Analysis of Genetic Diversity in Prunus Sibirica L. in Inner Mongolia Using SCoT Molecular Markers

Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica populations in Inner Mongolia. A total of 289 polymorphic bands were amplied with 23 SCoT primers, showing a polymorphism percentage of 97.94% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplied up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplied by SCoT3 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of Prunus sibirica in Inner Mongolia. The analysis of molecular variance (AMOVA) showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic (UPGMA) cluster analysis, principal coordinate analysis (PCoA) and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the ecient SCoT molecular marker-based genetic diversity analysis of Prunus sibirica in Inner Mongolia can provide a reference for Prunus sibirica variety breeding and resource development. A principal coordinate analysis (PCoA) was performed according to the binary matrix using GenAlEx software. STRUCTURE software was used to determine the genetic structure of the studied population, and K was tested from 1 to 10 with ten replicates. IBD software was used for Mantel test to analyze the correlation between genetic distance and geographic distance and altitude . PCoA GenAlEx The results showed that the 278 individuals were divided into two groups. The UPGMA clustering analysis showed that the 278 individuals were divided into group I and group II when the genetic similarity was 0.17. Group I included 144 individuals, while group II included 134 individuals.


Introduction
Prunus sibirica is a member of the Rosaceae family and is the dominant species on mountain dunes and dry steppes (Yu 1979 Prunus sibirica shows strong cold and drought resistance and high nutritional and medicinal value (Dong et al. 1991). However, the yield differences in Prunus sibirica in China are signi cant and very unstable because of long-term seed reproduction, delayed breeding, and the in uence of climatic factors. In addition, frost can severely reduce the yield of Prunus sibirica, greatly restricting its industrialization (Ma et al. 2007; Yao et al. 2007; Jin et al. 2018). Prunus sibirica shows self-incompatibility, resulting in large genetic differences among individual genetic resources .
Biodiversity refers to all of the variation among living things on earth and is the basis of survival and biological development (Rao et al. 2002). Genetic diversity is an important component of biological diversity and refers to the genetic differentiation of all living organisms (Lu 2018). Dong et al (2018) studied the diversity of 19 quantitative traits of Prunus sibirica from different populations, and the results showed that the coe cient of variation of the economic traits of fruit and kernel were large, and the coe cient of variation of fruit yield was the largest, indicating that Prunus sibirica has rich germplasm resources with great potential for breeding good varieties. Wang et al (2019) studied the seed traits of Prunus sibirica from 19 populations and showed rich genetic variations in seed traits between 19 populations. Li (2014) studied the genetic diversity of Prunus sibirica and Prunus armeniaca in North China according to inter-simple sequence repeat (ISSR), sequence-related ampli ed polymorphism (SRAP), and simple sequence repeat (SSR) analyses. The results showed that the natural population of Prunus sibirica in China exhibits a high level of genetic diversity, showing high genetic differentiation within its populations but low genetic differentiation and moderate gene ow among populations.
The initial SCoT marker was a molecular marker based on a single primer ampli cation reaction proposed by Collard and Mackill (2009) in rice. It was a novel molecular marker of the target gene. The strategy was to conduct genome ampli cation with a single primer according to the conservative nature of the ATG translation of the anking sequences of plant genes; the goal was to reveal the percentage of dominant polymorphic markers in candidate functional gene regions via a procedure with easy operation to identify rich polymorphisms. Compared with random ampli ed polymorphic DNA (RAPD), ampli ed fragment length polymorphism (AFLP), SSR, and ISSR markers, SCoT markers have been e ciently produced and linked to traits, making them convenient for use in molecular markerassisted breeding. SCoT markers have been used in various plant species, such as Phoenix dactyifera (Somayeh Saboori et al. 2020), Mangifera indica (Li Zhou et al. 2020) and Diospyros spp. (Changfei Guana et al. 2020).
Genetic resources for Prunus sibirica are extremely abundant and present great developmental potential, and they can provide an important genetic basis for the improvement of Chinese Prunus sibirica and the breeding of new varieties. In recent years, research on the genetic diversity of Prunus sibirica has mostly been conducted in northeastern and northern China, and Prunus sibirica is mainly distributed in Inner Mongolia. Moreover, few studies have been conducted on the genetic diversity of Prunus sibirica in Inner Mongolia. Therefore, we used SCoT molecular markers to analyze the genetic diversity of 278 individuals from 10 populations of Prunus sibirica in Inner Mongolia. The genetic diversity and genetic structure among populations and individuals of Prunus sibirica in Inner Mongolia were revealed. This study provides a scienti c basis for the cultivation and exploitation of the abundant genetic resources of Prunus sibirica in Inner Mongolia.

Plant materials
The materials were obtained from the Prunus sibirica Germplasm Resource Garden of the Inner Mongolia Fine Variety Breeding Center (Fig. 1). A total of 278 individuals were collected from 10 populations (Table 1). Fresh young leaves were placed in a bucket containing liquid nitrogen, brought back to the laboratory, and stored in a -80°C freezer for further experiments.

