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Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions

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Abstract

Macadamia nuts are known globally for their high quality and economic value. Global macadamia commercial nut production amounts to 60,000 metric tonnes and is increasing steadily. South Africa is the leading producer with 29% of worldwide kernel production. Commercial macadamia germplasm was originally selected from a small genepool (mainly Macadamia integrifolia species) from a limited geographic distribution in Australia. These accessions were subsequently bred, cloned and exported across the world to start local macadamia industries. The South African macadamia industry was established with pre-commercial and commercial macadamia from different parts of the world, and local selections were also performed. Many of these accessions have unique genetic compositions that have not been characterized yet. We used 13 nuclear microsatellite markers to study the genetic diversity and structure of macadamia germplasm cultivated in South Africa. We compared four groups of accessions including 31 originating from the Hawaiian Agricultural Experimental Station (HAES), 19 from Australia (AUS), two from California and one from Israel (OTH), 31 from South Africa’s locally selected accessions (SA) and 26 from two local Farmers (FARM). We used STRUCTURE, PCoA and neighbour-joining phylogenetic analyses to show that the South African selected accessions include diverse hybrid genotypes with strong Macadamia tetraphylla composition, unlike the Hawaiian commercially released and Australian representative collections that mostly have M. integrifolia or hybrid composition. Our results suggest that the South African selections represent a unique and diverse set of germplasm for future macadamia improvement efforts that will benefit from genomic breeding technologies.

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All of the data are included in the electronic supplementary material (Table S3).

Change history

  • 22 July 2022

    Handling editor name correction.

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Acknowledgements

The authors thank Mark Penter (Agricultural Research Council–Institute for Tropical and Subtropical Crops (ARC-ITSC) of South Africa) for assistance with sample collection from Mpumalanga, constructive comments on the manuscript and valuable information and discussions. The authors also thank Matthew Erasmus for the sample collection from University of KwaZulu-Natal–Ukulinga Research Farm. We would like to thank the local Farmer for allowing us to use the breeding population and the second farmer for his sample. Further thanks to Dr Catherine Nock (Southern Cross University) for assistance with the microsatellite markers. We would like to thank Dr Nanette Christie (University of Pretoria) and Annie Chan (Agricultural Research Council–Biotechnology Platform) for assistance with RStudio and the Forest Molecular Genetics Team (University of Pretoria) for their guidance with the GeneMarker. This work was funded by the National Research Foundation (NRF) of South Africa (UID 112133) and Macadamias South Africa (SAMAC). MR acknowledges PhD scholarship support from the Agricultural Research Council–Professional Development Programme (ARC-PDP) of South Africa.

Funding

This work was funded by the National Research Foundation (NRF) of South Africa (grant to CH, UID 112133). Further funding was received from Macadamias South Africa (SAMAC, strategic grant to GF).

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Authors and Affiliations

  1. Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa

    Mary Ranketse, Gerda Fourie & Alexander A. Myburg

  2. Biotechnology Platform, Agricultural Research Council – Onderstepoort Veterinary Institute, Pretoria, South Africa

    Mary Ranketse, Charles A. Hefer & Rian Pierneef

  3. AgResearch Ltd, Lincoln, New Zealand

    Charles A. Hefer

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  1. Mary Ranketse
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Contributions

The experimental design was contributed by CH, AAM and MR. MR did data collection and data analysis and wrote the first draft of the paper as part of her PhD thesis. The study was supervised by AAM, CH, GF and RP. The final manuscript was edited and approved by all the authors.

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Correspondence to Alexander A. Myburg.

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Communicated by M. Wirthensohn.

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Ranketse, M., Hefer, C.A., Pierneef, R. et al. Genetic diversity and population structure analysis reveals the unique genetic composition of South African selected macadamia accessions. Tree Genetics & Genomes 18, 15 (2022). https://doi.org/10.1007/s11295-022-01543-0

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