. abies (L.) Karst. revealed an identical number of linkage groups and a remarkable conservation of the gene content and gene order of linkage groups over the million years since the split between these taxa. Identical gene order among taxa was observed for 10 of the 12 assembled composite linkage groups. The discovery of one breakdown in synteny between P. glauca and the other two taxa indicated the occurrence of an inter-chromosomal rearrangement involving an insertional translocation. Analysis of marker colinearity also revealed a putative segmental duplication. The combined information from these three Picea genomes validated and improved large-scale genome comparisons at the inter-generic level in the family Pinaceae by allowing for the identification of 11 homoeologous linkage groups between Picea and Pinus, and nine such groups between Picea and Pseudotsuga menziesii. Notably, the analysis of synteny among the three genera revealed a putative case of chromosomal fission and an inter-chromosomal rearrangement in the genome of P. menziesii. Both of these changes are inter-connected, indicating much instability in this part of the P. menziesii genome. Overall, the macro-structure of the Pinaceae genome was well conserved, which is notable given the Cretaceous origin of its main lineages.

Linkage Maps of thedwarfand Normal Lake Whitefish (Coregonus clupeaformis) Species Complex and Their Hybrids Reveal the Genetic Architecture of Population Divergence

“…Consequently, the number of markers segregating 3:1 was also likely inflated, particularly when considering that the parents originated from divergent sources (Jiggins et al 2005;Pelgas et al 2006). Overall, over one-third of the markers showed a 3:1 segregation ratio, which was much higher than the proportion expected by chance alone when using dominant markers.…”

“…Small inversions were also observed between some linkage groups (e.g., LG4, Figure 2), and these were often associated with homologous loci informative in the opposite sexes between families. These inconsistencies in marker order were likely the result of doubtful positioning, particularly from loci considered as accessory markers within the current linkage map (Pelgas et al 2005(Pelgas et al , 2006). An additional explanation for noncolinearity may also be that despite the stringent criteria used for defining homology, homoplasy is still a likely source of mis-scoring.…”

“…First, with respect to increased heterozygosity in pure forms, our outbred crossing design, based on dominant markers and the pseudo-testcross strategy (Grattapaglia and Sederoff 1994), likely had considerable impacts on mapping with the main effect being an increase in the number of segregating markers (Myburg et al 2004;Yin et al 2004;Pelgas et al 2006). Consequently, the number of markers segregating 3:1 was also likely inflated, particularly when considering that the parents originated from divergent sources (Jiggins et al 2005;Pelgas et al 2006).…”

Towards a unified genetic map for diploid roses

“…Integrated maps not only increase the genome coverage but also make it possible to compare locations of major genes controlling important phenotypic traits or QTL positions between populations from multiple crosses. Although small chromosome rearrangements have been detected in some closely related species of the Pinaceae (Pelgas et al 2006) comparative mapping in the Rosaceae genus Prunus showed a very high degree of colinearity between the genomes of the diploid species peach, almond, apricot, and cherry (Dirlewanger et al 2004). Furthermore consensus maps of various genera of the Rosaceae have been linked with a conserved orthologue set of sequence-based markers (Sargent et al 2009).…”

Porsild spruce in Canada

“…There can be little doubt that a DNA approach such as that reported by Ran et al (2006) will ultimately decide the matter, but molecular genetics investigations into white spruce done already have only begun to set the stage for achieving improved taxonomic resolution (e.g., Tulsieram et al 1992, Sigurgeirsson and Szmidt 1993, Smith and Klein 1994, Gosselin et al 2002, Gupta et al 2005, Nkongolo et al 2005, Pelgas et al 2006. Individuals within natural "white spruce" populations can present strikingly diverse phenotypes, and during sampling in support of DNA research decisions must be made regarding whether to "force" the diversity of phenotypes into the category "white spruce" or to split them into subgroups based on phenotypic differences.…”