Introduction

Atractylodes chinensis (DC.) Koidz (typically referred to as “Bei Cang Zhu” in Chinese) is a major medicinal plant known as rhizome atractylodes, which are used to treat digestive disorders, rheumatic diseases and night blindness [5]. Modern pharmacological studies have reported that rhizome atractylodes was also used for anti-inflammatory, anti-bacterial [10, 17] and anti-tumor properties [11]. A. chinensis is widely distributed throughout most areas of northern China and is mainly produced in Hebei, Inner Mongolia, Liaoning and other provinces of China [35]. The contents of atractylodin in rhizome atractylodes, an important standard of quality assessment in the Chinese pharmacopeia, vary among provinces and even counties [13], but are similar in characteristics. The utilization of and research on A. chinensis have received less attention worldwide. Additionally, A. chinensis faces an unprecedented threat of even extinction due to its sharp reduction in wild resources as well as increasing medicinal demand. Although cultivation relieved some of this pressure over the past ten years, species of stable and consistent quality have not yet been cultivated due to unclear genetic basis. China is very rich in genetic variability of A. chinensis. Therefore, it is critical to adopt an effective methodology to assess the interpopulations genetic diversity of wild A. chinensis populations.

High-performance liquid chromatography (HPLC) fingerprinting [13], ITS [9, 12] and trnL-F [8, 22] sequences and chloroplast genome variation [30, 33] have been used to analyze interspecific phylogenetic relationships of Atractylodes species. However, these methods are not effective for intraspecific diversity analysis [34]. Simple sequence repeats (SSRs) are the ideal markers due to their high polymorphism, codominance and low cost. SSR markers have been widely used in variety identification, fingerprinting construction and intraspecific genetic diversity analysis [14, 25, 34]. The selection of a set of core SSR primers for germplasm identification and genetic diversity have been conducted for many medicinal plants, such as Glehnia littoralis [27], Glycyrrhiza [16], and Euryale ferox [15]. However, such a marker toolkit is not presently available for A. chinensis genetic diversity analysis.

In this paper, we screened SSR loci in clusters classified into the sesquiterpenoid biosynthesis pathway based on the transcriptomic database of A. chinensis. Ten SSRs with high polymorphism were used to analyze the interpopulations genetic diversity and fingerprinting of 19 A. chinensis populations. Interpopulation genetic diversity and fingerprinting will provide a scientific basis for species identification and selective breeding in A. chinensis.

Materials and methods

DNA extraction and PCR amplification

A. chinensis rhizomes were collected from different counties of northern China (Table 1), including Hebei, Shandong, Inner Mongolia and Jilin Provinces. No permission was required to collect wild resources of A. chinensis. All of the samples used in this study were identified as A. chinensis by Professor Qiaosheng Guo who works at Nanjing Agriculture University (Nanjing, Jiangsu Province, China). Professor Guo identified the experimental species through comparison with specimens inform the institute of botany Jiangsu Province, and the Chinese Academy of Sciences. All the samples were planted in the experimental farm of Hebei Normal University of Science & Technology (Qinhuangdao, Hebei, China). The quality and price of rhizome atractylodes were established according to the counties in the Chinese herbal medicine market. Young leaves of ten randomly selected plants from each population were mixed as one sample, immediately frozen in liquid nitrogen and stored at − 80 °C prior to DNA extraction.

Table 1 Details of 19 A. chinensis populations with location in the present study
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The total DNA of A. chinensis was extracted through the improved CTAB method using plant genomic extraction kits (Cat.No.0419-50 CB, Huayueyang, Beijing, China, http://www.huayueyang.com.cn/product/276782043). The purities of extracted DNA samples were tested in a 2.0% agarose gel with electrophoresis on a horizontal electrophoresis DYCP-31DN apparatus (Liuyi, Beijing, China) and a gel-imaging system (GBOX-HR, Syn-gene, UK). The OD260/280 ratios of DNA were measured by a spectrophotometer (Synergy HT, Gene Company Limited, Hong Kong, China).

