Conservation Genomics of Quercus macdougallii: Integrating Population Genomics, Functional Annotation, and Edaphic Analyses

Nelly Jazmín Pacheco Cruz, Jorge Eduardo Campos Contreras, Cecilia Liana Alfonso Corrado, and Ricardo Clark Tapia

Published May 2026 in International Oaks No. 37: 35–40

Abstract

Quercus macdougallii, a microendemic oak from the Sierra Juárez (Oaxaca, Mexico), provides an excellent model for examining the influence of genetic and environmental determinants on adaptability in species with limited distribution. This research integrates population genomics, comparative transcriptomics in silico, and edaphic analysis to evaluate the species’ susceptibility and adaptability. Using Genotyping-by-Sequencing (GBS) with Q. robur as a reference genome, we identified 5,426 SNPs in 79 individuals, revealing incipient north-south genetic differentiation and a low genetic diversity for the species (Hₒ ≈ 0.1). In-silico transcriptome annotation of Q. robur and Q. lobata identified outlier SNPs in pathogen-response genes (RPV1, RGA3), suggesting local adaptation. Edaphic analyses showed that Q. macdougallii inhabits acidic soils (pH ~4.2) characterized by loamy, sandy-loam, and silt-loam textures, along with fluctuating nutrient availability. The PZ site, the highest-elevation site in the southern zone, has more acidic, nutrient-poor soils, and hosted genetically distinct individuals. In contrast, the IT site, also in the southern zone, close to PZ but with soils similar to those in the north, showed greater genetic similarities with individuals from the northern zone. This research highlights how genomic, functional, and environmental data can provide early indicators of local adaptation in microendemic species, and offers practical ideas for the conservation of Q. macdougallii.

Keywords

microendemic  oaks,  SNPs,  local  adaptation,  in-silico  comparative transcriptomics, edaphic stress

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