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bioRxiv · 10.1101/2025.09.22.677927

Genetic diversity and variation in heterozygosity in Macadamia

Manatunga, S.·Furtado, A.·Topp, B.·Alam, M.·Mason, P.·Henry, R. J.
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Abstract

BackgroundMacadamia is a diploid (2n =28) rainforest tree of the Proteaceae family, native to Australia. Single-nucleotide polymorphisms (SNPs) have proven to be effective tools for evaluating genetic diversity and heterozygosity. SNPs from the whole genome were used to determine allelic diversity within different species and breeding populations, and to investigate the heterozygosity of genotypes ResultsA total of 349 samples, including wild and domesticated genotypes, were whole genome sequenced, generating 4,180,786 - 7,661,269, 2,446,762 - 7,356,187, 2,829,944 - 4,391,600, 1601519 - 3,182,089 and 3,123,715 to 9,620,640 single nucleotide polymorphism (SNP) positions at the whole genome level for M. integrifolia, M. tetraphylla, M. ternifolia, M. jansenii and the domesticated cultivars and breeding selections respectively. The overall SNP diversity for wild M. integrifolia, M. tetraphylla, M. ternifolia and M. jansenii was 4.43%, 4.33%, 1.80% and 1.1%, respectively. Domesticated M. integrifolia showed an overall SNP diversity of 3.4%, 1.03% lower than wild M. integrifolia, providing evidence of a genetic bottleneck during domestication. Genetic diversity at the individual level for the domesticated gene pool varied from 0.4% to 1.24%, with an overall diversity of 6.10%. Results across different breeding groups revealed that the Australian breeding selections (NMBPA) had the highest diversity, and HAES cultivars had the lowest diversity. Wild M. integrifolia and M. tetraphylla exhibited heterozygosity ranging from 0.36% to 0.71% and 0.30% to 0.71% respectively. The two non-edible species, M. ternifolia and M. jansenii, displayed relatively low heterozygosity (From 0.29% to 0.42% and 0.19% to 0.34% respectively). Domesticated macadamia exhibited a wide range of heterozygosity (0.33% to 1.15%). Additionally, heterozygosity correlated with yield efficiency (kernel yield/tree volume), cumulative kernel yield at age 8 and cumulative nut in shell (NIS) yield at age 8 and showed that performance increased with heterozygosity to an optimal level and declined thereafter. ConclusionThese findings confirmed that there is substantial genetic variation among the different macadamia genotypes. The results also revealed that the greatest diversity is present in wild germplasm. The data will greatly support future genome-wide studies and breeding programs.

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Manatunga, S., Furtado, A., Topp, B., Alam, M., Mason, P., Henry, R. J.. 2025-09-24. Genetic diversity and variation in heterozygosity in Macadamia. https://doi.org/10.1101/2025.09.22.677927

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