Core collection of Taiwanese Phalaenopsis orchids

This study establishes Taiwan's first Phalaenopsis orchid core collection, crucial for preserving genetic diversity and key traits. It analyzed 207 cultivars using phenotypic and genotypic data, employing novel techniques like multiple imputation and weighted k-means clustering. 22 core accessions were selected using the 'P+G strategy' and MGD algorithms, showcasing effectiveness in preserving diversity. The evaluation revealed significant diversity, surpassing alternatives, supported by pedigree analysis. The study underscores the importance of rigorous evaluation for quality and effectiveness. It contributes to orchid breeding, conservation, and sustainable agriculture, offering insights into genetic landscapes and breeding advancements.

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We devised a two-step ‘P+G strategy’ to capture key traits and genetic diversity in orchid germplasm. Steps include: (1) Imputing missing data using multiple imputations. (2) Exploring germplasm structure with weighted k-means clustering. (3) Estimating dissimilarity using the MGD algorithm. (4) Constructing core accessions based on MGD metric via 2-step ‘P+G strategy’.

, , # Core collection of Taiwanese *Phalaenopsis* orchids

We have submitted our core collection data (MGD_coreset.csv).

[https://doi.org/10.5061/dryad.fn2z34v2z](https://doi.org/10.5061/dryad.fn2z34v2z)

## Descriptions

This study establishes the first core collection for Taiwanese *Phalaenopsis* orchids, employing a novel approach crucial for preserving genetic diversity and key traits.

* *Variety:* sample ID
* *Flower diameter (cm):* flower diameter of orchids (cm)
* *Plant height (cm):* plant height of orchids (cm)
* *SSRN_N*: simple sequence repeats (SSR) markers (0 = absent, 1 = exist)
* *cluster:* clustering of the entire collection by weighted k-means

本研究构建了台湾地区首个蝴蝶兰属（Phalaenopsis）核心种质库，该种质库对保护兰花遗传多样性与关键性状具有核心价值。本研究利用表型与基因型数据对207个栽培品种展开分析，采用多重插补、加权k均值聚类等新兴技术手段。本研究通过“P+G策略”与MGD算法筛选出22份核心种质，证实该方法可有效保留种质遗传多样性。经系谱分析验证，本研究筛选获得的核心种质具有显著遗传多样性，优于其他备选方案。本研究强调了严谨评估对核心种质库质量与有效性的重要意义，可为兰花育种、种质保护与可持续农业提供支撑，并为解析兰花遗传格局与推动育种进步提供新见解。

本研究设计了两步法“P+G策略”，以捕获兰花种质资源中的关键性状与遗传多样性，具体步骤如下：（1）采用多重插补法处理缺失数据；（2）借助加权k均值聚类解析种质资源群体结构；（3）通过MGD算法估算种质间的遗传不相似性；（4）基于MGD指标，依托两步法“P+G策略”构建核心种质。

# 台湾蝴蝶兰属核心种质库
本研究已提交核心种质库数据（MGD_coreset.csv）。
https://doi.org/10.5061/dryad.fn2z34v2z

## 数据说明
本研究构建了台湾地区首个蝴蝶兰属核心种质库，采用创新方法以保护兰花遗传多样性与关键性状。
* 品种：样本编号
* 花径（厘米）：兰花的花径（单位：厘米）
* 株高（厘米）：兰花的株高（单位：厘米）
* SSRN_N：简单序列重复（Simple Sequence Repeats, SSR）标记（0表示标记不存在，1表示标记存在）
* 聚类：基于加权k均值对全部种质资源进行聚类的结果