Genome-wide diversity assessment for genetic resource management of Eucalyptus dunnii, E. grandis, E. nitens and E. urophylla

Abstract

The genus Eucalyptus with its over 900 species is a dominant genus of the Australian flora, many provide the foundation for closed forest habitats on the continent. In addition to its ecological significance, this genus is globally important as several species and interspecific hybrids are used in commercial hardwood forestry. More than 95% of the current Eucalyptus plantation stock comprise just nine species and their hybrids in the subgenus Symphyomyrtus. As such, the distribution of genetic variation in natural and breeding populations of these Eucalyptus species needs to be better understood to continue to inform developing breeding practices and effective conservation efforts. To achieve this goal, this study set out to investigate the distribution of genome-wide genetic variation within Eucalyptus nitens, E. dunni, E. grandis and E. urophylla as represented in ex situ collections spanning the diversity present in the native ranges of these species hosted in South African provenance trials and genetic conservation parks. The objectives of this MSc study were to: i) investigate genome-wide genetic variation in E. nitens, E. dunni, E. grandis and E. urophylla and analyse the population structure present within each species, ii) generate high density genome-wide reference sets for each species and their sub-populations to be used in ancestry assignment and species discrimination, iii) produce genome-wide profiles of genetic diversity and divergence within and between these species and between the sub-populations within each species. In this study we investigated genome-wide genetic diversity across n = 207, 195, 250, and 72 genotypes collected from across the native ranges of E. dunni, E. grandis, E. nitens in Australia, and from the Lesser Sunda Archipelago for E. urophylla, respectively. Using the EUChip60K genotyping resource we generated a dataset containing 23 225 single nucleotide polymorphisms (SNPs) across the four studied species that explained 56.29% of the variation among all genotypes in a PCA analysis. Across our samleed loci we observed medium to high levels of genetic diversity in the four species (He ranges between 0.094 and 0.258) with heterogenous patterns of diversity throughout the genomes. In a subsequent six-way-pairwise species comparison we found low levels of genetic divergence (Fst ranges between 0.29 and 0.39) while observing relatively similar patterns of genome-wide divergence within the six-pairwise species comparisons. We used sparse non-negative matrix factorization to detect within-species genetic structuring which detected K = 2, 3, 4, and 8 putative genetic structures within our datasets for E. dunni, E. grandis, E. nitens, and E. urophylla, respectively. We could relate these genetic structures to the underlying geographical features of the native habitats of the species, and how these features could have affected the observed genomic patterns of diversity and divergence among the detected genetic structures of each species. For all four study species we could identify major biogeographical barriers that have contributed to shaping the divergences within species at the population level. We also provide evidence for a novel E. grandis population exhibiting evidence of active hybridizing with another, unknown Eucalyptus species. We also provide novel insights to the distribution of genetic variation in E. urophylla across the Lesser Sunda Archipelago in Indonesia. These results will be valuable in informing forest tree breeding practices and conservation policy, especially in the search for adaptive variation from populations in marginal areas to safeguard forest tree productivity in the face of global climate change.