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High-density linkage mapping in a pine tree reveals a genomic region associated with inbreeding depression and provides clues to the extent and distribution of meiotic recombination

Emilie Chancerel12, Jean-Baptiste Lamy12, Isabelle Lesur13, Céline Noirot4, Christophe Klopp4, François Ehrenmann12, Christophe Boury12, Grégoire Le Provost12, Philippe Label56, Céline Lalanne12, Valérie Léger12, Franck Salin12, Jean-Marc Gion17 and Christophe Plomion12*

Author Affiliations

1 INRA, UMR1202 BIOGECO, F-33610 Cestas, France

2 Université de Bordeaux, UMR1202 BIOGECO, F-33170 Talence, France

3 HelixVenture, F-33700, Mérignac, France

4 Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326 Auzeville Castanet-Tolosan, France

5 INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075 Orléans, France

6 INRA, UMR547 PIAF, Les Cézeaux, 24 Avenue des Landais, F-63177 Aubière cedex, France

7 CIRAD, UMR AGAP, Campus de Baillarguet TA 10C, F-34398 Montpellier Cedex 5, France

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BMC Biology 2013, 11:50  doi:10.1186/1741-7007-11-50

Published: 18 April 2013



The availability of a large expressed sequence tags (EST) resource and recent advances in high-throughput genotyping technology have made it possible to develop highly multiplexed SNP arrays for multi-objective genetic applications, including the construction of meiotic maps. Such approaches are particularly useful in species with a large genome size, precluding the use of whole-genome shotgun assembly with current technologies.


In this study, a 12 k-SNP genotyping array was developed for maritime pine from an extensive EST resource assembled into a unigene set. The offspring of three-generation outbred and inbred mapping pedigrees were then genotyped. The inbred pedigree consisted of a classical F2 population resulting from the selfing of a single inter-provenance (Landes x Corsica) hybrid tree, whereas the outbred pedigree (G2) resulted from a controlled cross of two intra-provenance (Landes x Landes) hybrid trees. This resulted in the generation of three linkage maps based on SNP markers: one from the parental genotype of the F2 population (1,131 markers in 1,708 centimorgan (cM)), and one for each parent of the G2 population (1,015 and 1,110 markers in 1,447 and 1,425 cM for the female and male parents, respectively). A comparison of segregation patterns in the progeny obtained from the two types of mating (inbreeding and outbreeding) led to the identification of a chromosomal region carrying an embryo viability locus with a semi-lethal allele. Following selfing and segregation, zygote mortality resulted in a deficit of Corsican homozygous genotypes in the F2 population. This dataset was also used to study the extent and distribution of meiotic recombination along the length of the chromosomes and the effect of sex and/or genetic background on recombination. The genetic background of trees in which meiotic recombination occurred was found to have a significant effect on the frequency of recombination. Furthermore, only a small proportion of the recombination hot- and cold-spots were common to all three genotypes, suggesting that the spatial pattern of recombination was genetically variable.


This study led to the development of classical genomic tools for this ecologically and economically important species. It also identified a chromosomal region bearing a semi-lethal recessive allele and demonstrated the genetic variability of recombination rate over the genome.

Unigene; SNP array; Linkage mapping; Segregation distortion; Recombination; Maritime pine; Pinus pinaster