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

Xiao Wei,Fei Shen,Xiaoxue Ma,Yuping Zhang,Ning Liu,Qiuping Zhang,Shuo Liu,Weisheng Liu,Yujun Zhang,Ming Xu

doi:10.1007/s11295-021-01506-x

Xiao Wei, Fei Shen + Show 8 more

Open Access

https://doi.org/10.1007/s11295-021-01506-x

Copy DOI

Abstract

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 ~20× 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.

Highlights

Plum is one of the most important fruit crops globally and, possesses extensive genetic diversity and high economic value (Topp et al 2012)
The 67 plum accessions representing different geographic and morphological characteristics (Table S1) were sequenced using the Illumina HiSeq 2500 platform with a sequence depth higher than 20×; a total 462.6 Gb of clean data was retained with an average of 6.9 Gb for each accession after filtering out low-quality reads
43.81% of the Single-nucleotide polymorphisms (SNPs) were located in intergenic regions, and 10.52% were in coding regions

Summary

Introduction

Plum is one of the most important fruit crops globally and, possesses extensive genetic diversity and high economic value (Topp et al 2012). Within the genus Prunus, the Chinese plum According to historical records of cultivation, the Chinese plum may have originated in the Yangtze River Basin, and there are abundant plum germplasm resources in China (Hartmann and Neumulle 2009). The Chinese plum has a long growing history and extensive geographical distribution, with more than 1000 indigenous plum cultivars in China, derived from Prunus salicina L. Over 700 of these cultivars are currently preserved at the National Germplasm Repository for Plums and Apricots (NGRPA) located in Xiongyue, Liaoning Province, China (Wei et al 2020). Yu et al (2011) carried out comprehensive phenotyping of 405 Chinese plum cultivars and their hybrids from the NGRPA, and investigated a total of 32 morphological and agronomic characters.

Methods

Results

Conclusion