DNA/aDNA

The analysis of plant genomes has been widely used to investigate the origins and cultivation history of crops. This can be done by analysing ancient DNA extracted from archaeological/historical materials, or by looking at the genetic variation in heirloom (landraces) and wild varieties collected in different regions and preserved in national seed banks.

Just like studying human genomes – and those of our closest primate ancestors – can inform us about evolution, past migrations and how we adapted to different environments, looking at crop genomes can tell us a lot about when, where, and how these species were domesticated as well as their subsequent spread.

How does it work ?

We look for point mutations that make the genome of one variety (aka “accession”) different from another. These genetic markers are called “single-nucleotide polymorphisms” (SNP – read “snip”). To do this, poppy seeds sent by germplasm banks are germinated, DNA is extracted from leaves, and sequenced using next-generation DNA sequencing technologies (NGS). The DNA sequences are then analysed using bioinformatic pipelines and specialised software (R packages, Structure, TASSEL, vcftools) to identify groups of varieties that share the same ancestral populations. We then see how these populations are spatially distributed in a map and use archaeological and historical proxies to infer the processes that created that distribution

Packages of wild and cultivated Papaver provided by germplasm banks (USDA-GRIN, IPK, CRF, CRI-Prague). Photo; H.R. Oliveira (2022)

What we are planning to do ?

We will use genotype-by-sequencing (GBS) to uncover the genetic diversity of 408 landrace poppies from all over Europe and Asia as well as in 112 wild setigerum and 56 accessions of other wild Papaver species found in SW Asia and the Mediterranean.

Modern poppies growing.
Modern poppies are growing. Leaves will be crushed to extract DNA (photo: A.Salavert, 2022)
Modern poppies will be processed at the ICArEHB, University of Algarve (Photo: A. Salavert, 2022)

The use of phylogenetic and population structure methods will reveal which of the wild species is genetically closer to the cultivated poppy and if any of them is a feral form rather than true wild. The genetic proximity between cultivated poppies and wild plants from different regions (i.e. West Mediterranean, SW Asia) will pinpoint the place(s) where poppy originated. It will also distinguish between a multiple or single domestication scenario. Geographical Information Systems (GIS) will be used to map the spatial distribution of genetic diversity in cultivated poppies.

Accessions available in germplam banks from modern (red circles), wild setigerum (blue circles), and others wild Papaver species (orange squares), DAO: H.R. Oliveira

We will also extract and sequence DNA from historical samples (Musée de Matière médicale in Paris, European herbaria). These data will be compared with modern DNA and tell us how much diversity has changed over time and allows us to calibrate molecular clocks (rates of genetic change). Material will be prepared at the P2GM platform at the Musée de l’Homme.

By using RNA-seq (an NGS method) in three wild and three domesticated poppy accessions, we will see which genes are switched on in domesticated opium poppy and off in wild poppies (and vice-versa).

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