Characterising a Eucalyptus cladocalyx breeding population using SNP markers

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 (F̂_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.