Spatial and Ecological Drivers of Genetic Structure in Greek Populations of Alkanna tinctoria (Boraginaceae), a Polyploid Medicinal Herb

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.

Metabolic Profiles, Genetic Diversity, and Genome Size of Bulgarian Population of Alkanna tinctoria

“…This is the first report on the DNA content in the Bulgarian accessions of A. tinctoria . The estimated value of 1C = 1.326 pg was congruent with the data published for the species from Greek accessions (1C = 1.21–1.28 pg, [ 27 ]). Studies in the genome size in mature seeds, 10 seeds per population in a total of 11 populations (AT1 to AT11), revealed that 1C varied in the range of 1.28 to 1.49 pg ( Table 4 ).…”

“…In turn, the reduction in genetic variation might suggest a decline in adaptation to a changing environment, leading to an increased danger of extinction and increased inbreeding [ 62 , 63 ]. In the studied Bulgarian populations of A. tinctoria , the established genetic diversity was low, while in the Greek populations of the species, Ahmad et al [ 27 ] found moderate genetic diversity. This fact is consistent with the assumption of the same authors that limitation in population size and distribution is a major factor influencing population genetic diversity, which decreases with decreasing population size: the species is more common in Greece and other Mediterranean countries compared to Bulgaria, where it is considered very rare [ 64 ].…”

“…The citometrical studies in Alkanna species are few. The genome size of A. tinctoria and A. sieberi was previously reported by Ahmad et al [ 27 ].…”

“…Even though these markers have some limitations, they could bring additional insight into the phylogenetic relationships among the Alkanna species. The genetic structure and its determinants in A. tinctoria and A. sieberi from Greece were studied by Ahmad et al [ 27 ].…”

Transcriptional dynamics of Chitinophaga sp. strain R-73072-mediated alkannin/shikonin biosynthesis in Lithospermum officinale

“…Because of their interesting pharmaceutical properties and significant commercial value ( Papageorgiou et al, 1999 , 2008 ), there has been increasing interest in enhancing their production, e.g., through boosting its biosynthetic pathway, also by using beneficial microbes ( Rat et al, 2021 ). Recently, Fazal et al (2021) and Rat et al (2021) demonstrated that A/S producing Boraginaceae (e.g., Alkanna tinctoria ; Ahmad et al, 2021 ) host diverse microbial communities, among which a number of cultivable bacteria were shown to improve A/S production in a hairy root culture system. These findings were further supported by a study from Varela-Alonso et al (2022) , in which endophytic bacteria isolated from A. tinctoria also improved A/S biosynthesis in L. officinale , a Boraginaceae widely distributed in Europe and Asia ( Al-Snafi, 2019 ).…”