# Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers
## 4 Discussion  
The preservation of crop resources relies on the establishment of core germplasm collections, where effective sampling ratios and retention strategies are essential. [PERSON] [41] suggested retaining 5% to 10% of the original sample size, capping at 3000 samples. In contrast, [PERSON] et al. [42] recommended a 20-30% sampling ratio for populations with genetic distances (DR) between 0.2 and 0.9. Generally, the sampling ratio depends on the genetic structure and diversity of the species, often decreasing with larger population sizes. Sampling ratios for core germplasm collections in various plant species range from 5% to 40% [43]. Our study identified the overall retention scale and square root ratio method as the most effective for phenotypic core germplasm. Accordingly, we established a phenotypic core collection of 41 pepper varieties with retention ratios of 25% to 30%, consistent with the ratios seen in most populations. \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Germplasm** & **Number of** & **Number of** & **Percentage of** & **Shannon Weaver** & **Shannon Weaver Index** & **Average Number of** \\
**Group** & **Germplasm** & **Polarorphic** & **Loci** & **Diversity Index** & **Change Rate** & **AllELS** \\ \hline core collection & 32 & 54 & 100.00\% & 0.3005 & 125.68\% & 1.6875 \\ Primitive germplasm & 155 & 54 & 100.00\% & 0.2391 & 100\% & 0.3484 \\ \hline \hline \end{tabular}
\end{table} 
Table 11: Comparison of genetic diversity parameters between core and primary germplasm. \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Compression** & **Germplasm** & **Number of** & **Phenotypic** & **Number of** & **Polymorphic** & **Site** \\
**Ratio** & **Number** & **Phenylogenic** & **Retention** & **Loci** & **Retention** \\
90.00\% & 57 & 87 & 92.55\% & 54 & 100.00\% \\
100.00\% & 63 & 87 & 92.55\% & 54 & 100.00\% \\ \hline \hline \end{tabular}
\end{table} 
Table 12: Ratio of phenotype and number of polymorphic loci between the core and recompressed primary germplasm. Essential for constructing core germplasm collections are accurate evaluation data and detailed characteristic and identification information. Morphological and agronomic traits are critical for species definition and core germplasm evaluation [33; 34; 35; 36; 37; 38], serving a key role in initial collection efforts. For example, [PERSON] et al. (2004) [33] established a core collection of 137 accessions from 1202 chili germplasm at the USDA by using 21 phenotypic traits, stratified grouping, and representative sampling. Similarly, [PERSON] et al. analyzed 21 qualitative and 7 quantitative traits from 603 chili peppers to create a core collection of 91 accessions. [PERSON] et al. (2015) [44] developed a core collection of 43 accessions from 146 Huang-denglong pepper varieties based on 10 phenotypic traits. Despite their importance, phenotypic traits may not always reflect genotypic differences accurately due to environmental variability. Molecular markers, such as chloroplast trLH-psbA sequences, SSR, RAPD, SRAP, AFLP, and SNP, have become increasingly valuable because they are unaffected by environmental factors and provide benefits such as high abundance, broad distribution, stability, and rapid detection [39; 40; 45; 46; 47]. Among these, second-generation markers like SSR are favored for their cost-effectiveness, precision, and standardized procedures. [PERSON] et al. (2013) [30] used 28 SSR markers to develop a core collection of 332 chili germplasm from 1352 samples across 11 species in 89 countries. [PERSON] et al. (2015) [48] selected 28 core collections from 230 chili peppers using 10 SSR loci. [PERSON] et al. (2015) [49] examined genetic variation in 90 local chili germplasm from Guizhou and 7 from elsewhere, resulting in a core collection of 9 peppers. [PERSON] et al. (2016) [6] analyzed genetic diversity and population structure with 48 SNPs from 4652 pepper samples across 11 species in 97 countries, establishing the 'CC240' core collection of 240 germplasms.