Project name: Genotype of Slash pine population

Description: In this project, we used 370 slash pine samples from 33 half-sib families to capture their genotypes based on a 51K SNP liquid-phased array. Fresh needles were sampled from 340 individuals in 2023. Total genomic DNA was extracted using the M5 HiPer Universal DNA Mini Kit (Beijing Juhemei Biotechnology Co., Ltd., Beijing, China). Genotype data were generated using the 51K liquid-phased probe array for loblolly and slash pine. To ensure data quality, initial filtering of the captured SNP loci was conducted using VCFtools, excluding sites with a minor allele frequency (MAF) below 0.01 and missing rates exceeding 20%. Finally, 319,286 high-quality SNPs were retained. A total of 317,801 markers were mapped and evenly distributed across the 12 chromosomes in the slash pine genome (not published yet). The number of SNPs per chromosome ranged from 18,487 to 34,721. The reference for the 51K liquid-phased probe array is: Diao S, Ding X, Luan Q, et al. (2024) Development of 51K liquid-phased probe array for Loblolly and Slash pines and its application to GWAS of Slash pine breeding population. Industrial Crops and Products 216:118777. https://doi.org/10.1016/j.indcrop.2024.118777

Data type: Raw sequence reads; Genome sequencing

Sample scope: Monoisolate

Relevance: Agricultural

Release date: 2026-03-30

Last updated: 2026-03-30