Comparative mapping in the Fagaceae and beyond with EST-SSRs

Abstract

Background: Genetic 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.

Results: We 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.

Conclusions: This 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.

Figure 1

Relationships between the four objectives of this study. Inputs, outputs and species involved.

Figure 2

Information gained by genotyping several pedigrees (P1 to P5).

Figure 3

Distribution of common loci per LG for at least two maps.

Figure 4

Number of shared loci between two to ten parental maps.

Figure 5

LG consensus species maps of Q. robur and Q. petraea.

Figure 6

Synteny between Quercus and Castanea for LG1. Loci in red are common for both species, loci in green are located as accessory loci (theta/LOD), parts of linkage group which are represented by the same colour correspond to homologous segments between the two species.

Figure 7

Syntenic relationships between oak and Arabidopsis , grape, poplar, Medicago, soybean genomes. Schematic representation of the orthologs identified between the grape chromosomes (g1 to g12) used as a reference, and the Arabidopsis (a1 to a5), poplar (p1 to p19), Medicago (m1 to m8), soybean (s1 to s20) and oak (o1 to o12) chromosomes. Each line represents an orthologous gene. The seven different colors used to represent the blocks reflect the eudicot origin from the seven ancestral chromosomes.

Figure 8

Duplication relationships within the oak genome. The 5 major interchromosomal duplications in oak are illustrated. Each line represents a duplicated gene. The different colours reflect the origin of the eudicots from the seven ancestral chromosomes. Duplications were visualized using the circos software (http://mkweb.bcgsc.ca/circos/.

Figure 9

Oak genome paleohistory. The oak chromosomes are represented with a seven colour code to illuminate the evolution of segments from a common ancestor with seven chromosomes (A1-A7). The lineage specific shuffling events (such as chromosome fusion, CF) that have shaped the modern oak karyotype from the n = 7 or 21 ancestors are mentioned on the figure.