ORAL PRESENTATION: Spatial genetic structure of European beech and outlier SNPs analysis of multiple European beech (Fagus sylvatica L.) populations based on ddRAD analysis.

Submitted by : Fady Bruno
Abstract type : Oral presentation
Session type : Conference session 1: GENOMES and the ENVIRONMENT
Author Speaker : Ulaszewski Bartosz

Information about other authors :

Ulaszewski Bartosz1,  Meger Joanna1, Burczyk Jaroslaw1

1Kazimierz Wielki University, Department of Genetics, Chodkiewicza 30, Bydgoszcz, Poland

* e-mail: ulaszewski@ukw.edu.pl

Abstract :

Reduced representation sequencing techniques like ddRADseq or GBS can be very useful for discovering vast sets of genomic markers applicable in multiple types of studies. From thousands of gathered SNP, it is possible to search for patterns of structure, migration, genome-environmental (GxE) associations or signs of selection. In our study, we have used the available reference sequence of Fagus sylvatica (Mishra et al. 2018) to analyze 60 Gbp of ddRADseq data from 1068 individuals which originated from 85 cross-European sites. The SNP-calling gave 18021 SNPs present in at least 95% of the samples with minor allele frequency >0,05. Genetic structure analysis revealed three distinct clusters that seem to overlap potential glacial refugia and postglacial migration routes of this species. Associations of SNP outliers were tested using three methods: Sambada (Stucki et al. 2017) and LEA-LFMM (Frichot & François 2015) which also use temperature and rainfall climatic data (Hijmans et al. 2005) and BayeScan (Foll & Gaggiotti 2008). We have found >100 markers under selection confirmed by at least two methods. Analysis of those abovementioned SNPs showed that populations on the eastern border of the species range tend to have significantly higher Fst with lower heterozygosity and allelic richness. This is a signal that those populations are under serious threat with increasing negative effects of climate change on beech. Discovered structure and allele frequencies of outlier SNPs provide evidence that reference-based genomic variance analysis is a useful tool for predicting response to change of local and species-ranged bioclimatic conditions.

Bibliografic references :

Frichot, E.,  François, O. (2015). LEA: an R package for landscape and ecological association studies. Methods in Ecology and Evolution, 6(8), 925-929.

Foll, M., Gaggiotti, O. (2008). A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180(2), 977-993.

Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones, A. Jarvis, (2005). Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.

Mishra, B., Gupta, D. K., Pfenninger, M., Hickler, T., Langer, E., Nam, B., Paule, P., Sharma, R., Ulaszewski, B., Warmbier, J., Burczyk, J., Thines, M., (2018). A reference genome of the European beech (Fagus sylvatica L.). GigaScience, 7(6), giy063.

Stucki, S., Orozco‐terWengel, P., Forester, B. R., Duruz, S., Colli, L., Masembe, C.,   Taberlet, P. (2017). High performance computation of landscape genomic models including local indicators of spatial association. Molecular ecology resources, 17(5), 1072-1089.

Keywords : Fagus sylvatica, hybrid assembly, ddRAD, landscape genomics, local adaptation