Abstract
BackgroundThe 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.ResultsUsing 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 (H e ) and long distance linkage disequilibrium (LD) along the chromosomes. We found no particular pattern in the empirical variogram of H e 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.ConclusionsThese 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.
Highlights
The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms
Intermediate composite maps were established for G2F-F2 and G2M-F2 because there were few markers common to the G2F and G2M maps suitable for anchoring (25 in total), whereas 198 single-nucleotide polymorphism (SNP) were common to F2 and G2F maps and 240 SNPs were common to F2 and G2M maps
We established a 1,712 cM linkage map of maritime pine with 1,838 SNP markers using for the first time a new map merging algorithm that integrates linkage maps from separate populations without any recourse to original genotypic data
Summary
The accessibility of high-throughput genotyping technologies has contributed greatly to the development of genomic resources in non-model organisms. Conifers represent an ancient and widespread lineage of about 650 species [1,2] They are of immense ecological and economic importance as they dominate many terrestrial landscapes and are primarily used for timber and paper production worldwide. The application of genomic techniques in crop [4] and animal [5,6] breeding has resulted in more powerful methods for genetic evaluation, and recent advances in conifer genomics [6,7,8] have allowed tree breeders to use these tools and methodologies (namely association mapping and genomic prediction) to dissect the genetic basis of phenotypic variability and to accelerate the breeding process of these longlived organisms [9]
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