For SSR amplification, a 10 μL volume of reaction mixture included 50 ng/μL DNA, 2.5 mM dNTPs, 10 × buffer (Mg2+ included), 5.0 U/μL Taq enzyme, 10 μM of each primer, and ddH2O. Procedures for SSR amplification were carried out in a thermal cycler (BIO-RAD S1000 PCR, California, USA) by the following cycles: an initial 4 min pre denaturation at 94 °C, followed by 35 cycles of a 30-s denaturation at 94 °C, a 30-s annealing phase at 55 °C, and a 1 min extension at 72 °C, and a final extension at 72 °C for 10 min. The PCR products were preserved at 4 °C. PCR products were separated by polyacrylamide gel electrophoresis (6%) at a constant voltage (130 V) for 3 h. A 1000 bp DNA marker (TaKaRa, Japan) was used to determine allele size.

RNA sequencing and core SSR marker screening

RNA extraction and sequencing were performed as described by Zhao et al. (2021) [36]. RNA of A. chinensis was extracted using TRIzol Reagent (Invitrogen). Transcriptome data of A. chinensis were acquired based on the Illumina Hiseq Xten PE150 platform, by Novogene Co. (Beijing, China). All SSR primers used in this study were designed from the transcriptomic database as reported by Zhao et al. 2021 [36], and they are available in the SRA (BioProject ID PRJNA698794, https://www.ncbi.nlm.nih.gov/sra/PRJNA698794). SSR marker detection, identification and primer design were performed as described by Wu et al. (2021) [31].

This study was carried out to analyze the inter-populations genetic diversity based on those markers in clusters classified into sesquiterpenoid biosynthesis pathway. Twenty-five SSR primers in clusters annotated as terpene skeleton biosynthesis and eighty-one primers in clusters annotated as the sesquiterpenoid biosynthesis pathway were screened for polymorphism testing (Supplementary Table S1). SSR primers were constructed by Shanghai Invitrogen Biotechnology Company (Shanghai, China). The core primers, with high allelic frequencies (> 2), were screened by amplification with DNA extracted from 8 A. chinensis populations from different counties. Only ten SSR primers with distinct bands and high polymorphism were used to analyze interpopulations genetic diversity in this study (Table 3).

Data analysis

The amplified bands with good resolution from 10 SSR primers were counted and scored as 1 (present) or 0 (absence). Several genetic diversity assessment parameters such as the observed number of alleles, effective number of alleles, Nei's (1973) gene diversity (h) and Shannon's information index (I) were determined using software POPGENE version 1.32 [19]. The polymorphism information content (PIC) was calculated as described by Botstein et al. (1980) [3]. Similarity coefficients were calculated using the similarity program in PopGene version 1.32.

The clustering of 19 A chinensis populations was performed based on a similarity matrix using an unweighted pair group method with arithmetic average (UPGMA) algorithm following SAHN module of NTSYS version 2.10. The phylogenetic tree was constructed using the neighbor-joining method by MEGA version 7.0.21.

Results and discussion

SSR polymorphism

A total of 89,005 SSRs with 3 or more mono, di-, tri-, tetra-, penta-, and hexanucleotide repeat units were identified in the A. chinensis transcriptome. Among the SSRs, 46,188 (51.89%), 30,675 (34.46%), 9,791 (11.00%), 904 (1.02%), 886 (1.00%), and 561 (0.63%) were mono-, di-, tri-, tetra-, penta-, and hexanucleotides SSRs, respectively (Table 2). A/T (18,572, 20.87%), AG/CT (3,274, 3.68%) and ACC/GGT (1,303, 1.46%) were the most abundant of the mononucleotide, dinucleotide and trinucleotide motifs, respectively. Of the tetra-, penta- and hexanucleotide motifs, AAAT/ATTT (151, 0.17%), AAACC/GGTTT (339, 0.38%), and AACCCT/AGGGTT (15, 0.02%) were the most abundant, respectively (Table 2).

