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Increasing [CO2] may influence commercial crop and timber yield. While selection of genotypes sensitive to elevated [CO2] (e[CO2]) appears possible in agricultural crops, there is limited evidence for genotype-by-CO2 (G × CO2) interactions in commercial tree species. We examined [CO2] responsiveness in 124 open-pollinated Eucalyptus globulus ssp. globulus (E. globulus) families with the aim of assessing whether G × CO2 interactions are detectable in seedlings for early-age screening. Plants were grown in ambient (a[CO2]; ~ 405 μmol mol−1) and e[CO2] (640 μmol mol−1) and harvested 25 days after germination. Total, shoot, and root dry weights were determined for each plant. Carbon isotopic discrimination against 13C (Δ13C) was determined at the family level. We observed highly significant (p 2 for each mass trait. The main effects from the mixed-model output ([CO2] and individual-tree effects) were significant for all traits. However, [CO2]-by-individual tree interactions were non-significant for all traits, indicating little G × CO2 interaction. A secondary aim was to examine the correlation between greenhouse and mature-age growth from breeding trials that use common families conducted under ambient [CO2]. These correlations were non-significant, suggesting early growth is not necessarily indicative of later-age responses. Our results suggest that while early growth of E. globulus is enhanced under e[CO2], genotypes respond relatively uniformly to e[CO2] and little opportunity exists for seedling-based selection at the population level based upon the response of plants during the first weeks of growth.

Population structure, family relatedness and inbreeding within a first-generation Eucalyptus cladocalyx breeding population were analysed with single-nucleotide polymorphism markers to underpin quantitative trait analysis and breeding program management. The breeding population, comprising families selected from wild and cultivated stands, was found to be strongly structured ( $$ {{\widehat{F}}_{\mathrm{ST}}} $$ = 18 %), with two geographically defined groups of South Australian wild subpopulations: Kangaroo Island (KI) and South Flinders Ranges (SFR). The selections from cultivated stands were shown to be derived from SFR subpopulations of SFR and had similar levels of diversity, suggesting that they were established from a broad genetic base. Relatedness and inbreeding among families was heterogeneous, ranging from completely outcrossed and predominantly half-sib (HS) to completely selfed. Families from the cultivated stands had minimal inbreeding and were close to HS on average. Among SFR subpopulations, family-average inbreeding was negatively correlated with growth, suggesting inbreeding depression (ID). Inbreeding was high, on average, in the KI subpopulations; however, evidence of ID was absent, with highly inbred families amongst the most vigorous, perhaps indicative of purging of deleterious recessive alleles in a bottleneck event. The marker-based information suggested that modification of the usual assumptions of relatedness made in undertaking quantitative analysis of the first-generation populations would be desirable.

The effects of adjusting additive (numerator) relationship matrices (A) for inbreeding estimates taken from molecular markers were investigated using a small, model population of Eucalyptus cladocalyx. A number of individual-tree, mixed-models were compared, incorporating estimates of population- and family-level selfing and ancestral inbreeding applied either as average values to the entire population or as variable estimates for subpopulation and family groups. The consequences of ignoring inbreeding were inflated additive genetic variance estimates and underestimation of residual variance, with resulting inflation of heritability. We found models that correct for differential inbreeding at the subpopulation level give similar results to more complex ones including family-level estimates. Our analysis indicates that the commonly applied coefficient of relationship for first-generation eucalypt progeny of ρ = 1/2.5 appears to be quite suitable for correcting variance component and heritability estimates. However, if inbreeding is not specifically corrected for by adjustment of A, some minor rank changes of individual breeding values can occur, especially where levels of inbreeding vary among families, and some suboptimal selections and loss of genetic gain may ensue.

Analysis of stem diameter, height and axis persistence (AP) in a first-generation Eucalyptus cladocalyx breeding population comprising 137 wild and land-race families planted at 11 sites in southern Australia revealed significant genetic variation among subpopulations and among families within subpopulations. Alternative analyses were carried out using individual-tree mixed models that (i) assumed the trees within families were half-siblings (HS) and (ii) used molecular marker-based information to account for highly heterogeneous relatedness and inbreeding depression among families resulting from mixed mating (MM). For certain site and trait combinations, the HS models would not converge, as estimates of additive variance exceeded the total phenotypic variance, demonstrating the fundamental unsuitability of the HS assumption for this breeding population. Where HS models converged, moderate to very high heritability estimates resulted for growth traits. The MM assumption resulted in re-ranking of individual-tree breeding values and markedly lower estimates of narrow-sense heritability for all trait-site combinations. In some cases, however, heritability remained moderate to high, probably reflecting unquantified dominance variance in some highly inbred subpopulations. Genotype-by-environment interaction was significant overall due to reactivity of genotypes on a few sites, with type-B correlations between pairs of sites ranging from 0.06 to 0.99. Generally, families from the Australian land race were found to perform particularly well for both growth and AP traits. Some wild families were found to be vigorous, despite significant inbreeding. The study has demonstrated that traditional models assuming non-relatedness and/or homogeneous inbreeding in first-generation eucalypt breeding populations can be significantly improved upon by flexible mixed models that integrate marker-based data.