The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.

在最少的种质中保持最大的多样性是种质管理的挑战之一，评估种群结构，种质之间的关系以及核心品种的构建是关键步骤。合适的分子标记的选择通常是起点。在这项研究中，我们分析了INRAE核桃种质资源的一部分，该种资源在欧洲具有高度的多样性和独特性，其中包括来自美洲，欧洲和亚洲各大洲的150个种质。基于现有的基因型数据，使用13个SSR或364,275个SNP，我们表明第一级结构被同等检测。我们还从经验上强调，要在主坐标分析（PCoA）中获得与13个SSR相似的聚类，大约需要100个SNP。我们根据两种策略（总等位基因多样性的百分比或种质数量）和两种基于不同算法的构建方法（“最大长度子树”和“从最近进入”的方法）构建了八个核心集合。我们表明，基于少数SSR标记的核心集合能够捕获至少99.5％的SNP等位基因多样性，而与所使用的构建方法无关。然后，使用两种构建方法，基于每种标记物类型的核心馆藏高度相似。所有这些步骤对于确定改善植物遗传资源管理的合适工具和方法至关重要。