A GBAS marker system for assessing genetic diversity and population differentiation in Norway Spruce

Abstract Effective management of Picea abies (Norway spruce), a widely planted conifer species in Europe, requires high-resolution, scalable genotyping tools capable of capturing genetic variation across complex genomes. The primary aim of this study was to establish a cost-effective marker toolkit for P. abies suitable for population genetics, provenance studies, and long-term monitoring. We employed a Genotyping by Amplicon Sequencing (GBAS) approach to investigate sequence-level variation in Norway spruce, using 124 highly multiplexed markers, comprising 43 novel genomic SSRs, 33 elongated established SSRs, and 48 Exon-Primed Intron-Crossing (EPIC) markers. As a proof of concept, the markers were applied to 85 individuals from five Austrian populations. Genotyping was performed using the GBAS pipeline, enabling the extraction of both traditional length-based genotypes and whole amplicon information. Diversity metrics and clustering analyses revealed spatial genetic structure among populations, reflecting neutral demographic processes.