The LIFE Seedforce project: a comprehensive genotyping initiative to assist the conservation of endangered Habitat Directive plant species

Paloma Perez-Bello Gil ¹, Fabio Marroni ¹, Emanuele De Paoli ¹, Valentino Casolo ¹, Giuseppe Fabrini ², Lara Dixon ³, Roberta M. Ceriani ⁴, Luciano di Martino ⁵, Blanka Ravnjak ⁶, Joseph Buhagiar; Gianluigi Bacchetta; Antonia Cristaudo; Gabriele Casazza; Cristina Salmeri; Mariacristina Villani; Sara Magrini; Costantino Bonomi ⁷

Dipartimento di Scienze AgroAlimentari Ambientali e Animali, Università degli Studi di Udine, Udine, Italy ¹, Dipartimento di Biologia Ambientale, Sapienza Università, Rome, Italy ², Conservatoire botanique national méditerranéen de Porquerolles, Hyères, France ³, Centro Flora Autoctona della Lombardia, Parco Monte Barro, Galbiate, Italy ⁴, Ente Parco Nazionale della Majella, Guardiagrele, Italy ⁵, University of Ljubljana, Biotechnical faculty, Botanic Garden, Ljubljana, Slovenia ⁶, Universita' ta' Malta, MSIDA, Malta; Centro Conservazione Biodiversità (CCB), Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Cagliari, Italy; Università degli Studi di Catania, Catania, Italy; Università degli Studi di Genova, Genova, Italy; Università degli Studi di Palermo, Palermo, Italy; Centro di Ateneo Orto Botanico dell'Università di Padova, Padova, Italy; Università degli Studi della Tuscia - Dipartimento di Scienze Ecologiche e Biologiche, Viterbo, Italy; Museo delle Scienze (MUSE), Trento, Italy ⁷

We present the approach and preliminary results of the LIFE Seedforce project (LIFE20 NAT/IT/001468), which aims to improve the conservation status of 29 endangered native plant species in Italy, Malta, France and Slovenia (https://lifeseedforce.eu/en/). Assessing genetic diversity of populations is an essential aspect while defining a specific conservation strategy. Minimizing the selection of closely related individuals reduces the risk of inbreeding, ensuring the adaptability and long-term survival of the translocated populations. We conducted a genetic diversity survey of the target species using double digest Restriction Associated DNA sequencing (ddRAD-seq), a high-throughput genotyping method capable of identifying thousands of single-nucleotide polymorphisms (SNPs), the most frequent type of genetic variation between individuals. This approach is particularly suitable for non-model organisms for which no reference genomes are available and allows for cost-effective sequencing by processing DNA from either single or pooled individuals. With the aim of optimizing sequencing resources most of the species were sequenced after pooling DNA from eight individuals, and information on expected heterozygosity and beta diversity were obtained. For six of the project species, samples were sequenced individually; which allowed to perform expected heterozygosity and beta diversity analyses, information on observed heterozygosity, kinship, inbreeding and population structure. In total, approximately 500 samples were sequenced individually, and 800 were sequenced as 100 pools of eight individuals each and two different pipelines were created (one for individual approach and another for pooled individuals). Our results showed that overall, for the species that were sequenced following the individual approach heterozygosity was low, ranging from 10% to 4% with inbreeding values higher than zero in all the species. For most of species inbreeding coefficient was around 0.2, with the notable exception of one species (Linaria flava subsp. sardoa), in which inbreeding coefficient was higher than 0.9. The individual approach also showed high inter-population differentiation within the same species. The pattern of low genetic diversity and high isolation is compatible with the expectation for small, fragmented populations. The pooled approach revealed low to moderate expected heterozygosity, ranging from 10% to 35%, with high population differentiation, again supporting the expectation for small, fragmented populations. Information on genetic diversity of the populations of each species will be used to inform the translocation policies foreseen in the project.

Main author career stage: Postdoc / Fellow

Contribution type: Poster

First choice session: 5. Genetics, genomics, and bioinformatics

Second choice session: 1. Systematics, phylogenetics, biogeography and evolution