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Open Access Research article

Genome-wide distribution of genetic diversity and linkage disequilibrium in a mass-selected population of maritime pine

Christophe Plomion12*, Emilie Chancerel12, Jeffrey Endelman3, Jean-Baptiste Lamy12, Eric Mandrou12, Isabelle Lesur14, François Ehrenmann12, Fikret Isik15, Marco CAM Bink6, Joost van Heerwaarden6 and Laurent Bouffier12

Author Affiliations

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

2 Univ. Bordeaux, BIOGECO, UMR1202, Talence F-33170, France

3 Department Horticulture, University of Wisconsin, Madison, WI 53706, USA

4 HelixVenture, Mérignac F-33700, France

5 Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA

6 Biometris, Wageningen University and Research Centre, Wageningen NL-6700 AC, Netherlands

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BMC Genomics 2014, 15:171  doi:10.1186/1471-2164-15-171

Published: 1 March 2014

Abstract

Background

The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. High-density genotyping arrays have only recently been developed for some economically important species such as conifers. The potential for using genomic technologies in association mapping and breeding depends largely on the genome wide patterns of diversity and linkage disequilibrium in current breeding populations. This study aims to deepen our knowledge regarding these issues in maritime pine, the first species used for reforestation in south western Europe.

Results

Using a new map merging algorithm, we first established a 1,712 cM composite linkage map (comprising 1,838 SNP markers in 12 linkage groups) by bringing together three already available genetic maps. Using rigorous statistical testing based on kernel density estimation and resampling we identified cold and hot spots of recombination. In parallel, 186 unrelated trees of a mass-selected population were genotyped using a 12k-SNP array. A total of 2,600 informative SNPs allowed to describe historical recombination, genetic diversity and genetic structure of this recently domesticated breeding pool that forms the basis of much of the current and future breeding of this species. We observe very low levels of population genetic structure and find no evidence that artificial selection has caused a reduction in genetic diversity. By combining these two pieces of information, we provided the map position of 1,671 SNPs corresponding to 1,192 different loci. This made it possible to analyze the spatial pattern of genetic diversity (He) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of He across the 12 linkage groups and, as expected for an outcrossing species with large effective population size, we observed an almost complete lack of long distance LD.

Conclusions

These results are a stepping stone for the development of strategies for studies in population genomics, association mapping and genomic prediction in this economical and ecologically important forest tree species.

Keywords:
Pinus pinaster; Genetic diversity; Linkage disequilibrium; Recombination; Linkage map; Domestication; Breeding program; Forest tree; Genomics; Genomic selection