Koontz Austin C, Schumacher Emily K, Spence Emma S, Hoban Sean M
Morton Arboretum Center for Tree Science Lisle Illinois USA.
Cornell University Department of Public and Ecosystem Health Ithaca New York USA.
Evol Appl. 2024 Mar 22;17(3):e13650. doi: 10.1111/eva.13650. eCollection 2024 Mar.
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For , SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for . The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
植物园和树木园保存的植物种质资源是迁地保护的关键组成部分。在这些种质资源中维持遗传多样性，能使其作为补充野生种群的资源。然而，大多数推荐的用于维持足够迁地遗传多样性的最小样本量是基于微卫星标记得出的，鉴于最近开发的新一代测序（NGS）方法，这些样本量是否仍然有效尚不清楚。为了填补这一知识空白，我们研究了在两种受威胁橡树的园林样本和野生样本中，基于微卫星和单核苷酸多态性（SNP）得出的迁地保护状况和采样建议有何不同。对于[此处原文似乎缺失具体内容]，SNP显示出野生等位基因多样性的迁地代表性较低，且最小样本量估计略低于微卫星，而对于[此处原文似乎缺失具体内容]，每个标记的结果在很大程度上相似。缺失数据过滤的应用往往会导致更高的迁地代表性，而不同SNP分型方法的影响则取决于所分析的物种。物种内种群分化的测量在标记之间大致相似，但更多数量的SNP位点能够更清晰地分辨种群结构，并更明确地将迁地个体分配到野生源种群。我们的结果为未来利用SNP数据进行迁地保护评估提供了指导，例如缺失数据过滤的应用和参考基因组的使用，并表明对于寻求确保其种质资源遗传多样性的植物园和树木园来说，微卫星和SNP仍然是可行的选择。