Table 2 Repetition times and distribution frequency of mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeat units in A. chinensis transcriptomic database
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For medicinal plants without a reference genome, SSR molecular marker technology may not be directly used for genetic diversity analysis. High-throughput RNA sequencing effectively provides SSR markers. This is the first time that genetic diversity analysis of A. chinensis populations has been reported using SSR markers. In this paper, among the 106 SSR markers (Supplementary Table S1) screened on 8 randomly selected A. chinensis populations (data not shown), ten SSR markers generated polymorphisms (Table 3, Supplementary Fig S1). These ten SSR markers were used for DNA fingerprinting and genetic diversity analysis of 19 A. chinensis populations.

Table 3 List of primers used for genetic diversity analysis in the present study
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The size of the amplified fragments was estimated by using the DNA ladder that produced the expected size (100–1000 bp). SSR locus diversity data from ten SSR primers are summarized in Table 4. The overall size of the amplified fragments varied from 200 to 1000 bp. A total of 65 loci in 78 alleles (80.33%) were detected revealing the presence of a large difference. The number of polymorphic alleles per SSR locus ranged from 2 (S4) to 13 (S2) with an average of 6.5 alleles per locus (Table 4), showing that 19 A. chinensis populations exhibited a high level of genetic diversity. The average number of allelic genes in this study was more than that of many other crop species, namely, 3.7 in Euryale ferox [15], 5.1 in Lactuca sativa var capitata [37] and 4.5 in Sesamum indicum [2].

Table 4 Characteristics of each ten polymorphism SSR markers in genetic information
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SSRs with PIC values > 0.5 were considered highly informative markers [24]. The PIC values among the 19 A. chinensis populations varied from 0.4908 (S54) to 0.8918 (S2) with an average of 0.6265 (Table 4), which was much higher than 0.5. The calculated average PIC value (0.6265) in A. chinensis was higher than that in some crops, namely, 0.495 in Camellia sinensis [7], 0.32 in Gossypium hirsutum [23], 0.5619 in Sorghum bicolor ssp. bicolor [21], which indicated their high informativeness. The value of PIC related to the relative frequency and number of alleles [24] was proportional to the polymorphic locus. The highest number of polymorphic alleles and PIC value were 13 and 0.8918, respectively, in primer S2. Eight out of ten (80.00%) markers had a PIC value > 0.5, except for S4 (0.4908) and S54 (0.4748), indicating that they were suitable for genetic diversity and fingerprinting studies.

Genetic diversity and relatedness

A dendrogram elucidating the genetic relationships among the 19 A. chinensis populations was constructed using the neighbor-joining method by MEGA version 7.0.21. To better understand their relationships, we divided the tested 19 A. chinensis populations into three clusters (Fig. 1). Populations P11 were grouped into Cluster I. Cluster II consisted of 9 populations distributed into two subgroups. One population, P6, was grouped into the subgroup. The remaining 8 populations were grouped into the second subgroup. Populations belonging to different provinces constituted cluster II. For example, P5 (Shandong Province) and P19 (Jilin Province) were grouped into the Hebei Province cluster. Similarly, cluster III consisted of 9 populations derived from different provinces. Populations P2 and P15 from Inner Mongolia Province were grouped into Hebei Province.

Fig. 1
figure 1

Neighbor-joining tree of 19 A. chenesis populations using MEGA

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The 15 populations from Hebei Province were divided into two clusters, and grouped with Shandong and Jilin Provinces or with Inner Mongolia Province. The three clusters formed in the dendrogram revealed that the geographic origin does not exactly corroborate genetic diversity. This phenomenon appeared in many SSR marker-based genetic diversities, such as Sesamum indicum [2, 20], Camellia oleifera [4], Vicia amoena [31] and Trifolium repens [32]. Wu et al. carried out genetic diversity analysis of Trifolium repens using PCoA, UPGMA and STRUCTURE, and indicated that UPGMA analysis was implemented based on genetic distance, which provided more detailed relationships [32]. In this study, we used MEGA software to determine the genetic diversity of A. chinensis based on UPGMA. Weak genetic differentiation was observed in Pennisetum glaucum among the geographical regions, suggesting high seed and pollen-mediated gene flow among the regions [1]. A. chinensis is an often cross-pollinated plant, and 90% of the plants had only female flowers in our investigation (data not shown). Mixed samples for genetic diversity analysis may have resulted in the elimination of genetic variation; moreover, the complex genetic structure in wild resources of A. chinensis decreased the regional differentiation among populations. Additionally, the use of different SSR markers leads to the different dendrograms. Thus, the dendrogram constructed in the present study may not reflect the geographic origins of 19 A. chinensis populations.

