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Benchmarking genetic diversity in a third-generation breeding population of Melaleuca alternifolia


The success of a long-term breeding program for outcrossing tree species depends not only on genetic gains through selection but also on the maintenance of genetic diversity over consecutive generations of plant breeding. To inform future breeding and deployment of Melaleuca alternifolia, this study benchmarked genetic variation in 114 selected individuals from a third-generation breeding population with 18 microsatellite markers. Five loci were used to compare diversity measures in the breeding population to values of genetic variation for natural populations in Australia. The expected heterozygosity in the breeding population was high (HE = 0.823) and comparable to the average heterozygosity for 427 individuals from 36 natural populations (HE = 0.844). The inbreeding coefficient FIS was 0.044 and 0.151 in breeding and natural populations, respectively. These favourable findings confirmed that objectives of past breeding practices were successful in maintaining diversity and preventing inbreeding. Sample size effects were evident, nonetheless, and the average number of alleles per locus (NA) was markedly reduced, especially those of low frequency. To study the impact deploying clones would have on genetic diversity, simulated populations of clones were created by repeatedly sampling the breeding population for subsets of 10, 15 or 20 individuals and generating diversity parameters for all 18 loci. Results for each number of individuals were compared to the diversity in the entire breeding population. Sample size had no effect on HE, but NA was significantly and progressively reduced with smaller sample size.

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We acknowledge past ATTIA and Agrifutures Australia (formerly RIRDC) support in the development of the germplasm used in this study. We thank Tony Larkman and John Doran for constructive comments and improvements to a draft manuscript, and Gary Baker for many helpful conversations on tea tree breeding.


The authors received financial support from the Australian Tea Tree Industry Association (ATTIA), the Commonwealth Government of Australia and the Southern Cross University for CRC-Project 53955.

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Correspondence to Julia Voelker.

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An inquiry for SSR primer sequence submission to the NCBI probe database was made by the authors. However, this database is decommissioned in its current form, and the authors were informed by NCBI that the current advancements and availability of sequencing data does not require the archiving of small numbers of primers anymore. Therefore, the primer sequences for the markers used in this study were included in the supplementary material of this manuscript.

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Voelker, J., Shepherd, M. Benchmarking genetic diversity in a third-generation breeding population of Melaleuca alternifolia. Tree Genetics & Genomes 16, 22 (2020). https://doi.org/10.1007/s11295-020-1416-8

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  • Melaleuca alternifolia
  • Microsatellites
  • Genetic diversity
  • Breeding
  • Clonal deployment