Genetic linkage maps constitute an ideal framework for studies of the genetic architecture of quantitative traits [1
] and genome evolution [3
]. They are also a prerequisite for map-based gene cloning [5
] and for the ordering of physical scaffolds in genome sequencing projects [8
]. Furthermore they are essential tools for marker assisted plant breeding [9
Comparative analyses of genetic maps across phylogenetically related species are based on the development of transferable and orthologous genetic makers. Simple sequence repeats (SSRs) are the markers of choice, because they are reproducible, abundant in the genome and they provide highly polymorphic information and are readily transferable between phylogenetically related species [10
]. Their properties are highly prevalent in EST-derived SSRs, making these markers particularly useful, as shown for Theobroma
] and Citrus
]. SSRs are also easy to handle and, once developed, are cost-effective markers for high-throughput genotyping.
In the last 12 years, several linkage maps have been generated for the three main genera of the Fagaceae family: oaks (Quercus
), beeches (Fagus
), and chestnuts (Castanea
). These long-lived species constitute important economic and ecological resources and have been the focus of genetic investigations relating to their evolution and more applied objectives, such as those of conservation and breeding programs [16
]. Linkage maps have been established to support forward genetic approaches for studying the genetic architecture of adaptive traits (number, location and effect of QTLs) and to increase our knowledge of the structural features of the oak genome and its evolutionary history.
First-generation linkage maps have been obtained with anonymous RAPD and AFLP markers for oak [17
], chestnut [18
] and beech [20
]. QTL studies, mostly in oak, have focused on dissecting the genetic architecture of adaptive traits, such as growth and bud phenology [21
] and of traits related to species divergence between pedunculate and sessile oaks, two species occurring in sympatry in Europe [24
]. A limited number of genomic SSRs (about 50) and EST-based (about 50) markers [26
], have also been added to these maps. These markers allowed to align homologous linkage groups between oak and chestnut and to compare and validate the QTLs that had been previously characterized in the two genera [27
]. A first step toward the construction of a dense SSR-based genetic map was taken recently, with the development and mapping of 256 EST-SSRs [29
]. The authors used a selective mapping strategy with a bin set of 14 highly informative offspring from a single full-sib (FS) mapping population for which an AFLP framework map was available. SSR markers were assigned to 44 bins of the female and 37 bins of the male parental maps, spanning the entire genome.
The main goal of this study was to advance the establishment of a dense EST-SSR-based map for oak, by genotyping trees with a broader genetic background and using a larger set of genomic and EST-SSRs. Our specific objectives were as follows:
i) To optimize comparative mapping between two Quercus
species by identifying a subset of SSRs that were transferable and orthologous across different mapping pedigrees. We genotyped a total of 400 offspring from five families obtained from controlled crosses of the Q. robur
and Q. petraea
genotypes. We then generated 10 individual linkage maps (one for each of the parents used in the crosses) by the two-way pseudo-testcross mapping strategy [30
] and constructed consensus maps for each species from 419 genomic and EST-based SSR markers.
ii) To determine gene content (synteny) and order (collinearity) between these two sympatric species [7
iii) To assess the transferability of a subset of EST-SSRs in several Fagaceae and Nothofagaeae species and to describe the genetic diversity of several oak populations depending on the type of the repeated motifs. We also mapped transferable EST-SSRs, in European chestnut for which two linkage maps were available [28
] making it possible to refine the first comparative map for oak and chestnut [27
iv) To unravel the evolutionary paleohistory of oak chromosomes, by genetic mapping of 321 EST-SSR and 60 SNP-based markers identified from oak transcriptome sequence information (31,798 Sanger-based unigenes from Ueno et al. [33
These four objectives are interconnected, as shown in Figure .
Relationships between the four objectives of this study. Inputs, outputs and species involved.