# 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  
5.1 Cluster Analysis of Chili Germplasm Based on SSR Markers and Reserve Ratio Analysis of Pre-Selected Core Collection  
Figure S1 displays the amplification results for 155 pepper varieties using eight pairs of SSR primers. These primers exhibited strong polymorphism, with distinct peaks and amplification fragments ranging from 122 to 352 bp. Using GeneMarker 2.2.0 software, 54 polymorphic fragments were identified. Primers CIDAM-7, CIDAM-2, CIDAM-8, CIDAM-6, CIDAM-3, CIDAM-1, CIDAM-4, and CIDAM-5 generated 14, 11, 7, 6, 5, 4, 4, and 3 polymorphic fragments, respectively (Table 7). The average number of polymorphic bands per primer was 6.75, achieving a 100% polymorphism rate.  
Cluster analysis, using the \"0, 1\" matrix from NYSY software, organized the 155 chili germplasms into 11 levels: 10.97%, 14.19%, 18.06%, 24.52%, 30.32%, 40.65%, 52.90%, 58.71%, 69.68%, 74.19%, and 90.32% (Figure 3). For compression percentages of the pre-selected core germplasm from 10.97% to 52.90%, allelic variation retention (RVA) increased with  
\begin{table}
\begin{tabular}{c c c c} \hline \hline
**Primer Name** & \
\begin{tabular}{c} **Total Amplified** \\ **Bands** \\ \end{tabular} & **Polymorphic Bands** &
\begin{tabular}{c} **Proportion of** \\ **Polymorphic Bands** \\ \end{tabular} \\ \hline CIDAM-1 & 4 & 4 & 100.00\% \\ CIDAM-2 & 11 & 11 & 100.00\% \\ CIDAM-3 & 5 & 46 & 100.00\% \\ CIDAM-4 & 4 & 47 & 100.00\% \\ CIDAM-5 & 3 & 51 & 100.00\% \\ CIDAM-6 & 6 & 52 & 100.00\% \\ CIDAM-7 & 14 & 54 & 100.00\% \\ CIDAM-8 & 17 & 54 & 100.00\% \\ \hline \hline \end{tabular}
\end{table}
Table 7: Number of bands amplified by eight pairs of primers on 155 pepper germplasm DNA.  
Figure 2: Phenotypic comparison between pre-selected core and entire collections.  
5.2 Shannon-Weaver Index Analysis of Pre-Selected Core Collection of Peppers Obtained with Different Clustering Compression Ratios  
In the compression spectrum of 10.97% to 100%, the Shannon-Weaver diversity index decreases as the proportion of compressed samples increases, accompanied by a rise in genetic repetition and allele omissions (Table 9). Notably, the Shannon index for phenotypes fluctuates irregularly within this range. Specifically, from 14.19% to 58.71% compression, the Shannon index consistently exceeds 80%, while it falls below this threshold outside these ratios. The Shannon index shows minimal variation across all retention schemes, with a range of 4.26%.  
When the CR exceeds 24.52%, the RPR surpasses 91.40%. Similarly, CR values above 30.32% result in an allele retention ratio exceeding 94.44%. In the 14.19% to 24.52% compression range, the allele retention ratio fluctuates between 83.33% and 87.04%. Consistently, within the 14.19% to 58.71% compression range, the phenotype Shannon index remains above 80%, while it drops below 80% at other compression ratios. The minimal variation in the phenotype Shannon index across different compression ratios highlights its limited variability. Specifically, when the CR is between 10.97% and 18.06%, the Shannon-Weaver index exceeds 0.2837; outside this range, it falls below this threshold. Consequently, a compression percentage of 14.19% was selected for the predetermined molecular core collection, encompassing 22 preserved germplasm and accounting for 10 allelic variations that were not retained.