**5. Conclusions**

In the present study, 278,425 SSRs were identified by searching the *C. frutescens* genome sequences. The AT/TA, TTG/CAA, and AAAT/ATTT were observed to be the most common repeat motifs in the dinucleotide, trinucleotide, and tetranucleotide repeats, respectively. Among them, dinucleotides were the most abundant number of repeats, accounting for 55.16%. In this research investigation, the genetic diversity of *C. frutescens* germplasms was investigated using 33 SSR markers, which were evenly distributed on all of the chromosomes. The 147 experimental materials used in this study were wild peppers with rich genetic diversity. Their eminent properties (withstanding pathogenic attacks, high yielding capacity, and so on) will potentially provide excellent genes for the acquisition of pepper breeding accessions. They may also provide a basis for improving the existing cultivated pepper species, as well as having important significance in expanding the narrow genetic basis of pepper breeding in China. In addition, it was considered that the genome-wide identification and development of SSR markers could be very useful and may possibly provide insights into various research areas regarding *C. frutescens* in the future, such as high-density genetic mapping, genome comparative mapping, and genome-wide association analyses.

**Supplementary Materials:** The following are available online at https://www.mdpi.com/article/10 .3390/{h}orticulturae7070187/s1, Supplementary File S1, Detailed information for the 147 pepper (C. *frutescens*) cultivars used in this study.

**Author Contributions:** Y.Z., Y.C. and H.W. conceived and designed the research; M.R., Q.Y. and R.W. performed the experiments; Z.Y. and G.Z. analyzed the data and wrote the paper; Y.Z., J.L. and J.Y. revised the manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was partially supported by China Agriculture Research System of MOF and MARA (CARS-23-G-44), National Key Research and Development Program of China (2017YFE0114500, 2018YFD1000800) and National Natural Science Foundation of China (31772294, 31960601, 32060446).

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** The data used for the analysis in this study are available within the article and supplementary materials.

**Conflicts of Interest:** The authors declare no conflict of interest.
