Towards second-generation STS (sequence-tagged sites) linkage maps in conifers: a genetic map of Norway spruce (Picea abies K.)

Abstract

Genetic linkage maps have been produced for a wide range of organisms during the last decade, thanks to the increasing availability of molecular markers. The use of microsatellites (or Simple Sequence Repeats, SSRs) as genetic markers has led to the construction of "second-generation" genetic maps for humans, mouse and other organisms of major importance. We constructed a second-generation single-tree genetic linkage map of Norway spruce (Picea abies K.) using a panel of 72 haploid megagametophytes with a total of 447 segregating bands [366 Amplified Fragment Length Polymorphisms (AFLPs), 20 Selective Amplification of Microsatellite Polymorphic Loci (SAMPLs) and 61 SSRs, each single band being treated initially as a dominant marker]. Four hundred and thirteen markers were mapped in 29 linkage groups (including triplets and doublets) covering a genetic length of 2198.3 cM, which represents 77.4% of the estimated genome length of Picea abies (approximately 2839 cM). The map is still far from coalescing into the expected 12 chromosomal linkage groups of Norway spruce (2n = 2x = 24). A possible explanation for this comes from the observed non-random distribution of markers in the framework map. Thirty-eight SSR marker loci could be mapped onto 19 linkage groups. This set of highly informative Sequence Tagged Sites (STSs) can be used in many aspects of genetic analysis of forest trees, such as marker-assisted selection, QTL mapping, positional cloning, gene flow analysis, mating system analysis and genetic diversity studies.

Does maternal environmental condition during reproductive development induce genotypic selection in Picea abies?

“…II) represented between 40% (1957) and 54.3% (2736) of the genome. These results are in good accordance with the 2839 cM of the map previously published by Paglia et al [32]. The probability that a new marker added at the map would be linked to another marker present in the framework map was also estimated.…”

“…Furthermore, no marker was significantly distorted using a Bonferroni correction. In our study, we revealed a lower or similar level of genetic distortion compared to those reported in other P. abies genome studies (without Bonferroni corrections) where segregation distortion affected 5.6% [32] to 6.6% [1] of markers. Additionally, when loci inheritance was directly compared between the two maternal environments, we detected differences for 1.3% (2735) to 5.7% (1957) of loci per parent at P < 0.05 (Tab.…”

A high density genetic map of maritime pine based on AFLPs

“…In spite of its large genome size, the use of appropriate PECs allowed the production of easy-to-score AFLP gels. The use of Pst-Mse PECs has been reported to provide less complex gel patterns but also yields non-randomly distributed markers in conifers [43]. PstI is sensitive to methylation and the use of this endonuclease may target low-copy clustered regions.…”

“…Alternatively, other research groups started to use codominant markers such as RFLPs [10,19,54], PCR-RFLP [26], ESTs (Expressed Sequence Tags) [12,47,61] and more recently SSRs (Simple Sequence Repeats) [19,22,43], allowing gene action to be precisely defined (estimation of additive and dominant effects of QTLs, [55]) and providing anchor points in comparative mapping experiments [39].…”

Genetic studies of “noble cane” for identification and exploitation of genetic markers

“…Microsatellites have become the marker system of choice due to their high reproducibility, abundance in genome, hypervariability, and co-dominance. Due to their hypervariability and efficiency in polymorphism detection, SSR markers have become ideal for genetic map construction (Devey et al, 1996;Paglia et al, 1998), identification of clones (Dayanandan et al, 1998), identification of species and hybrids, determination of paternity (van de Ven and McNicol, 1996), and marker-assisted selection (Weising et al, 1997).…”