Abstract
Background and Aims: Quantifying genetic variation is fundamental to understand a species’ demographic trajectory and its ability to adapt to future changes. In comparison with diploids, however, genetic variation and factors fostering genetic divergence remain poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies.Methods: We collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing. In addition, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high-quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations, complemented by genome size measurements and chromosomal counts. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables.Key Results: We found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modeling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria.Conclusion: Current findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.
Highlights
Polyploids are very frequent in flowering plants as at least 35% of extant species are of recent polyploid origin (Wood et al, 2009)
The genome size of A. tinctoria was found to vary from 1.21 to 1.28 pg. (1C-value), whereas greater variation was observed among the A. sieberi samples, with sizes from 1.08 to 1.21 pg. (Table 1)
We provide evidence that only dysploid tetraploid A. tinctoria and A. sieberi are prevalent in Greece, the main distribution area for these species
Summary
Polyploids are very frequent in flowering plants as at least 35% of extant species are of recent polyploid origin (Wood et al, 2009) Despite their high abundance in nature, economic, esthetic, and medicinal importance, polyploids are still rarely investigated in population genomics (van de Peer et al, 2017). Genotype likelihood-based methods (as implemented, e.g., in ANGSD; Nielsen et al, 2011; Korneliussen et al, 2014) that are accounting for uncertainties regarding genotype calling have been shown to greatly improve accuracy of population genetics parameters estimated from low to medium coverage NGS data in diploid species (Warmuth and Ellegren, 2019). Restriction site-associated DNA sequencing (RAD-seq; Baird et al, 2008) is a popular method to generate NGS data and investigate genetic variation and population structure, especially for species not benefiting from an available suitable reference genome (Rochette and Catchen, 2017). From a practical perspective, such investigation can inform biodiversity management strategies
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
