Genetic relationships in the gene pool of domesticated Macadamia based upon chloroplast and nuclear genome sequencing

Macadamia is a recently domesticated horticultural crop cultivated to produce edible nuts. M. integrifolia and M. tetraphylla are the two cultivated members of the genus Macadamia. Here, we performed whole genome sequencing of 199 domesticated cultivars and selections from the Australian macadamia breeding program. Analysis of 45 nuclear gene coding sequences from the nuclear genome showed that 153 genotypes from different breeding programs and Australian breeding selections were closely related to the M. integrifolia genome, while 29 genotypes were closer to the M. tetraphylla genome, and three genotypes were related to the M. ternifolia genome. The nuclear phylogeny revealed most of the Hawaiian cultivars were closely related to each other reflecting their genetic similarity. Non-Hawaiian cultivars from different breeding programs were spread throughout the phylogenetic tree. Complete chloroplast genomes were assembled, and the chloroplast phylogeny was analysed in relation to 59 wild macadamia accessions, revealing the maternal origin of the Hawaiian cultivars to be from the Gympie and Gundiah regions. Only a small proportion of the wild M. integrifolia diversity was utilised in the process of domestication of most of the Hawaiian cultivars. Chloroplast haplotype analysis identified 11 functional haplotype groups in the domesticated gene pool. This study highlights the potential value of including wild germplasm in breeding to develop improved cultivars that capture more of the available diversity.