Prunus salicina Genome sequencing and assembly

Plum is gaining importance due to their extensive genetic diversity and nutritional attributes beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, we used the high-quality SNPs generated from high-depth whole-genome resequencing of 67 Prunus accessions to evaluate the genome-level diversity and population structure. The 67 plum accessions were classified into four groups, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG), basing on the results of the phylogenetic analysis, the principal component analysis, and the population structure analysis. Several cultivars from South China were observed distributing in the other three groups, and gene flow was detected between the SCG and the FG. For the two groups mainly consisted of plum landraces, the genetic diversity indices including the private allele number, the observed heterozygosity, the expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. We speculated that, for SCG, the genetic background was relatively broader, the genetic exchange was more frequent with other groups, and the possible origin center of Chinese plum was at the Yangtze River Basin in South China. This study provided detailed genetic variation features of plum cultivars, and preliminarily dissected their genetic diversity and population structure, laying a foundation for breeders to use diverse germplasm and allelic variants towards developing improved plum varieties.