*Article* **High-Throughput SSR Marker Development and the Analysis of Genetic Diversity in** *Capsicum frutescens*

**Yangmin Zhong 1, Yuan Cheng 1, Meiying Ruan 1, Qingjing Ye 1, Rongqing Wang 1, Zhuping Yao 1, Guozhi Zhou 1, Jia Liu 2, Jiahong Yu 1,2 and Hongjian Wan 1,3,\***


**Abstract:** *Capsicum frutescens*, one of the domesticated species of pepper grown worldwide, is thought to be highly advantageous due to its strong resistance against plant pathogenesis, high productivity, and intense aroma. However, a shortage of molecular markers limits the efficiency and accuracy of genetic breeding for pepper. With the newly developed next-generation sequencing technology, genome sequences of *C. frutescens* can be generated, which are now available for identifying SSR markers via data mining. In this study, a total of 278,425 SSRs were detected from the pepper genome using MISA software. It was observed that trinucleotides were the dominant repeat motif. This was followed by dinucleotides, tetranucleotides, pentanucleotides, and the hexanucleotides repeat types. (AT)n (TTG)n (AAAT)n (AAATA)n (TATAGA)n is known to be the most common repeat motifs corresponding to dinucleotide to hexanucleotide repeats, respectively. In addition, a total of 240 SSR primers evenly distributed over all 12 chromosomes were designed and screened against 8 *C. frutescens* cultivars. Of these, 33 SSR markers that have high polymorphism, have been scrutinized for 147 accessions from 25 countries. The dendrogram constructed clustered these accessions into seven major groups. The groups were found to be consistent with their origins. The results obtained in this study provided resources of SSR molecular markers and insight into genetic diversity of the *C. frutescens*.

**Keywords:** *C. frutescens*; SSR; germplasm; genetic diversity
