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A multiplexed set of microsatellite markers for discriminating Acacia mangium, A. auriculiformis, and their hybrid

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Abstract

In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a set of multipurpose SSR markers for use in both Acacia mangium and A. auriculiformis. A total of 51 SSR markers (developed in A. mangium and natural A. mangium x A. auriculiformis hybrid) were tested. A final set of 16 well-performing SSR markers were identified, six of which were species diagnostic. The markers were optimized for assay in four multiplex mixes and used to genotype range-wide samples of A. mangium, A. auriculiformis, and putative F1 hybrids. Simulation analysis was used to investigate the power of the markers for identifying the pure species and their F1, F2, and backcross hybrids. The six species diagnostic markers were particularly powerful for detecting F1 hybrids from pure species but could also discriminate the pure species from F2 and backcross progenies in most cases (97 %). STRUCTURE analysis using all 16 markers was likewise able to distinguish these cross types and pure species sets. Both sets of markers had difficulties in distinguishing F2 and backcross progenies. However, identifying F1 from pure species is the current primary concern in countries where these species are planted. The SSR marker set also has direct application in DNA profiling (probability of identity = 4.1 × 10−13), breeding system analysis, and population genetics.

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Acknowledgments

This research was funded by the Australian Centre for International Agriculture Research (ACIAR) and the Ministry of Agriculture and Rural Development (Vietnam). We acknowledge the provision of DNA extracts by Mandy Maid and Suguna Apparow from Plant Genetics Laboratory (UKM). We would like to thank Dr. Nghiem Quynh Chi (Vietnamese Academy of Forest Sciences—VAFS) for supplying control pollinated hybrid seeds, Dr. Siju Senan (UKM) for helping in experimental design, Mr. David Bush (Australian Tree Seed Centre) for supplying information on natural population locations, Peter Harrison (PhD candidate—University of Tasmania) for helping in map design, and Mr. Do Son and Mr. Phan Quyen (VAFS) who helped in sample collection.

Data archiving statement

All individual genotype data relating to this study will be available at: http://eprints.utas.edu.au/ (accession number will be supplied later).

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Authors and Affiliations

  1. School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia

    Son Le, Christopher E. Harwood, Matthew J. Larcombe, Rod A. Griffin, Anthony Koutoulis, Jane L. Harbard & René E. Vaillancourt

  2. Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, 43600, Malaysia

    Wickneswari Ratnam, Koh Sin Cyer & Liew Wai Yee

  3. CSIRO Land and Water, Private Bag 12, Hobart, TAS, 7001, Australia

    Christopher E. Harwood

  4. Vietnamese Academy of Forest Sciences, Chinhthang, Bactuliem, Hanoi, Vietnam

    Son Le & Thinh Huy Ha

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  1. Son Le
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  2. Wickneswari Ratnam
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  3. Christopher E. Harwood
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  4. Matthew J. Larcombe
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  5. Rod A. Griffin
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  9. Liew Wai Yee
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  11. René E. Vaillancourt
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Corresponding author

Correspondence to Son Le.

Additional information

Communicated by W. Ratnam

Electronic supplementary material

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ESM 1

Supplementary Table 1 List of wild populations of A. mangium and A. auriculiformis used in this study (seeds improted from ATSC). Supplementary Table 2 List of control crossed samples used for validating markers (2 samples/combination) (Am = A. mangium, Aa = A. auriculiformis). Supplementary Table 3 Primer sequences of 40 published microsatellite loci. Supplementary Table 4 Mixes of 16 markers used in second stage of genotyping. Supplementary Figure 1 Summary of simulations for K = 1 to 10 from STRUCTURE for Evanno approach for wild population of A. auriculiformis, A. mangium and their putative hybrids. (DOC 211 kb)

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Le, S., Ratnam, W., Harwood, C.E. et al. A multiplexed set of microsatellite markers for discriminating Acacia mangium, A. auriculiformis, and their hybrid. Tree Genetics & Genomes 12, 31 (2016). https://doi.org/10.1007/s11295-016-0990-2

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