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SummaryTo improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic SNP markers. These markers fail to capture the large amount of haplotype diversity in these species and thus multi-allelic markers are required. We aimed to develop a gene-based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6 293 genes implicated in growth and wood properties, pest and disease resistance and abiotic stress responses. We identified and phased 195 834 SNPs using a read-based phasing approach to reveal SNP-based haplotypes. A total of 8 915 target regions (at 4 637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13 to 4.52 haplotypes per target region in each species and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species and provide multi-allelic markers that can be used for genome-wide association studies and gene-based breeding approaches.Significance StatementWe developed a haplotype sequencing panel for Eucalyptus targeting 8915 regions at 4637 gene loci associated with growth and wood properties, pest and disease resistance and abiotic stress response providing a genome-wide, multi-allelic, gene centric genotyping resource for eucalypts. We tested the panel in four Eucalyptus species (E. grandis, E. dunnii, E. nitens and E. urophylla) and found an average of 3.65 haplotypes per target region per species, and 9.98 across all four species.

From its origins in Australia, Eucalyptus grandis has spread to every continent, except Antarctica, as a wood crop. It has been cultivated and bred for over 100 yr in places such as South Africa. Unlike most annual crops and fruit trees, domestication of E. grandis is still in its infancy, representing a unique opportunity to interrogate the genomic consequences of artificial selection early in the domestication process. To determine how a century of artificial selection has changed the genome of E. grandis, we generated single nucleotide polymorphism genotypes for 1080 individuals from three advanced South African breeding programmes using the EUChip60K chip, and investigated population structure and genome-wide differentiation patterns relative to wild progenitors. Breeding and wild populations appeared genetically distinct. We found genomic evidence of evolutionary processes known to have occurred in other plant domesticates, including interspecific introgression and intraspecific infusion from wild material. Furthermore, we found genomic regions with increased linkage disequilibrium and genetic differentiation, putatively representing early soft sweeps of selection. This is, to our knowledge, the first study of genomic signatures of domestication in a timber species looking beyond the first few generations of cultivation. Our findings highlight the importance of intra- and interspecific hybridization during early domestication.

Genomic selection (GS) can substantially reduce breeding cycle times in forest trees compared to traditional breeding cycles. Practical implementation of GS in tree breeding requires an assessment of significant drivers of genetic gains over time, which may differ among species and breeding objectives. We present results of a GS study of growth and wood quality traits in an operational Eucalyptus grandis breeding program in South Africa. The training population consisted of 1575 full and half-sib individuals, genotyped with the Eucalyptus (EUChip60K) SNP chip resulting in 15,040 informative SNP markers. The accuracy of the GS models ranged from 0.47 (diameter) to 0.67 (fibre width). We compared a 4-year GS breeding cycle equivalent to half of a traditional 8-year E. grandis breeding cycle and obtained GS efficiencies ranging from 1.20 (wood density) to 1.62 (fibre length). Simulated over 17 years, the ratio of the accumulated genetic gains between three GS cycles and two traditional breeding cycles ranged from 1.53 (diameter) to 3.35 (wood density). To realise these genetic gains per unit time in E. grandis breeding, we show that significant adjustments have to be made to integrate GS into operational breeding steps.