Genetic diversity, population structure, and relationships of apricot (Prunus) based on restriction site-associated DNA sequencing

Abstract

Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. Here, high-throughput sequencing was used to examine the genome-level diversity, population structure, and relationships of apricot, which are important for germplasm conservation and molecular breeding. Restriction site-associated DNA sequencing (RAD-seq) was adopted to sequence 168 Prunus spp. accessions distributed in five ecological groups, including 74 accessions of cultivated Prunus armeniaca L. and 94 accessions of wild apricots (P. armeniaca L. and Prunus sibirica L.), which generated 417,961 high-quality SNPs. We used cluster, genetic structure, and principal component analyses to examine the genetic diversities and genetic relationships of the 168 accessions. The Dzhungar-Ili ecological group accessions showed the highest genetic diversity in terms of private allele number, observed heterozygosity, and nucleotide diversity. We speculate that the Central Asian ecological group accessions were domesticated from the Dzhungar-Ili ecological group accessions. The population structure and gene flow of the North China and European ecological group accessions suggested a genetic background of P. sibirica. We argue that the two groups should be considered hybrid swarms connected to P. sibirica by continuous and extensive gene flow. P. armeniaca originated in Northwest China (Ili Valley), subsequently spread throughout Central Asia, and eventually spread to Europe. In addition, selective sweep signatures in P. armeniaca during domestication from wild to cultivated apricots, combined with differentially expressed genes, underlie distinct fruit traits, including sugars, aromas, organic acids, and carotenoids. This study provides substantive and valuable genomic resources that will significantly advance apricot improvement and effective utilization.

Keywords: Comparative genomics; Genome evolution.

Fig. 1. SNP mutation type for the five ecological groups.

a Number of transitions and transversions for the five ecological groups. b transition/transversion rate

Fig. 2. ML tree created for 168 Prunus spp. accessions.

Red indicates an outgroup (Malus sieversii). Group-0 represents Northeast Asian ecological group (wild P. sibirica), Group I represents Dzhungar-Ili ecological group (wild P. armeniaca), Group II represents Central Asian ecological group (cultivated P. armeniaca), Group III represents European ecological group (cultivated P. armeniaca), and Group IV represents North China ecological group (cultivated P. armeniaca). Node values correspond to bootstrap values

Fig. 3. Population structure of 168 accessions of Prunus spp.

Each column represents an individual, with the length of the different color segments representing the proportion of an ancestor in the individual’s genome. K = 2–8 indicates the number of ancestral groups assumed in this study from 2 to 8; The x-coordinate indicates the name of the sample, and the order of the sample of the same group was specified together. HC Huocheng county, YN Yining county, GL Gongliu county, XY Xinyuan county

Fig. 4. PCA analysis in 168 accessions of Prunus spp.

Red indicates an outgroup (Malus sieversii). The CAG, DZG, EG, NAG, and NAG indicate Central Asian ecological group, Dzhungar-ili ecological group, European ecological group, Northeast Asian ecological group, and North China ecological group

Fig. 5. Detection of gene flow between five ecological groups accessions.

Lines represent gene flow; arrows indicate the direction of ene flow. The scale bar shows a tenfold average standard error of the entries in the sample covariance matrix. The color bar shows the migration weight: a red color denotes a strong gene flow, while a yellow color denotes a weak gene flow

Fig. 6. Summary of nucleotide diversity and population divergence across the five ecological groups.

Values in parentheses represent measures of nucleotide diversity for the group, and values between pairs indicate population divergence (Fst). The thickness of the lines is proportional to the value of Fst. The circle size is proportional to the value of π

Fig. 7. Distribution of Fst values of selective sweeps of P. armeniaca during domestication from wild to cultivated apricots.

a Distribution of Fst values of selective sweeps in DZG and CAG accessions during domestication. b Distribution of Fst values of selective sweeps in DZG and EG accessions during domestication. c Distribution of Fst values of selective sweeps in DZG and NCG accessions during domestication. The horizontal line indicates the threshold of Fst (5%)