# Construction and Evaluation of Pepper Core Collection Based on Phenotypic Traits and SSR Markers
## 1 Introduction  
Peppers (_Capsicum_ L.), originating from Central and South America, belong to the _Solanaceae_ family and include both herbaceous and semi-shrubby plants. Globally significant as a vegetable, pepper fruits are primarily consumed fresh or as conditions [1]. The _Capsicum_ genus includes key species such as _C. annuum_, _C. frutescens_, _C. pubescens_, _C. chinense_, _C. bacatum_, and _C. assamicum_, along with 32 wild species. _C. annuum_ is extensively cultivated and holds economic importance in countries such as China, India, South Korea, Spain, Thailand, and Mexico. Meanwhile, _C. frutescens_ and _C. chinense_ are commercially grown in select areas of Central America, West Africa, Central Africa, Oceania, and Asia [2, 3]. _C. pubescens_ and _C. bacatum_ are limited to Central and South America and the Caribbean [4]. Recently, _C. assamicum_, a domesticated species identified in northeastern India, has gained attention for its extreme spiciness, prolific branching, yellow-green corrollas, pale blue alnters, and sunken epidermal fruits [5]. Pepper fruits are rich in vitamins C and E, carotenoids, flavonoids, essential nutrients, and bioactive compounds such as capsaicin and phenols, providing significant health benefits and broad market potential [1]. Given their economic and nutritional importance, breeders have focused on enhancing agronomic traits such as yield, fruit type, pungency,and resistance to biotic and abiotic stresses. Advances in genetic engineering and gene editing, as well as efforts to address male infertility, have played crucial roles in these improvements. However, these breeding efforts have also reduced the genetic diversity of local resources, leading to the loss of valuable genes. Therefore, the comprehensive collection, identification, protection, and sustainable use of pepper genetic resources are vital for further advancements [6; 7]. In recent decades, significant global progress has been made in collecting and protecting pepper germplasm resources. Notable contributions include the Asian Vegetable Research and Development Center (AVRDC, Tainan, China) with 5100 accessions, the United States with 4700, the Hunan Province of China with 3600, and Russia with 2300 [8]. Brazil's Amombra Horticultural Research Institute (AHRI, Sao Paulo, Brazil) has curated 1220 accessions, categorizing 654 based on IPGRI traits. Despite its relatively low pepper consumption, France has amassed over 1150 accessions [9]. A major milestone is the establishment of the world's first pepper botanical garden in the United States, preserving wild peppers and diverse germplasm resources as vital genetic reservoirs for future breeding. However, the introduction of peppers from various global breeding and research institutions has obscured the genetic background of these resources. This increase in quantity does not fully reflect the genetic richness available in breeding institutions. Establishing core germplasm banks is vital for conserving genetic resources and advancing research. These banks preserve the genetic diversity of entire populations, minimize duplication, reduce management costs, streamline germplasm screening, and enhance breeding potential [6; 7; 8; 9; 10]. Over 100 primary core collections have been developed worldwide, including those for major crops such as rice [11], wheat [12], maize [13], soybeans [14], and rapeseed [15]. Core collections also exist for fruits such as apples [16; 17], apricots [18], pomerangates [19], chestnuts [20], and litchi [21], as well as vegetables including Chinese cabbage [22], potatoes [23], tomatoes [24], garlic [25], eggplants [26], amaranth [27] and carrots [28]. Additionally, diverse phenotypes and genetic variations of pepper core collections have been established for research purposes [29; 30; 31; 32; 33; 34]. For example, [PERSON] et al. developed a chili core germplasm bank with 100% morphological variation using a clustering method of 21 phenotypic traits, achieving selection rates of 10% (CA), 16% (CC), and 16% (CB) [34].