ORAL PRESENTATION: Range wide genetic variation and divergence in Pinus pinaster elucidated by gene capture data

Submitted by : Fady Bruno
Abstract type : Oral presentation
Session type : Conference session 1: GENOMES and the ENVIRONMENT
Author Speaker : Katharina Birgit Budde

Information about other authors :

Katharina B. Budde1, Delphine Grivet2, Sara Pinosio3, Simone Scalabrin3, Agathe Hurel1, Francesca Bagnoli, Andrea Piotti, Giovanni G. Vendramin4, Santiago C. González-Martínez1

1 INRA, UMR-BioGeco, Bordeaux, France

2 INIA-CIFOR, Madrid, Spain

3 IGA Technology, Udine, Italy

4 IBBR-CNR, Florence, Italy

Abstract :

Background/Objectives: The population genetic structure of tree species has often been studied using neutral genetic markers; however, little is known about how genetic diversity at potentially adaptive loci is distributed in natural forest tree populations. Comparing closely related species with different life history traits or distantly related species with similar life history traits could reveal mechanisms and drivers shaping genetic adaptations. Yeaman et al. (2016) reported convergent evolution at several loci associated with similar climatic clines in two distantly related conifer species in North America. In two closely related European pine species (Pinus pinaster and P. sylvestris) occupying different ecological niches and with different evolutionary histories, Grivet et al. (2017) revealed unusually high rates of adaptive evolution and several loci under selection in both species. Here we aim to further elucidate adaptive processes in Pinus pinaster and later on compare our results to other European tree species.

Material and Methods: In the framework of GENTREE H2020 project, samples were collected in range wide populations in a paired sampling design contrasting local stands growing under markedly different conditions (high altitude vs. low altitude or wet vs. dry). A total of 599 Pinus pinaster samples from 25 populations are available. Gene capture data was generated on over 1,130 homologous genes common to seven deeply sequenced European forest tree species. For each species, ca. 1,000 extra genes were added comprising previously known candidate genes, as well as random sequences. SNP calling was done against a de-novo assembly of reads from selected Pinus pinaster samples. STRUCTURE and other spatial analysis methods were used to identify gene pools and to evaluate distinctness of marginal populations, as well the site frequency spectrum was assessed to reveal the demographic history of the species. Preliminary selection analyses were also performed .

Results: For P. pinaster, the gene capture experiment yielded over 130 000 high quality SNPs after filtering. We used sequences from the haploid tissue  of the megagametophytes to identify loci with paralogs and compared the results to other approaches commonly used for paralog filtering e.g. based on heterozygote excess and deviation from allele balance. We revealed the population genetic origin of the 25 range wide populations including populations with great conservation interest from south-east France, southern Italy, southern Morocco and Tunisia which have never been part of phylogeographic studies with nuclear markers before. Furthermore, we  described the demographic history for multiple and differentiated gene pools in the species, as well as produced preliminary results on loci associated to environmental factors taking advantage of the paired sampling design and the range wide samples.

Conclusions: The high number of genome wide markers allowed us to study the population genetic structure of P. pinaster in more detail than previous studies, as well as to provide insight on demographic history of the differentiated gene pools in the species.

Bibliografic references :

Grivet D, Avia K et al. (2017) Molecular Ecology 26, pp. 6857-6870, DOI: 10.1111/mec.14402

Yeaman S, Hdgins KA et al. (2016) Science, 353, pp. 1431-1433, DOI:10.1126/science.aaf7812

Keywords : Pinus pinaster, gene capture, paralog filtering, genetic structure, demography