Genetic diversity analysis of macadamia germplasm in China based on whole-genome resequencing

Abstract

Macadamia (Macadamia integrifolia, and M. tetraphylla) production has increased rapidly in China over the past two decades. However, our understanding of the genetic diversity and genomic background of available macadamia germplasm resources remains limited. Here, we conducted whole genome resequencing of 208 macadamia accessions in a macadamia germplasm from China. In all, 1,110.83 Gb of clean reads and 458,205,696 single nucleotide polymorphisms (SNPs) were identified, including 5,470,885 high-quality SNPs. The overall genetic diversity of 208 macadamia accessions showed nucleotide diversity (Pi), expected heterozygosity (He), and observed heterozygosity (Ho) values of 1.716 × 10^–3, 0.270, and 0.202, respectively. Australian germplasm generally possessed the highest genetic diversity, followed by Chinese germplasm, with macadamia germplasm resources introduced from the United States exhibiting the lowest genetic diversity. Furthermore, both phylogenetic and PCA analyses consistently clustered American accessions together. Genetic structure analysis divided the 208 accessions into nine groups, with moderate to high genetic differentiation found between different groups. These findings and genomic resources obtained from this study will be crucial for the strategic utilization of macadamia germplasm and will significantly contribute to future genome-wide associate studies.