SNP analysis of Macadamia integrifolia chloroplast genomes to determine the genetic structure of wild populations

Macadamia is an iconic Australian plant, being the only international commercial food crop developed from the indigenous flora. The preferred species for commercial production of the highly valued kernel is Macadamia integrifolia, which is endemic to the subtropical rainforests of south-east Queensland. The first domesticated macadamia is probably a tree planted in the Brisbane Botanical gardens by Walter Hill in 1858. Crop development was led in Hawaii following introductions in the late 19^th century. Complete chloroplast (cp) genome sequencing, using next generation sequencing technology, of 13 trees was used to examine the structure of the wild populations. The 516 Single Nucleotide Polymorphisms (SNPs) identified with reference to the cp genome sequence of Hawaiian 'H.741 Mauka' cultivar produced 12 unique chlorotypes in addition to the reference. The results of this study suggest there is a strong geographic structure to the genetic variation in M. integrifolia. Northern populations were a source of germplasm for the development of the 'Mauka' cultivar, and the origin of the Walter Hill tree was likely a southern population of M. integrifolia.