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).FORGENIUS H2020项目整合了基因型、表型与环境数据，用于描述欧洲遗传保护单元（European Genetic Conservation Units, GCUs）内的森林遗传资源，重点关注其应对气候变化的适应能力。依托高通量基因组学、光谱学、表型组学及遥感技术的整合应用，可实现对遗传多样性、表型可塑性与环境互作关系的评估。 本研究公开了欧洲黑杨（Populus nigra）与海松（Pinus pinaster）各两个欧洲遗传保护单元的遗传数据，二者基于鲜明的生态特征差异被筛选纳入本数据集。在每个欧洲遗传保护单元中，研究团队使用赛默飞世尔（Thermo Fisher，美国加利福尼亚州圣克拉拉）提供的多物种4TREE Axiom基因分型芯片，对约500株成体个体与250株幼树个体进行基因分型。该芯片总计包含45893个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点，其中13408个位点针对欧洲黑杨，13407个位点针对海松。研究使用Axiom Analysis Suite v5.2软件对低质量样本与不合格SNP位点进行了数据过滤。关于采样、基因分型、数据整理与质控及分析的全部细节，可参阅已提交至《GigaScience》待审的数据论文"An integrative set of high-throughput spectroscopic, phenotypic, genetic and remote sensing environmental data: 1. Populus nigra and Pinus pinaster"，其DOI将在获取后立即公布。 整理后的遗传数据以四个独立的.ped/.map文件格式提供： 1. 奥地利欧洲黑杨遗传保护单元对应文件：AUT00284.ped与AUT00284.map，包含750个个体的11451个SNP位点； 2. 西班牙欧洲黑杨遗传保护单元对应文件：ESP00395.ped与ESP00395.map，包含740个个体的11733个SNP位点； 3. 意大利海松遗传保护单元对应文件：ITA00019.ped与ITA00019.map，包含745个个体的10992个SNP位点； 4. 法国海松遗传保护单元对应文件：FRA00051.ped与FRA00051.map，包含750个个体的11085个SNP位点。 此外还提供了两个额外的.ped/.map文件，仅包含两个物种各自的两个欧洲遗传保护单元中均成功分型的位点基因型数据：欧洲黑杨对应文件Populus_nigra_filt.ped与Populus_nigra_filt.map（包含10490个SNP位点），以及海松对应文件Pinus_pinaster_filt.ped与Pinus_pinaster_filt.map（包含9199个SNP位点）。