View Program - 2022 Population, Evolutionary, and Quantitative Genetics Conference

Eucalyptus is an iconic genus of woody perennials that harbours vast genetic, chemical and morphological diversity and occupies diverse ecological niches in Australia and islands to its north. A handful of fast-growing eucalypt species and their interspecific hybrids form the genetic basis for the most widely planted hardwood fibre crop globally (>20 mha). Breeding material from these species remains essentially undomesticated, or is undergoing early domestication. Population genomics studies using genome-wide SNP markers have provided the first insights into patterns of genome diversity in the natural range and how this diversity is reshaped by early domestication, selective breeding and interspecific hybridization in breeding populations. Complex trait dissection in these trees is however hampered by high levels of genetic load and long generation times. Furthermore, haplotype and structural variation, key components of pan-genome variation, are relatively unexplored as sources of complex trait variation in these outbred organisms. To address this, we are characterizing haplotype and structural variant (SV) diversity in Eucalyptus grandis and E. urophylla, the parents of the most widely planted eucalypt hybrid combination in subtropical zones. Using Flex-seq technology (RAPiD Genomics), we developed a haplotype mining panel using over 10,000 oligonucleotide probe sets targeting coding and/or non-coding sequences at 5000 genes with multiple evidence lines supporting their involvement in growth, wood properties and biotic and abiotic interactions. We also produced ~200X long read (Oxford Nanopore) coverage and ~100X short-read (Illumina) coverage of three F₁ progeny and used a trio-binning approach to assemble haplogenomes inherited from their E. grandis pollen parents and E. urophylla seed parents, and then identified SVs within and between the parental species. Linkage maps of the parental genomes were derived from SNP72K chip genotypes for approx. 384 F1 hybrid progeny from each of a series of interconnected full-sib families for QTL detection and nested association mapping. We aim to impute haplotypes and SVs segregating in the population as a first step towards assessing and understanding how these two types of pan-genome variation may affect quantitative trait variation in Eucalyptus tree species.

A pan-genome view of complex trait dissection in Eucalyptus