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.

The purposes of this study were to provide palynological information about apricots and to reveal the relationships between six ecological groups of apricots by describing the morphological characteristics of their pollen. The pollen grains of 175 accessions belonging to 3 species (Prunus armeniaca L., Prunus sibirica L., and Prunus mume Sieb. et Zucc.) of Prunus were examined using light microscopy and scanning electron microscopy. The pollen grains were isopolar monads, radially symmetric, medium to large in size, prolate or subprolate, and 3-colporate. Most pollen grains exhibited striate exine ornamentation, and a few exhibited striato-reticulate or cerebroid exine ornamentation. Cluster analysis divided that the six ecological groups into two groups: one including the Central Asian, North China and Dzhungar-Ili ecological group accessions and another including the Northeast Asian, European and East China ecological group accessions. Principal component analysis revealed that equatorial diameter, colpus length, colpus width and ridge width were the most important metrical pollen traits, and can be used as powerful diagnostic characters in apricot identification. We speculated that the cultivated apricots in Xinjiang were domesticated from wild apricots from the Ili Valley. This study described the morphological characteristics of apricot pollen grains and provided some morphological information for future studies on the phylogenetic relationships of apricots.

To clarify the phytogeography of Prunus armeniaca L., two chloroplast DNA fragments (trnL-trnF and ycf1) and the nuclear ribosomal DNA internal transcribed spacer (ITS) were employed to assess genetic variation across 12 P. armeniaca populations. The results of cpDNA and ITS sequence data analysis showed a high the level of genetic diversity (cpDNA: H_T = 0.499; ITS: H_T = 0.876) and a low level of genetic differentiation (cpDNA: F_ST = 0.1628; ITS: F_ST = 0.0297) in P. armeniaca. Analysis of molecular variance (AMOVA) revealed that most of the genetic variation in P. armeniaca occurred among individuals within populations. The value of interpopulation differentiation (N_ST) was significantly higher than the number of substitution types (G_ST), indicating genealogical structure in P. armeniaca. P. armeniaca shared genotypes with related species and may be associated with them through continuous and extensive gene flow. The haplotypes/genotypes of cultivated apricot populations in Xinjiang, North China, and foreign apricot populations were mixed with large numbers of haplotypes/genotypes of wild apricot populations from the Ili River Valley. The wild apricot populations in the Ili River Valley contained the ancestral haplotypes/genotypes with the highest genetic diversity and were located in an area considered a potential glacial refugium for P. armeniaca. Since population expansion occurred 16.53 kyr ago, the area has provided a suitable climate for the population and protected the genetic diversity of P. armeniaca.

The volatile compounds in the fruits of 24 apricot cultivars were quantitatively and qualitatively determined via headspace solid-phase microextraction and gas chromatography–mass spectrometry (HS-SPME-GC–MS). A total of 429 volatile compounds were detected in these fruits, and the greatest number of detected terpenoids was 77. Significant differences were found among the cultivars in terms of the total volatile compound content of the fruits, with variation from 112.76 (‘ZSHYX’) to 317.36 µg/g (‘JNL’). Using relative odor activity value (rOAV) analysis, 42 key aroma compounds were identified. The rOAVs of (2S,4R)-4-methyl-2-(2-methylprop-1-enyl)oxane, (E)-non-2-enal, (3-methyl-3-sulfanylbutyl) formate, and thiophen-2-ylmethanethiol were above 1000, and most had green, fruity, and woody odors; these results indicated that these substances were important contributors to the overall aroma of the apricot fruits. Our study provides a comprehensive analysis of the volatile compounds from 24 representative apricot cultivars and can aid in the further scientific understanding of the metabolites and aroma in apricots. These findings provide a reference for controlling fruit quality and for future apricot cultivar breeding.

Wild apricot in Yili wild fruit forest in Xinjiang have been seriously affected by leaf spot-hole disease, with the incidence reaching 100%. To identify the pathogen of apricot perforation in the Yili wild fruit forest, two bacterial strains with strong virulence were obtained by the dilution separation method. The bacterial strains were gram-negative bacteria with yellow colonies, smooth surfaces and neat edges. The results of the pathogenicity test showed that the bacteria could cause symptoms of leaf spot-hole disease in wild apricot, similar to the symptoms in the field, and could cause HR in tobacco. Based on the 16S rDNA gene sequence and multilocus sequence analysis of fusA, gyrB, leuS, pyrG, rpoB and rlpB, combined with the physiological and biochemical characteristics, the isolated strain was identified as Pantoea agglomerans. The pathogen causing bacterial leaf spot-hole disease in wild apricot was determined to be P. agglomerans in the wild fruit forest of Yili, Xinjiang. The whole genome of the pathogen strain GL9-2 was sequenced based on the Illumina HiSeq500 and PacBio RS platforms. The genome size was 4765392 bp, and the G+C value was 55.27%. There was one chromosome and two plasmids in the genome, and 4353 CDs were identified. The annotation results showed that 52 glycoside hydrolase-related genes, 38 bacterial secretory system-related genes and 600 toxin-related genes were predicted.