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Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers

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Abstract 

Since the start of avocado cultivation in South Africa, superior rootstocks and fruit cultivars have been selected based on morphological traits, which is time consuming and expensive. Technological advances, such as the development of a single nucleotide polymorphism (SNP) genotyping platform for avocado, may reduce these limitations. Therefore, the aim of this study was to implement molecular marker technologies for the validation of clonal material, verification of horticultural varieties, and determining the genetic diversity and population structure of an avocado cultivar germplasm in South Africa. An avocado cultivar breeding population, containing 375 individuals, was genotyped using 384 SNP markers. Our affinity propagation analysis (APA) indicated a 10.74% mislabelling in the germplasm. The principal component analysis (PCA) and discriminate analysis of principal components (DAPC) suggested that the germplasm was admixed in relation to the three known avocado varieties, Guatemalan, Mexican, and West Indian. Additionally, the ancestral origins were determined for 27 individuals with unknown ancestry. Furthermore, the population diversity was assessed and revealed moderate levels of differentiation in the germplasm, suggesting a high level of gene flow between the different populations. This research highlights the value of clonal verification and horticultural variety identification—for the reliable propagation of material with desired traits. The accurate propagation of material and clonal identity could aid avocado growers to link morphological characters and stress tolerance to accurate genetic backgrounds, which could improve the selection of avocados for current and future environmental stressors, especially as Africa is set to be significantly impacted by climate change.

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Data availability

The cultivar germplasm analysed during this study is available in the University of Pretoria Research Repository [Supplementary File 1—https://doi.org/10.25403/UPresearchdata.19145087].

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Acknowledgements

The authors would like to thank the Forestry and Agricultural Biotechnology Institute (FABI) and the University of Pretoria for the use of their facilities and equipment. Furthermore, the authors would like to thank Dr David Kuhn for the custom affinity propagation scripts. Lastly, I would like to thank Allesbeste™ for providing the plant material.

Funding

The authors would like to thank the Hans Merensky Foundation© and Allesbeste™ for funding.

Author information

Authors and Affiliations

  1. Hans Merensky Chair in Avocado Research, University of Pretoria, Pretoria, South Africa

    Raven Wienk & Noëlani van den Berg

  2. Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa

    Raven Wienk, Marja Mostert-O’Neill & Noëlani van den Berg

  3. Faculty of Natural and Agricultural Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa

    Raven Wienk, Marja Mostert-O’Neill & Noëlani van den Berg

  4. Dominican University of California, San Rafael, CA, USA

    Nilwala Abeysekara

  5. Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA

    Patricia Manosalva

  6. Subtropical Horticulture Research Station, USDA-ARS, Miami, FL, USA

    Barbie Freeman

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  1. Raven Wienk
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Contributions

RW contributed to the study design, experimental design, sample curation, formal analysis, investigation, visualisation, and drafting/writing/editing of the manuscript. NVDB contributed to the study conceptualisation and design, experimental design, project administration, resources, supervision, and funding. MMON and NA were responsible for methodology and technical assistance. PM provided the horticultural reference. BF extracted, processed, and performed the SNP genotyping. All co-authors contributed to writing/editing of the manuscript. All authors contributed to and approved the final manuscript.

Corresponding author

Correspondence to Raven Wienk.

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This study received specific approval by the appropriate ethics committee for research involving plants.

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The authors declare no competing interests.

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Communicated by C. Chen

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Supplementary Information

Below is the link to the electronic supplementary material.

11295_2022_1573_MOESM1_ESM.pdf

Supplementary file1 Supplementary Fig 1 DAPC analysis of 159 genotypes indicating the cluster’s composition from K = 2 until K = 7 a) Bayesian information criterion (BIC) plot b) DAPC scatterplot - The eigenvalues and variance of each PC are found within parentheses on each axis. Individuals are represented as dots c) Genomic composition plot - Each thin vertical line in the bar plot represents one individual and each colour represents one inferred ancestral population. The length of each colour in a vertical bar represents the proportion of that individual’s ancestry that is derived from the inferred ancestral population corresponding to that colour. The same colour in different individuals indicates that they belong to the same cluster, indicating admixture (PDF 3451 KB)

11295_2022_1573_MOESM2_ESM.xlsx

Supplementary file2 Supplementary File 1: Formatted data of 326 genotyped individuals - Including industry suspected variety, DAPC assigned variety, assigned affinity propagation groups, silhouette scores, and genotype data (10.25403/UPresearchdata.19145087) (XLSX 663 KB)

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Wienk, R., Mostert-O’Neill, M., Abeysekara, N. et al. Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers. Tree Genetics & Genomes 18, 41 (2022). https://doi.org/10.1007/s11295-022-01573-8

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