DNA extraction
Genomic DNA was extracted from fresh leaves using a Plant DNA Extraction Kit (TIANGEN, China). The extracted DNA was tested for quality and purity with a spectrophotometry at a wavelength of 260/280 nm using a BioPhotometer (Thermo Fisher Scienti c, America) and 1% agarose gel electrophoresis (with a nucleic acid stain) and stored in a -20°C freezer for further experiments.

SCoT-PCR
The 80 primer sequences were selected by referring to Collard and Mackill (2009) and were synthesized by Shanghai Sangon Biological Engineering Technology and Services. A total of 23 highly polymorphic and repeatable primers were selected from 80 SCoT primers to evaluate the selected Prunus sibirica accessions ( Table 2). A 96-well gradient PCR instrument was used for the ampli cation reactions. PCR was performed in a 20 µL volume containing 10 µL of 2× Taq Mix, 1.6 µL (30 ng/µL) of genomic DNA, 0.8 µL (10 mol·L − 1 ) of each primer, and 7.6 µL of ddH 2 O. SCoT-PCR ampli cation was conducted with initial denaturation for 5 min at 95 ℃, followed by 40 cycles of 45 s at 94℃, 45 s at 50 to 54℃ and 2 min at 72℃, with a nal extension of 7 min at 72℃ and holding at 4℃. The PCR products were separated in a 1.5% agarose gel using 1 × TBE running buffer, stained, and photographed, and the records were preserved.

Data analysis
SCoT amplicons were scored in a binary matrix as present (1) or absent (0) for each sample based on the corresponding standard size. Vague bands that could not be easily detected were not scored. POPGEN32 software was used to calculate the total number of bands (NPB) and the number of polymorphous bands (PPB) obtained with the SCoT primers to analyze the genetic diversity index of Prunus sibirica and to calculate Nei's gene diversity index (H), Shannon's information index (I), the number of alleles (Na), the effective number of alleles (Ne), total genetic diversity (Ht), population genetic diversity (Hs), the coe cient of genetic differentiation (Gst ), and gene ow (Nm).
Ntsys-2.0 software was used to calculate Nei's genetic distances from the binary (0, 1) matrices obtained, and the unweighted pair-group method with arithmetic means (UPGMA) method performed in the SHAN program was used for the cluster analysis of the 10 populations to construct the cluster relationship tree diagram. MEGA7 software was used for the cluster analysis of the 278 individuals based on Nei's genetic similarity matrix obtained via the arithmetic mean (UPGMA) method. An analysis of molecular variance (AMOVA) and GenAlEx software were used for the analysis of genetic differentiation among and within populations. A principal coordinate analysis (PCoA) was performed according to the binary matrix using GenAlEx software. STRUCTURE software was used to determine the genetic structure of the studied population, and K was tested from 1 to 10 with ten replicates. IBD software was used for Mantel test to analyze the correlation between genetic distance and geographic distance and altitude .

SCoT polymorphism analysis
In the SCoT analysis, 23 SCoT primers were used for marker ampli cation in 278 Prunus sibirica individuals. A total of 292 bands that could be scored were produced, among which 289 bands were polymorphic, with a mean of 12.6 polymorphic bands per primer. The polymorphism percentage was 98.87%. Among the 23 SCoT primers, SCoT21, SCoT32, and SCoT53 ampli ed a maximum of 17 bands, and the polymorphism percentage was 100%. The number of bands ampli ed by the SCoT 25 primer was at least 9, and the polymorphism percentage was 90%.     Analysis of the among-population genetic structure POPGEN32 was used to analyze the genetic distance and genetic similarity of the 10 Prunus sibirica populations in Inner Mongolia. The analyses of Nei's genetic similarity and Nei's genetic distance showed that the population genetic distance ranged from 0.0311 to 0.2486 while the genetic similarity ranged from 0.7799 to 0.9694. The genetic similarity between WJG and KSK was the highest, at 0.9694, and their genetic distance was the lowest, at 0.0311. The lowest genetic similarity between ZLT and WJG was 0.7799, and the greatest genetic distance was 0.2486 (Table 7).
Based on Nei's genetic distance, the UPGMA method was used for cluster analysis. The results showed that the 10 populations were divided into two major groups at a genetic distance threshold of 0.22 (Fig. 2 . 3), with the PCoA performed using GenAlEx software (Fig. 4) To further explore the genetic relationships within populations of Prunus sibirica, the population structure of 278 Prunus sibirica individuals was evaluated using STRUCTURE software. ∆K values computed for all classes indicated a strong signal for K = 2 (Fig. 5),and K = 2 values provided the most rational arrangement of Prunus sibirica in different regions. A total of 278 Prunus sibirica individuals were divided by the STRUCTURE analysis into 2 groups (Fig. 6).
Group I included all individuals in the KSK, WJG, KZH, and KYZ populations and some individuals from ZLA. Group II included all individuals from AL, WLS, ZLT, BLY, and LC and some individuals from ZLA. This result is similar to the clusters identi ed using UPGMA and PCoA.

