Comparative mapping in the Fagaceae and beyond with EST-SSRs

Abstract

BackgroundGenetic markers and linkage mapping are basic prerequisites for comparative genetic analyses, QTL detection and map-based cloning. A large number of mapping populations have been developed for oak, but few gene-based markers are available for constructing integrated genetic linkage maps and comparing gene order and QTL location across related species.ResultsWe developed a set of 573 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and located 397 markers (EST-SSRs and genomic SSRs) on the 12 oak chromosomes (2n = 2x = 24) on the basis of Mendelian segregation patterns in 5 full-sib mapping pedigrees of two species: Quercus robur (pedunculate oak) and Quercus petraea (sessile oak). Consensus maps for the two species were constructed and aligned. They showed a high degree of macrosynteny between these two sympatric European oaks. We assessed the transferability of EST-SSRs to other Fagaceae genera and a subset of these markers was mapped in Castanea sativa, the European chestnut. Reasonably high levels of macrosynteny were observed between oak and chestnut. We also obtained diversity statistics for a subset of EST-SSRs, to support further population genetic analyses with gene-based markers. Finally, based on the orthologous relationships between the oak, Arabidopsis, grape, poplar, Medicago, and soybean genomes and the paralogous relationships between the 12 oak chromosomes, we propose an evolutionary scenario of the 12 oak chromosomes from the eudicot ancestral karyotype.ConclusionsThis study provides map locations for a large set of EST-SSRs in two oak species of recognized biological importance in natural ecosystems. This first step toward the construction of a gene-based linkage map will facilitate the assignment of future genome scaffolds to pseudo-chromosomes. This study also provides an indication of the potential utility of new gene-based markers for population genetics and comparative mapping within and beyond the Fagaceae.

A linkage disequilibrium perspective on the genetic mosaic of speciation in two hybridizing Mediterranean white oaks

“…However, the extremely large degree of macro-synteny and macro-collinearity observed between Q. petraea and Q. robur, as well as between Castanea and Quercus (Casasoli et al, 2006;Bodénès et al, 2012), together with the large genome similarity among the European white oaks, would argue in favor of the assumption. Indeed, linkage maps from Q. petraea and Q. robur show some non-linear relationships (for example, Bodénès et al, 2012), but we believe their most likely explanation is variation in cross-over rates among different crosses and among male and female individuals. Furthermore, even if the two Mediterranean oaks would show some micro-synteny and collinearity differences, these would become almost irrelevant on the basis of the LD results (see below).…”

“…These species show evidences of recurrent and ongoing gene flow, as indicated by the sharing of chloroplast DNA variants with strong biogeographic structure (Olalde et al, 2002;Petit et al, 2002) and by the occurrence of hybrid/admixed trees in sympatric populations (Valbuena-Carabaña et al, 2005;Curtu et al, 2007;Lepais and Gerber, 2011). Furthermore, all our data suggest their genomes maintain a large degree of synteny (Casasoli et al, 2006;Bodénès et al, 2012).…”

“…We used several available linkage maps established for Q. petraea and Q. robur (Bodénès et al, 2012 and references therein) to assemble a composite consensus map with the aid of the R library LPmerge (Endelman and Plomion, 2014). We are aware that violations of the collinearity assumption could have important implications for some interpretations of our results.…”

“…The EST-SSRs markers used in this study were selected from available European white oaks linkage (Bodénès et al, 2012) and bin maps (Durand et al, 2010;), whereas the nSSRs were selected from multilocus scans previously carried out in Q. petraea and Q. robur (Scotti- Saintagne et al, 2004b;Goicoechea et al, 2012). Part of our data set was used in Bodénès et al (2012), with the only intention of providing a proof of concept on the subject of the EST-SSRs transferability to the Mediterranean white oaks.…”

“…Part of our data set was used in Bodénès et al (2012), with the only intention of providing a proof of concept on the subject of the EST-SSRs transferability to the Mediterranean white oaks. Lab details about DNA extractions and purifications, PCR amplifications, electrophoretic methods and the binning of alleles, were provided on that publication.…”