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Characterising a Eucalyptus cladocalyx breeding population using SNP markers

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Abstract

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.

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Acknowledgments

We would like to acknowledge Bronwyn Matheson and Charlie Bell for the assistance with DNA extraction and preparation of samples for sequencing. Tim Jackson, Des Stackpole, Paul Macdonell and David Spencer are thanked for the assistance with management, sampling and measurement of the field trial. Chris Harwood and Shannon Dillon made useful suggestions on a draft version of the paper.

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Authors and Affiliations

  1. CSIRO Plant Industry, GPO Box 1600, Canberra, ACT, 2601, Australia

    David Bush & Bala Thumma

  2. Australian National University, Fenner School of Environment and Society, Canberra, ACT, Australia

    David Bush

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  1. David Bush
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  2. Bala Thumma
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Correspondence to David Bush.

Additional information

Communicated by R. Burdon

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online Resource 1

Subpopulation/spatial data for the first-generation E. cladocalyx breeding population. (DOCX 32 kb)

Online Resource 2

Description of genes (n = 39) and SNPs (n = 75) located within chromosome scaffolds (1–10) and a minor scaffold, as yet unallocated to a chromosome (scaffold 12), with annotation from the E. grandis genome (Phytozome Version 7). Gene names are either from known E. nitens sequences and/or based on similarity to Arabidopsis thaliana gene sequences. SNP descriptors are as follows: U = unannotated E. grandis region, I = intron, E = unannotated exon, S = synonymous, NS = non-synonymous, P = probable promoter (from within 1 kb of the 5′ region of a gene). (DOCX 37 kb)

Online Resource 3

Detection of SNPs under selection in E. cladocalyx first-generation breeding population using the method of Excoffier et al. (2009) implemented in Arlequin; a hierarchical island model with 3 groups and 14 subpopulations simulated. Solid blue lines delineate the 99 % confidence interval envelope. The SNP above the upper bound (from the EcxCBS gene) is an outlier likely to be under selection, or possibly the result of other processes such as a genetic bottleneck or founder effect. (DOCX 103 kb)

Online Resource 4

Family-average relatedness estimates between pairs of trees within families of E. cladocalyx. E(2θ|HS) = 0.25, E(f|HS) = 0. KI = Kangaroo Island, SFR = South Flinders Ranges, PS = planted stand. Values given are not corrected for bias (see Table 3). (DOCX 40 kb)

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Bush, D., Thumma, B. Characterising a Eucalyptus cladocalyx breeding population using SNP markers. Tree Genetics & Genomes 9, 741–752 (2013). https://doi.org/10.1007/s11295-012-0589-1

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