Genetic diversity analysis and core collection construction of Macadamia spp. from Yunnan using fourfold degenerate SNP sites

Macadamia (Macadamia spp.) is a popular nut native to Australia. Yunnan Province has emerged as the largest macadamia cultivation region globally and possesses the most extensive collection of macadamia germplasm in China. However, knowledge regarding the genetic diversity and core collection characteristics of macadamia in this region remains limited. In this study, we analyzed 210 macadamia accessions from three geographical origins-Australia, the USA, and China-to assess the genetic diversity of Yunnan macadamia germplasm through resequencing and identified 90,783 fourfold degenerate single-nucleotide polymorphism (SNP) sites. We classified populations from the three geographical origins based on these SNPs using phylogenetic and population structure analyses. Our assessment of genetic diversity and population differentiation revealed a mean expected heterozygosity ranging from 0.222 to 0.257, mean observed heterozygosity from 0.203 to 0.224, mean polymorphic information content from 0.183 to 0.216, average minor allele frequency from 0.155 to 0.171, and nucleotide diversity from 0.224 to 0.259. Accessions from the USA exhibited the lowest genetic diversity, whereas those from Australia exhibited the highest. Finally, we developed a core collection of 43 accessions based on genetic diversity analyses. Our findings provide valuable insights into the genetic diversity of macadamia and may facilitate the collection and utilization of macadamia resources in Yunnan Province.