Nei's unbiased measures of genetic similarity are shown in Table 5. The similarity coefficient ranged from 0.46 to 0.90 among 19 A. chinensis populations based on ten SSR primer amplification results. P8 and P10 showed the highest similarity (0.90), and the lowest similarity (0.46) was estimated between P2 and P11.

Table 5 Simple matching similarity matrix among 19 A. chinensis populations calculated from ten SSR markers
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SSR marker analysis is an effective method for genetic diversity analysis and molecular marker-assisted selection breeding [6, 28]. In the present study, we used ten well-chosen SSR markers in clusters annotated as sesquiterpenoid biosynthesis to analyze 19 A. chinensis populations in northern China. The results showed that these markers were highly polymorphic. The SSR marker analyses revealed the presence of genetic diversity among 19 A. chinensis populations which could be helpful for selective breeding in the future.

Establishment of DNA fingerprinting

According to the amplification results, the set of SSR markers used here provided a discernible assessment of the ability of SSR primers to produce unique DNA profiles of A. chinensis populations. The ten SSR markers were able to differentiate 19 A. chinensis populations. DNA fingerprints of the 19 A. chinensis populations were constructed according to the original data matrix of amplification results (Supplementary Table S2).

DNA fingerprinting is a popular technique for identifying species. The genus Atractylodes comprises species of perennial herbs used as important crude drugs prescribed in Chinese, Japanese, Korean and Thai traditional medicine, including Atractylodes lancea, A. chinensis, Atractylodes japonica and Atractylodes macrocephala [35]. A. lancea and A. chinensis are known as Cangzhu in Chinese and Sojutsu in Japanese. A. japonica is recorded in the Japanese and Korean Pharmacopoeias but not in the Chinese pharmacopeia. The plants of the genus Atractylodes showed similar morphological features of stems, leaves and rhizomes, leading to disagreement regarding whether they are unique species and to their frequent misuses in medical products [29]. DNA fingerprinting is immensely helpful in detecting populations with high similarity. The results of the present study revealed that SSR marker-based fingerprinting databases are useful to detect genetic polymorphisms representing a method for analyzing unique populations. Marker-based fingerprinting provides a desirable reference for species and germplasm identification in the genus Atractylodes.

Unique alleles

SSR markers, in contrast to morphological markers, have strong species specificity [26]. Seventeen populations produced unique bands with certain SSR markers (Table 6). For P11, five SSR markers generated unique bands, and three markers generated unique bands for P14. Four SSR markers received unique bands for P6, and three markers received unique bands for P7.

Table 6 List of populations that produced specific fragments with certain SSR markers
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Among the ten SSR primers used in the present study, seven were detected to generate unique fragments in certain populations (Table 7). Numerous specific SSR loci enabled us to select markers that yield highly specific amplifications independently (Supplementary Fig. S1, Table 7). S54 generated unique fragments of 320 and 350 bp specific to P6. Similarly, S99 produced bands sizes of 200, 750 and 1000 bp in P1. The specific bands were generated from S53 (320 and 350 bp) in P6, S52 (750 bp) and S63 (380 and 500 bp) in P11. S74 generated unique fragments 420 and 850 bp in P2, 480 bp in P3 and 650 bp in P11. The unique fragment generated through natural selection [18] was utilized for the evaluation of germplasm resources and molecular marker-assisted selection breeding.

Table 7 List of populations that produced unique fragment sizes with certain SSR markers
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Conclusion

The selection of set of core SSR primers is a crucial step for genetic diversity, DNA fingerprinting and germplasm identification. The ten SSR markers used in this study enable conclusions regarding the overall polymorphism and number of alleles observed in the 19 studied A. chinensis populations but do not relate explicitly to functional diversity and specific traits. The genetic diversity combination of agronomic traits (such as yield and quality traits) and SSR markers can be a key source of information to exploit superior A. chinensis germplasm resources for selective breeding.