Genetic diversity, population structure, and interspecific differentiation in introduced breeding populations of Eucalyptus sideroxylon and Eucalyptus camaldulensis established in northern Chile

Breeding populations of Eucalyptus sideroxylon and Eucalyptus camaldulensis have been established in the Coquimbo Region of northern Chile, immediately south of the Atacama Desert, owing to their ecological adaptability and tangible economic value. However, their genetic resources remain poorly characterized outside their native ranges. This study aimed to characterize genetic diversity, intraspecific population structure, and interspecific differentiation using a high-density 72K SNP array in a mixed-species breeding trial established in northern Chile. After stringent quality-control filtering, 19,299 and 29,254 polymorphic SNPs were retained for E. sideroxylon and E. camaldulensis , respectively, including 10,373 shared SNPs for comparative analyses. Genome-wide linkage disequilibrium (LD) analyses revealed distance-dependent LD decline in both populations; however, E. camaldulensis maintained slightly higher and more persistent LD across most genomic distance classes than E. sideroxylon . Population structure analyses based on Principal Coordinate Analysis (PCoA), Discriminant Analysis of Principal Components (DAPC), and Analysis of Molecular Variance (AMOVA) revealed clear genetic differentiation between populations and weak but detectable intra-specific genetic structure. AMOVA indicated that 35.15% of the total genetic variation was attributable to interspecific differentiation (ΦPT = 0.352, p = 0.001), whereas 64.85% was distributed within population. Genetic diversity analyses revealed moderate genome-wide variation in both populations, with E. sideroxylon exhibiting higher allelic diversity and heterozygosity than E. camaldulensis. These findings provide a genome-wide characterization of introduced Eucalyptus germplasm and establish a genetic baseline for breeding and conservation strategies involving Eucalyptus populations introduced into arid and semi-arid environments.