Discussion
In this study, a genetic diversity analysis was performed using SCoT markers to assess phylogenetic relationships genetic diversity of Prunus sibirica in different regions, and the results showed that the polymorphism ranged from 58-90%. In contrast, the SCoT molecular markers were found to be more polymorphic than other molecular markers.
Therefore, SCoT markers may be suitable for the study of genetic diversity according to molecular markers in Prunus sibirica. A previous study of the genetic diversity of Prunus armeniaca (Li 2014 )  As a perennial wild resource, Prunus sibirica is widely distributed in Inner Mongolia and exhibits a large distribution area, long-term evolution and considerable diffusion as well as ecological diversity, leading to rich genetic diversity.
According to Wright (1972), when the F ST (G ST , genetic differentiation coe cient) value is 0 to 0.05, the genetic differentiation within populations is low; when the F ST value is 0.05 to 0.15, the genetic differentiation within populations is moderate; when the F ST value is 0.15 to 0.25, the genetic differentiation within populations is high; and when the F ST value is greater than 0.25, the genetic differentiation within populations is great. In our research, the G ST was 0.3601. The results showed that the genetic differentiation coe cient of Prunus sibirica within populations in Inner Mongolia was relatively high, with among-population genetic differentiation of 39% and a within-population genetic differentiation of 61%. Wang (2019), Liu et al. (2012) and Ma (2013), who used SSR and ISSR markers for Prunus sibirica and wild apricot genetic diversity analyses, showed that within-population variation dominated, and the among-population variation was much lower than the within-population variation. which is similar to the results of a previous study in Prunus sibirica.
The reasons for the high within-population genetic differentiation of Prunus sibirica in Inner Mongolia may include the following: 1. Gene ow is an important factor affecting genetic differentiation in a population when Nm < 1, which can conversely effectively prevent genetic differentiation caused by genetic drift. The Nm value for Prunus sibirica in Inner Mongolia was 0.8884, indicating that genetic drift was not the main factor in uencing the genetic differentiation of the Prunus sibirica populations in Inner Mongolia. Some gene ow exists among the Prunus sibirica population in Inner Mongolia, but the Nm intensity was relatively low. 2. The self-incompatibility breeding characteristic of Prunus sibirica may eliminate self-pollination as a possible cause of genetic differentiation, and its breeding mainly relies on natural pollination or pollination by visiting insects such as bees, ies and a few butter ies Liu 2010).
Although pollen can be spread by insects and by wind over long distances, the large distribution area and discontinuities in the population distribution of Prunus sibirica are restricted due to geographic isolation or habitat fragmentation (Wu et al. 2015), thus weakening the gene ow within populations of Prunus sibirica. 3. Some populations have been destroyed or their habitats have been degraded, resulting in a gradual fragmentation of the population distribution and limiting the gene ow within the populations. Therefore, Prunus sibirica in Inner Mongolia shows high within-population genetic differentiation under the in uence of multiple factors, such as physical geographic isolation and human activities.
In the present study, the genetic structure of Prunus sibirica populations in Inner Mongolia was analyzed. From the clustering diagram, principal component analysis, and structure analysis, we can see that most of the populations are clustered together with a similar geographic distribution, and the Mantel test showed a signi cant correlation between the genetic distance and geographic distance and between the genetic distance and altitude of the Prunus sibirica studied (r = 0.0426, P ≦ 0.4790;r = 0.0305, P ≦ 0.4260). Therefore, we hypothesized that a geographic isolation effect exists among populations of Prunus sibirica populations in Inner Mongolia, weakening the opportunities for gene ow within the populations and causing the intensi cation of genetic differentiation within populations. The clustering diagram, principal component analysis and structure analysis of the 278 individuals divided the populations into two groups ( I and II ). KSK, WJG, KYZ, and KZH were clustered in group I; LC, BLY, WLS, AL, and ZLT were clustered in group II; and only the 22 individuals in the ZLA group were divided between the two groups. A certain degree of gene ow exists among the subgroups, and gene ow also affects the population structure of Prunus sibirica (Liu et al 2012). This may occur because of the existence of many mountains and areas of sandy land in Inner Mongolia, and the topography and landforms are very complex. Thus, topographic barrier characteristics are prominent in the regional distribution, resulting in a natural isolation effect on different provenances of species and weakening the gene ow opportunities among populations. Second, habitat fragmentation is also an important factor that affects the composition and structure of the ecosystem and the genetic structure of a species.

Conclusion
This study revealed that Prunus sibirica shows high genetic diversity in Inner Mongolia. Therefore, improving the preservation and utilization of speci c germplasms of different populations is necessary to avoid the disappearance of a large number of valuable genetic resources. Moreover, strengthening the protection of the genetic resources of Prunus sibirica and expanding the collection of Prunus sibirica resources to implement transfer protection will be conducive to better scienti c research and resource protection in Prunus sibirica, increase the gene ow among populations, and improve the genetic diversity of Prunus sibirica. Based on resource collection, genetic diversity analyses, and genetic structure analyses, the breeding of Prunus sibirica varieties with high yields and frost resistance is being actively performed to meet the increasing demand for the industrial production of Prunus sibirica resources. Evanno's test based on delta k among Prunus sibirica cultivars studies Figure 6 Population structure of the 278 individuals at K = 2. Note: The same color indicates the same group