Genetic data from two cohorts of Populus nigra and Pinus pinaster trees growing in contrasting environments [FORGENIUS H2020 project - WP3]

The FORGENIUS H2020 project combines genotypic, phenotypic, and environmental data to describe forest genetic resources across European Genetic Conservation Units (GCUs), with an emphasis on their capacity for adaptation in the face of climate change. The combination of high-throughput genomic, spectroscopic, phenotypic, and remote sensing techniques should allow assessing genetic diversity, phenotypic plasticity, and environmental interactions. Here, we make available genetic data for two GCUs of black poplar (Populus nigra) and maritime pine (Pinus pinaster), selected based on their contrasted ecological characteristics. In each GCU, we genotyped approximately 500 adults and 250 juveniles using the multispecies 4TREE Axiom array available at Thermo Fisher (Santa Clara, CA, USA). The array comprised a total of 45,893 Single Nucleotide Polymorphisms (SNPs), of which 13,408 are for black poplar and 13,407 for maritime pine. Raw data were filtered out for both bad-quality samples and SNPs using the Axiom Analysis Suite software v5.2. All details regarding sampling, genotyping, data curation and analyses are available in the data paper "An integrative set of high-throughput spectroscopic, phenotypic, genetic and remote sensins environmental data: 1. Populus nigra and Pinus pinaster" that is currently under revision in GigaScience (a DOI will be provided as soon as it is available). Curated genetic data are provided in four independent .ped/map files: AUT00284.ped and AUT00284.map for the Austrian black poplar GCU (11,451 SNPs for 750 individuals) ESP00395.ped and ESP00395.map for the Spanish black poplar GCU (11,733 SNPs for 740 individuals) ITA00019.ped and ITA00019.map for the Italian maritime pine GCU (10,992 SNPs for 745 individuals) FRA00051.ped and FRA00051.map for the French maritime pine GCU (11,085 SNPs for 750 individuals). Two additional .ped/map files containing only the genotype calls for the positions successfully genotyped in both GCUs of each of the two species are also provided: Populus_nigra_filt.ped and Populus_nigra_filt.map (10,490 SNPs) and Pinus_pinaster_filt.ped and Pinus_pinaster_filt.map (9,199 SNPs).