Haplogenome analysis and genetic dissection of growth and wood property traits in Eucalyptus urophylla x E. grandis hybrids

Abstract

Genetic dissection of complex traits is important for tree breeding and trait improvement. Marker-trait association is typically performed using quantitative trait locus (QTL) mapping in biparental crosses or genome-wide association (GWA) mapping in large open-pollinated populations using biallelic single nucleotide polymorphism (SNP) markers. However, these analyses often have low genetic resolution and poor statistical power, respectively. One way to mitigate these limitations is to make use of multi-parent mapping populations which combine the high power of biparental crosses with the increased resolution of population-wide (across-family) analyses. Additionally, multi-allelic haplotype markers and structural variants (SVs) are beginning to be used in several crop plant species for genetic dissection studies as these variants contain more information than individual SNPs and have, in some cases, been found to be causal variants. Current genetic dissection studies in Eucalyptus, an important genus for the forestry industry, make use of SNP markers, and there is a limited amount of research into the extent of haplotype and SV diversity in Eucalyptus species.

The aim of this PhD study was to perform genome-wide characterization of the haplotype and structural diversity in the genomes of E. grandis and E. urophylla parents used for hybrid breeding and to use the haplotypes for genetic dissection in F1 interspecific hybrid progeny. The first research objective was to develop a gene-based haplotype genotyping panel for Eucalyptus species. The second research objective was to sequence, assemble, annotate and identify SVs in the haplogenomes of parents of a E. urophylla x E. grandis interspecific multi-parent mapping population. The third research objective was to perform genetic dissection of growth and wood properties using 1 331 interspecific hybrid progeny from the Eucalyptus multi-parent mapping population using SNP and haplotype markers and to integrate haplotype and haplogenome information to interrogate QTLs further.

This study has improved our understanding of haplotype and SV diversity within E. urophylla and E. grandis parents used for hybrid breeding and has demonstrated how this information can be used to identify candidate genes underlying complex traits. The development of a haplotype mining panel provides a tool which targets 8 915 target regions at 4 637 genes, that can be used to understand the haplotype diversity present within the genus, analyse genome evolution and provide multi-allelic haplotype markers that can be used for genetic dissection studies. Additionally, the study revealed extensive intra- and inter-species gene (between 41 945 to 43 194 protein coding genes annotated) and structural diversity (between 30% and 40% of the genomes consist of SVs) which supports the need for a pangenome view of these species and their interspecific hybrids. We used 12 053 SNP and 11 017 haplotype markers for genetic dissection in the multi-parent mapping population. Haplotype markers and parental haplogenomes enabled the identification of a region with fewer than 100 candidate genes underlying a large effect QTL for diameter growth (DBH). We hypothesise that this QTL has pleiotropic effects on growth and viability of the trees and identify several candidates that can be prioritised for future function genetic studies.