# Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers
## 4 Discussion
In 2016, the Vegetable and Flower Research Institute of the Chinese Academy of Agricultural Sciences (CAAS) utilized 29 SSR markers to analyze 1904 pepper germplasm from China's vegetable germplasm bank, resulting in a core collection of 334 germplasms. [PERSON] (2017) [50] analyzed 512 pepper germplasms with 21 SRP primer pairs, initially creating a core collection of 288 samples, which was further refined to 200 samples using 65 SSR markers. In our study, we first established a phenotype-based core collection. We then used SSR molecular markers to create a molecular core collection of 22 materials, achieving a compression ratio of 14.19%. The two collections were integrated and further compressed. At a final compression ratio of 90%, the germplasm bank preserved all polymorphic loci from the original samples, with a phenotype retention ratio of 92.6%. This core collection comprehensively represents the original germplasm. The core germplasm strategy optimizes the use of original germplasm resources by minimizing redundancy and preserving genetic diversity and geographical variation with minimal material. This method streamlines the collection, evaluation, and utilization of germplasm resources. In this study, a core germplasm collection of 57 accessions was developed, including 36 var. _longum_ [PERSON], 10 var. _grossum_ [PERSON], 4 var. _fascicultatum_ [PERSON], 10 var. _conoides_ [PERSON], and 1 var. _cerasiforme_ [PERSON] (Table S4). The collection encompasses both domestic and foreign resources, showing significant diversity in key traits such as flower organ structure, mature fruit color, fruit shape, and spiciness (Table 5). This diversity provides a robust foundation for gene mining and improves breeding efficiency. The following supporting information can be downloaded at [[https://www.mdpi.com/article/10.3390/app14177473/s1](https://www.mdpi.com/article/10.3390/app14177473/s1)]([https://www.mdpi.com/article/10.3390/app14177473/s1](https://www.mdpi.com/article/10.3390/app14177473/s1)), Tables S1-S4 and Figure S1. Table S1. Information of pepper germplasm used in this study. Table S2. Assignment of values for quality traits in pepper germplasm resources. Table S3. Construction of core germplasm. Table S4. The final core germplasm. Figure S1. Visualization of Polyacrylamide gel electrophoresis PCR products in some pepper germplasm using SSR primers. **Funding:** This study was funded by the Hainan Provincial Natural Science Foundation of China (grant number: 320 RC474) and Key R&D Projects in Hainan Province (grant number: ZDYF2022 XDNY159). **Institutional Review Board Statement:** Not applicable. **Informed Consent Statement:** Not applicable. **Data Availability Statement:** The datasets presented in this study can be found in online repositories of the National Center for Biotechnology Information (NCBI). The accession number is PRJNA932246. **Acknowledgments:** We would like to thank all the students for assisting with the collection and processing of data. We are grateful to the reviewers for their helpful suggestions. **Conflicts of Interest:** The authors declare no conflicts of interest. * (21) [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON]; [PERSON] Identification and development of a core set of informative generic SNP markers for assaying genetic diversity in Chinese cabbage. _Hortic. Environ. Biotechnol._**2019**, _60_, 411-425. [CrossRef]
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