Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of similar to 20x to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

Automated summary

This study conducted whole-genome resequencing of 67 Chinese plum accessions to construct high-quality SNPs, revealing that the plum accessions could be classified into four groups based on their origin location. The southern cultivar group showed higher genetic diversity indices compared to the northern cultivar group, with gene flow detected from the southern cultivar group to the foreign cultivar group. The domestication center of origin of Chinese plum was concluded to be southwestern China, providing genetic variation features and population structure insights for breeders to improve Chinese plum varieties.