# Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers
## 3 Results
### Construction and Evaluation of Chili Core Collection Based on SSR Markers
#### 3.5.3 Evaluation of Pre-Selected Core Collection by Molecular Markers  
Table 10 presents a comparative analysis of molecular genetic diversity between the original germplasm and the pre-selected core collection. The molecular core collection, with at least 22 resources, effectively preserved the original diversity while reducing genetic repetition. However, the new cluster lost nine allelic polymorphisms, resulting in an 83.33% polymorphism site percentage. Simultaneously, the Shannon-Weaver index increased to 121.66%, indicating enhanced phenotypic diversity. Additionally, the average number of alleles increased to 2.0455.  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Germplasm Group** & **Number of** **Gemplasms** & **Number of** **Polymorphic Loci** & **Percentage of** **Polymorphic Loci** & **Shannon Weaver Diversity Index** & **Average Number of Alleles** \\ \hline core collection & 22 & 45 & 83.33\% & 121.66\% & 2.0455 \\ Primitive germplasm & 155 & 54 & 100.00\% & 100.00\% & 0.3484 \\ \hline \hline \end{tabular}
\end{table}
Table 10: Comparison of genetic diversity parameters between core and primary germplasm.  
\begin{table}
\begin{tabular}{c c c c c} \hline \hline
**Compression Ratio** & **Number of Pre-Selected** **Core Germplasm** & **Number of Missing** **Allees** & **Shannon–Weaver Diversity Index** & **Phenotypic Shannon Index** \\ \hline
10.97\% & 17 & 11 & 0.2956 & 77.99\% \\
14.19\% & 22 & 10 & 0.2909 & 81.27\% \\
18.06\% & 28 & 8 & 0.2840 & 81.09\% \\
24.52\% & 38 & 7 & 0.2837 & 81.46\% \\
30.32\% & 47 & 3 & 0.2759 & 82.25\% \\
40.65\% & 63 & 2 & 0.2737 & 81.08\% \\
52.90\% & 82 & 0 & 0.2667 & 80.09\% \\
58.71\% & 91 & 0 & 0.2638 & 80.29\% \\
69.68\% & 108 & 0 & 0.2546 & 78.36\% \\
74.19\% & 115 & 0 & 0.2523 & 79.62\% \\
90.32\% & 140 & 0 & 0.2449 & 79.52\% \\
100.00\% & 155 & 0 & 0.2391 & 79.54\% \\ \hline \hline \end{tabular}
\end{table}
Table 9: Genetic diversity index of molecular and phenotypic traits in the core collection.  
3.5.4. Improvement of Molecular Marker Pre-Selection of Core Collection  
To address the loss of 10 polymorphic loci in the reserved germplasm of 22 varieties, a strategic approach was implemented. The selection process from the pre-selected core collection was enhanced with phenotype data to reintroduce the lost polymorphic loci. This refinement resulted in an SSR molecular core collection of 32 pepper varieties, successfully retaining all 54 polymorphic loci with a 100% retention rate (Table 11). The Shannon-Weaver index increased by 25.68% compared to the original germplasm, and the average number of alleles also rose significantly. This refined collection eliminated redundant germplasm and accurately represented the original genetic diversity.  
5.5 Integrating Phenotypic and Molecular Core Germplasm to Construct the Final Pepper Core Collection  
The phenotypic and molecular core germplasm of 63 varieties underwent further compression at ratios of 40%, 50%, 60%, 70%, 80%, and 90% (Table 12). At a 90% compression ratio, all polymorphic loci from the original germplasm were retained, achieving a phenotype retention ratio of 92.55%. As a result, the final core collection consists of 57 varieties, effectively preserving the genetic diversity of the original germplasm (Table S4).