Abstract Detail

Population Genetics/Genomics

Shigita, Gentaro [1], Ortiz, Edgardo M. [1], Gibis, Florian M. [1], Kastner, Toni [2], Hoewener, Alina [1], Ewald, Joerg [2], Schaefer, Hanno [1].

Genetic diversity of European holly (Ilex aquifolium) in the German Alps.

Genetic diversity of ornamental plants may reflect human preferences and cultural backgrounds, making them interesting not only from a biological, but also from an anthropological perspective. The European holly (Ilex aquifolium L., Aquifoliaceae) has been a popular ornamental and decorative plant since the time of the Celts, due to its shiny, spiny evergreen leaves and bright red berries. This species is naturally distributed throughout Western Europe from Spain to England, and north to central Norway. To the east there are smaller occurrences as far as Greece and Turkey, and to the south the species reaches as far as Morocco, Algeria, and Tunisia. With the help of genetic analyses, this study aimed to clarify whether (1) the European holly in the Bavarian Alpine region is a genetically distinct population and, if so, whether (2) this population is threatened by admixing with exotic hollies. To answer these questions, a total of 85 hollies were examined: 60 collected from gardens and semi-natural areas in the Alpine region as well as 25 herbarium specimens covering the natural distribution of the species. After DNA extraction, five regions in the chloroplast genome, and the ITS and three microsatellite regions in the nuclear genome were amplified by PCR and sequenced by Sanger sequencer. Analysis of chloroplast and ITS regions showed no intraspecific variation, and although the microsatellite showed some allelic variations, there was no clear relationship between alleles and geographic distribution. These results suggested that European hollies have quite narrow genetic diversity, and motivated us to conduct whole genome sequencing on 21 samples, which selected for their balance of geographic distribution and scale of the analysis. Sequence data were analyzed with the following procedure: First, low-quality bases and adapter sequences were removed from the raw reads using the “clean" function of Captus, an in-house developed pipeline. Next, since there is no reference genome available for this species, the draft genome sequence was constructed using the “assemble" function of the same pipeline for the sample with the highest sequencing yield. The cleaned reads of each sample were then mapped to the draft genome sequence using BBMap and genome-wide SNPs were called using freebayes. Finally, in order to visualize the genetic relationships among the samples, principal component analysis (PCA) was performed using PLINK based on the SNP matrix. This analysis yielded 24 million SNPs, which enabled a well-resolved PCA. In contrast to the results obtained with the traditional methods described above, a clear geographic separation was observed. While the majority of the Alpine samples were grouped with a French sample, four Alpine samples were placed closer to the English and Spanish samples, suggesting an introgression from nursery plants or other regions.

1 - Technical University of Munich, Life Science Systems, Plant Biodiversity Research, Emil-Ramann Strasse 2, Freising, D-85354, Germany
2 - Weihenstephan-Triesdorf University of Applied Sciences, Faculty of Forestry, Institute of Ecology and Landscape, Hans-Carl-von-Carlowitz-Platz 3, Freising, D-85354, Germany

Genetic diversity
intraspecific variation.

Presentation Type: Oral Paper
Number: PGG3005
Abstract ID:463
Candidate for Awards:Margaret Menzel Award

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