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Processing the Loblolly Pine PtGen2 cDNA Microarray
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Genetic Assignment at Different Geographical Levels: A Case Study in a Forest Tree Species (Pinus pinaster Ait.)
Sanna Olsson1, Delphine Grivet1, Marjana Westergren2
1Instituto de Ciencias Forestales (ICIFOR-INIA) Consejo Superior de Investigaciones Cientificas (CSIC) Madrid Spain.
Evolutionary Applications
|December 4, 2025
Summary
Genetic markers reliably identify the origin of Pinus pinaster at gene pool and region levels. This study provides a crucial genetic baseline for managing this important tree species.
Area of Science:
- Forestry and Genetics
- Conservation Biology
- Population Genetics
Background:
- Forest tree populations exhibit significant genetic variation across geographic levels, crucial for conservation and resource management.
- Identifying the origin of forest tree genetic resources is vital for sustainable use but faces challenges in marker development and baseline data creation.
- Hierarchical population structure (gene pools, regions, populations) is key for understanding genetic diversity and informing management strategies.
Purpose of the Study:
- To assess the reliability of genetic markers for discriminating and assigning individuals of *Pinus pinaster* to different hierarchical levels (gene pool, region of provenance, population).
- To evaluate the performance of genetic stock identification software (*RUBIAS* and *assignPOP*) using a comprehensive genomic dataset.
- To establish a publicly available genetic baseline for *Pinus pinaster* to aid in forest genetic resource management.
Main Methods:
- Analysis of a genomic dataset of 10,185 single nucleotide polymorphisms (SNPs) from 1579 *Pinus pinaster* samples.
- Utilized two software packages, *RUBIAS* and *assignPOP*, for genetic stock identification and population assignment.
- Performed numerical validation analyses to assess assignment accuracy at different geographical levels.
Main Results:
- Reliable genetic origin assignment was achieved for *Pinus pinaster* at the gene pool and region of provenance levels using 10K SNP markers and a comprehensive baseline.
- Assignment accuracy was lower at the population level, highlighting the need for high-resolution genetic data and complete reference populations.
- Incomplete genetic baselines were shown to lead to erroneous assignments across all hierarchical levels.
Conclusions:
- The developed SNP markers and comprehensive genetic baseline enable reliable origin assignment for *Pinus pinaster* at broader geographical scales (gene pool, region).
- Accurate management of forest genetic resources requires robust genetic baselines and appropriate marker density for desired resolution.
- The provided extensive and public baseline dataset serves as a valuable tool for the conservation and sustainable management of *Pinus pinaster* genetic resources.
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