A genotype-by-sequencing dataset and identity-by-state matrix of genetic variation in Pinus radiata from 16 counties

Pinus radiata is a commercially important softwood species planted extensively worldwide, while its native populations remain endangered and of high conservation concern. This dataset provides genome-wide SNP genotyping data generated via genotype-by-sequencing (GBS) using double-digest RAD sequencing (ddRADseq) on needle-derived DNA. Samples were collected from 16 countries and include both domesticated breeding material and wild-origin individuals from native populations. The dataset includes a SNP-by-sample matrix and an identity-by-state (IBS) matrix describing pairwise genetic similarity among individuals. These data support applications in population structure analysis, breeding program design, genetic resource management, and conservation planning for P. radiata., , # Dryad dataset

Dataset DOI: [10.5061/dryad.bzkh189pc](10.5061/dryad.bzkh189pc)

## Description of the data and file structure

Needles were collected from four positions around each tree canopy and pooled per tree. DNA was extracted from homogenized needle tissue using the Qiagen DNeasy Plant Pro Kit, with replicate extractions pooled to maximize yield and representation. Genotyping was performed using genotype-by-sequencing (GBS/ddRADseq) with EcoRI and MseI digestion, ligation of barcoded adapters, size selection (280–375 bp), and sequencing on an Illumina NovaSeq 6000. Reads were demultiplexed, clustered de novo, and SNPs called using a Bayesian genotyping model. Variant data were filtered and combined with sample metadata to produce the final SNP dataset. Identity-by-state (IBS) genetic similarity matrices were also generated using PLINK.

### Files and variables

#### File: Similarity_reduced_GBS_GLOBAL_June25_updated.csv

**Description:** Similarity matrix of all samples compare...,